Contacts of the helix formed by residues 97 - 123 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L ALA 3.9 8.7 - - - +
96L TRP* 1.3 73.1 - - - +
98L GLU* 1.3 65.0 + - - +
99L GLU* 3.7 6.8 + - - +
100L ARG* 3.0 27.7 + - - +
101L LYS* 3.0 22.4 + - - +
278L GLN* 3.5 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L TRP 3.9 1.4 + - - -
97L THR* 1.3 72.9 - - - +
99L GLU* 1.3 63.7 + - - +
101L LYS* 3.6 16.3 + - - +
102L GLY 3.1 16.6 + - - -
142L PHE* 3.6 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L THR* 3.1 6.5 + - - +
98L GLU* 1.3 81.8 + - - +
100L ARG* 1.3 64.8 + - - +
102L GLY* 3.0 3.1 + - - -
103L GLN* 2.9 47.7 + - + +
141L LEU* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L THR* 3.0 27.1 + - - +
99L GLU* 1.3 78.1 - - - +
101L LYS* 1.3 61.8 + - + +
103L GLN* 3.3 23.3 + - - +
104L VAL* 3.0 31.7 + - - +
275L VAL* 3.0 30.5 + - - +
276L LEU* 3.7 28.5 - - + +
278L GLN* 3.4 33.9 + - - +
280L GLU 3.5 11.9 + - - -
281L GLU* 3.0 37.7 + - - +
282L GLY 5.2 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L TRP* 4.0 34.4 + - + -
97L THR 3.0 16.0 + - - +
98L GLU* 3.8 26.0 - - - +
100L ARG* 1.3 74.6 - - - +
102L GLY* 1.3 54.6 + - - +
104L VAL* 3.8 0.7 - - - +
105L TRP* 2.8 37.9 + - - +
142L PHE* 3.9 4.3 - - + -
201L GLY 4.8 6.7 + - - +
202L LEU* 4.0 46.4 + - + +
205L ALA* 6.3 1.0 - - - +
276L LEU* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L GLU 3.1 7.9 + - - -
99L GLU 3.0 7.6 + - - -
101L LYS* 1.3 73.2 - - - +
103L GLN* 1.3 63.1 + - - +
106L THR* 2.6 33.5 + - - -
141L LEU* 4.0 10.8 - - - -
142L PHE* 3.2 33.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L GLU* 2.9 44.5 + - - +
100L ARG* 3.6 31.9 + - - +
102L GLY* 1.3 74.5 - - - +
104L VAL* 1.3 59.1 + - + +
106L THR* 3.8 2.1 - - - -
107L ALA* 2.9 31.6 + - - +
141L LEU* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L ARG* 3.0 24.1 + - - +
101L LYS 3.9 2.5 - - - +
103L GLN* 1.3 81.2 - - + +
105L TRP* 1.3 64.9 + - - +
107L ALA* 3.3 1.9 + - - +
108L ILE* 3.0 41.6 + - + +
202L LEU* 4.0 10.1 - - + -
272L VAL* 4.0 18.6 - - + -
275L VAL* 3.4 30.7 - - + -
276L LEU* 3.9 17.0 - - + -
283L VAL* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L LYS 2.8 23.2 + - - +
102L GLY 4.0 1.6 - - - +
104L VAL* 1.3 73.4 - - - +
106L THR* 1.3 74.6 + - + +
108L ILE* 3.2 9.4 + - + +
109L ILE* 2.9 58.5 + - + +
142L PHE* 3.6 34.8 - + + -
143L ASP* 3.7 20.4 - - + -
148L GLU* 4.0 12.3 - - - -
202L LEU* 4.0 22.4 - - + +
203L LYS* 3.7 36.8 - - + +
216L ASP* 3.5 38.7 + - + +
219L GLU* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L GLY 2.6 22.5 + - - -
103L GLN* 3.9 3.1 - - - -
105L TRP* 1.3 84.8 - - + +
107L ALA* 1.3 67.0 + - - +
109L ILE* 3.4 2.3 + - + +
110L ALA* 3.0 23.6 + - + +
139L LEU* 4.4 23.5 - - + +
140L ARG 3.9 22.7 - - - +
141L LEU* 3.5 8.2 - - + -
142L PHE 3.1 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L GLN 2.9 18.5 + - - +
104L VAL* 3.3 7.4 + - - +
106L THR* 1.3 74.7 - - - +
108L ILE* 1.3 61.3 + - - +
110L ALA* 3.3 8.1 - - - +
111L GLN* 3.2 27.9 + - - +
283L VAL* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L VAL* 3.0 36.4 + - + +
105L TRP* 3.4 12.3 - - + +
106L THR 3.1 0.2 - - - -
107L ALA* 1.3 75.2 - - - +
109L ILE* 1.3 67.1 + - + +
111L GLN* 3.0 22.2 + - - +
112L LYS* 3.1 9.0 + - - +
202L LEU* 4.8 3.1 - - + -
216L ASP* 3.5 22.2 - - + +
217L LEU* 4.1 25.8 - - + +
219L GLU* 4.1 5.2 - - + -
220L PRO* 3.7 22.9 - - + +
268L TYR* 3.9 13.9 - - - +
272L VAL* 4.3 8.3 - - + -
283L VAL* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L TRP* 2.9 51.0 + - + +
106L THR 4.0 3.1 - - - +
108L ILE* 1.3 76.5 - - + +
110L ALA* 1.3 64.6 + - - +
112L LYS* 3.0 9.5 + - + +
113L ILE* 2.9 40.3 + - + +
139L LEU* 4.4 13.7 - - + -
143L ASP* 5.3 0.2 - - - +
148L GLU* 3.2 46.7 - - + +
219L GLU* 3.7 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L THR 3.0 12.8 + - - +
107L ALA* 3.3 14.1 - - - +
109L ILE* 1.3 77.6 - - - +
111L GLN* 1.3 56.9 + - + +
113L ILE* 3.2 3.2 + - - -
114L THR* 2.8 34.5 + - - -
136L ARG* 3.6 19.4 - - + +
139L LEU* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L ALA* 3.2 14.1 + - - +
108L ILE* 3.0 9.2 + - - +
110L ALA* 1.3 76.6 - - + +
112L LYS* 1.3 57.1 + - - +
114L THR* 3.5 7.9 - - - -
115L ASN* 2.9 35.5 + - - +
220L PRO* 4.0 10.2 - - + +
268L TYR* 3.3 17.5 + - - -
283L VAL* 3.3 17.8 - - - +
284L PRO 2.9 22.6 + - - -
285L GLU* 3.5 23.8 - - + +
286L PHE 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L ILE 3.1 6.1 + - - +
109L ILE* 3.0 15.7 + - + +
111L GLN* 1.3 75.9 - - - +
113L ILE* 1.3 53.8 + - - +
115L ