Contacts of the helix formed by residues 97 - 123 (chain B) in PDB entry 5XVO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 3.9 9.0 - - - +
96B TRP* 1.3 73.2 - - - +
98B GLU* 1.3 64.2 + - - +
99B GLU* 3.8 6.3 + - - +
100B ARG* 3.0 28.1 + - - +
101B LYS* 3.0 22.3 + - - +
276B LEU 5.4 0.2 + - - -
278B GLN* 3.5 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP 3.9 1.0 + - - -
97B THR* 1.3 74.7 - - - +
99B GLU* 1.3 62.5 + - - +
101B LYS* 3.4 31.7 + - - +
102B GLY 3.1 16.8 + - - -
142B PHE* 3.6 24.6 - - + -
202B LEU 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 3.1 6.4 + - - +
98B GLU* 1.3 79.8 - - - +
100B ARG* 1.3 58.8 + - - +
102B GLY* 3.1 3.6 + - - -
103B GLN* 2.9 52.1 + - + +
141B LEU* 4.1 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP* 5.9 0.4 - - + -
97B THR* 3.0 24.0 + - - +
99B GLU* 1.3 78.3 - - - +
101B LYS* 1.3 62.3 + - - +
103B GLN* 3.3 23.4 + - - +
104B VAL* 3.0 32.5 + - - +
275B VAL* 3.0 30.6 + - - +
276B LEU* 3.7 28.5 - - + +
278B GLN* 3.4 33.8 + - - +
280B GLU 3.5 15.0 + - - -
281B GLU* 3.1 34.6 + - - +
282B GLY 5.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP* 4.0 34.4 + - + -
97B THR 3.0 14.5 + - - +
98B GLU* 3.4 37.6 + - - +
100B ARG* 1.3 75.6 - - - +
102B GLY* 1.3 54.3 + - - +
104B VAL* 3.4 0.7 + - - +
105B TRP* 2.7 38.1 + - - +
142B PHE* 3.8 8.1 - - + -
201B GLY 4.7 7.1 + - - +
202B LEU* 4.0 41.5 + - + +
276B LEU* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 3.1 7.9 + - - -
99B GLU 3.1 6.7 + - - -
101B LYS* 1.3 73.4 - - - +
103B GLN* 1.3 56.8 + - - +
106B THR* 2.6 39.9 + - - +
141B LEU* 4.0 12.1 - - - -
142B PHE* 3.2 33.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 2.9 44.8 + - - +
100B ARG* 3.6 30.9 + - - +
102B GLY* 1.3 72.7 - - - +
104B VAL* 1.3 61.7 + - + +
106B THR* 2.9 19.1 + - - -
107B ALA* 2.9 19.9 + - - +
141B LEU* 4.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 3.0 23.7 + - - +
101B LYS 3.9 2.5 - - - +
103B GLN* 1.3 79.8 - - + +
105B TRP* 1.3 66.0 + - - +
107B ALA* 3.4 1.6 + - - +
108B ILE* 3.0 45.5 + - + +
202B LEU* 4.0 9.9 - - + -
272B VAL* 4.0 18.8 - - + -
275B VAL* 3.4 31.4 - - + -
276B LEU* 3.9 16.4 - - + -
283B VAL* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS 2.7 23.2 + - - +
102B GLY 4.0 2.0 - - - +
104B VAL* 1.3 75.3 - - - +
106B THR* 1.3 74.6 + - + +
108B ILE* 3.2 8.1 + - + +
109B ILE* 2.9 62.3 + - + +
139B LEU* 5.7 1.3 - - + -
142B PHE* 3.7 32.1 - + + -
143B ASP* 3.7 20.6 - - + -
148B GLU* 3.9 17.3 - - - -
202B LEU* 4.1 14.3 - - + +
203B LYS* 3.6 44.1 - - + +
204B HIS* 5.0 3.8 + + - -
216B ASP* 3.6 34.4 + - + +
219B GLU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY 2.6 23.2 + - - +
103B GLN* 2.9 13.7 + - - -
105B TRP* 1.3 88.0 - - + +
107B ALA* 1.3 64.9 + - - +
109B ILE* 3.3 1.5 + - - +
110B ALA* 3.0 25.2 + - - +
139B LEU* 4.4 11.6 - - + +
140B ARG 3.9 7.2 - - - +
141B LEU* 3.5 18.0 - - - +
142B PHE 3.0 33.0 - - - +
143B ASP 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN 2.9 18.4 + - - +
104B VAL* 3.5 6.3 - - - +
106B THR* 1.3 77.7 + - - +
108B ILE* 1.3 61.2 + - - +
110B ALA* 3.3 7.7 - - - +
111B GLN* 3.2 26.8 + - - +
283B VAL* 4.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.0 33.2 + - + +
105B TRP* 3.4 10.1 - - + +
107B ALA* 1.3 81.3 - - - +
109B ILE* 1.3 66.3 + - + +
111B GLN* 2.9 21.5 + - - +
112B LYS* 3.1 8.8 + - - +
202B LEU* 4.7 5.6 - - + -
216B ASP* 3.6 22.7 - - + +
217B LEU* 4.2 25.6 - - + +
219B GLU* 4.2 4.9 - - + -
220B PRO* 3.7 22.8 - - + +
268B TYR* 3.9 13.9 - - - +
272B VAL* 4.4 8.7 - - + -
283B VAL* 4.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TRP* 2.9 61.2 + - + +
106B THR 4.1 2.7 - - - +
108B ILE* 1.3 79.2 - - + +
110B ALA* 1.3 64.6 + - - +
112B LYS* 3.0 8.0 + - + +
113B ILE* 2.9 32.8 + - + +
139B LEU* 4.8 6.3 - - + -
148B GLU* 4.0 32.8 - - + +
216B ASP 5.0 0.2 - - - +
219B GLU* 3.4 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR 3.0 13.2 + - - +
107B ALA* 3.3 13.7 - - - +
109B ILE* 1.3 76.4 - - - +
111B GLN* 1.3 56.8 + - + +
113B ILE* 3.2 3.1 + - - +
114B THR* 2.9 34.3 + - - +
136B ARG* 3.7 21.0 - - + +
139B LEU* 3.9 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 3.2 14.0 + - - +
108B ILE* 2.9 9.4 + - - +
110B ALA* 1.3 77.8 - - + +
112B LYS* 1.3 61.6 + - - +
114B THR* 2.5 22.8 + - - -
115B ASN* 3.0 19.1 + - - -
220B PRO* 4.0 10.3 - - + +
268B TYR* 3.3 17.3 + - - -
283B VAL* 3.4 18.0 - - - +
284B PRO 2.9 22.8 + - - -
285B GLU* 3.5 24.2 - - + +
286B PHE 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE 3.1 6.6 + - - +
109B ILE* 3.0 15.7 + - + +
111B GLN* 1.3 77.8 - - - +
113B ILE* 1.3 52.1 + - - +
115B ASN* 3.0 5.8 + - - +
116B GLN* 2.8 69.0 + - + +
148B GLU* 3.4 34.0 + - - +
152B ALA* 4.7 1.6 - - - +
219B GLU* 3.4 54.6 + - + +
220B PRO* 3.9 9.8 - - + +
222B ARG* 4.4 10.7 - - + +
223B PRO* 4.3 4.4 - - + +
5H G 4.0 22.4 + - - -
6R G 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 2.9 23.9 + - + +
110B ALA 3.7 6.1 - - - +
112B LYS* 1.3 78.1 - - + +
114B THR* 1.3 62.4 + - - +
116B GLN* 3.1 18.6 + - - +
117B SER* 2.9 22.7 + - - +
132B LEU* 3.6 35.4 - - + +
133B LEU 4.9 0.2 - - - +
135B MET 5.2 0.4 - - - -
136B ARG* 4.0 14.8 - - + +
139B LEU* 4.3 25.1 - - + -
147B ARG* 4.6 2.5 - - + +
148B GLU* 4.1 26.2 - - - +
151B ALA* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA 2.9 8.8 + - - +
111B GLN* 2.5 31.1 + - - -
113B ILE* 1.3 75.3 - - - +
115B ASN* 1.3 63.2 + - - +
117B SER* 3.1 3.5 + - - -
118B LEU* 2.8 37.7 + - - +
133B LEU* 4.3 13.3 - - + +
136B ARG* 3.1 46.9 - - - +
286B PHE 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN 3.0 18.7 + - - +
112B LYS 3.0 6.0 + - - +
114B THR* 1.3 78.1 + - - +
116B GLN* 1.3 65.2 + - - +
118B LEU* 3.9 7.8 - - - +
119B HIS* 3.0 20.3 + - - +
220B PRO* 3.0 23.8 + - - +
223B PRO* 3.7 17.6 - - + +
286B PHE* 3.1 25.1 + - - +
287B GLY* 3.2 21.3 - - - -
288B ILE* 3.3 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 2.8 49.4 + - + +
113B ILE* 3.4 21.0 - - - +
115B ASN* 1.3 78.2 - - - +
117B SER* 1.3 61.6 + - - +
119B HIS 3.3 1.2 + - - -
120B LEU* 3.0 19.8 + - - +
132B LEU* 3.7 6.5 - - + -
148B GLU 4.8 0.3 - - - +
151B ALA* 4.3 12.8 - - - +
152B ALA* 4.1 14.0 + - - +
155B TYR* 3.3 62.7 - - + -
156B PHE* 5.1 3.2 - - - -
222B ARG* 6.3 1.2 - - - +
223B PRO* 4.3 8.7 - - + -
226B ASP* 5.0 2.0 + - - -
5H G 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE 2.9 11.2 + - - -
114B THR 3.4 8.1 - - - -
116B GLN* 1.3 77.0 - - - +
118B LEU* 1.3 52.3 + - - +
120B LEU* 2.8 10.4 + - - +
121B ALA* 2.8 31.8 + - - +
129B ALA* 3.1 23.3 + - - +
132B LEU* 2.7 36.8 - - - +
133B LEU* 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 2.8 28.1 + - - +
115B ASN* 3.8 20.9 - - - +
117B SER* 1.3 74.3 - - - +
119B HIS* 1.3 57.2 + - - +
121B ALA* 3.4 10.5 + - + +
122B GLN* 2.9 27.9 + - - +
287B GLY* 5.2 2.2 - - - -
288B ILE* 4.1 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN 3.0 17.7 + - - +
116B GLN 3.4 4.9 - - - +
118B LEU* 1.3 75.7 - - - +
120B LEU* 1.3 64.3 + - - +
122B GLN* 3.2 19.5 - - - +
123B ARG* 3.2 41.5 + - - +
155B TYR* 2.8 29.9 + - - +
159B LEU* 3.7 21.2 - - + +
223B PRO* 4.7 2.0 + - + -
226B ASP* 3.8 6.5 - - - +
227B GLN* 3.5 39.8 - - + -
230B TYR* 4.2 4.9 - - + +
288B ILE* 3.9 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN 3.0 11.7 + - - +
117B SER 2.8 11.2 + - - +
119B HIS* 1.3 69.6 - - - +
121B ALA* 1.3 68.4 + - - +
123B ARG* 2.9 14.9 + - - -
125B TYR* 3.1 28.5 + - + +
128B LYS* 4.1 18.2 - - + +
129B ALA* 4.1 9.0 - - + +
132B LEU* 3.7 38.8 - - + -
155B TYR* 3.8 16.4 - - + +
158B THR* 3.8 28.7 - - + +
159B LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.8 15.0 + - - +
118B LEU* 3.4 16.4 - - + +
120B LEU* 1.3 71.9 - - - +
122B GLN* 1.3 60.3 + - - +
124B ASP* 2.8 25.5 + - - +
125B TYR 4.5 4.9 - - - +
126B GLY* 4.8 5.5 + - - +
129B ALA* 3.9 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 2.9 15.0 + - - +
119B HIS* 3.2 16.7 - - - +
121B ALA* 1.3 76.9 - - - +
123B ARG* 1.3 93.8 + - - +
124B ASP* 3.3 8.5 + - - +
227B GLN* 3.0 29.1 + - - +
231B GLU* 4.4 2.8 - - - +
288B ILE* 5.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B HIS* 3.2 32.2 + - - +
120B LEU 2.9 8.7 + - - +
122B GLN* 1.3 101.8 + - - +
124B ASP* 1.3 70.0 + - - +
125B TYR* 3.2 28.4 + - + -
159B LEU* 4.2 11.4 - - + -
227B GLN* 3.5 11.5 + - - +
230B TYR* 3.2 38.9 - - + +
231B GLU* 3.1 40.2 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il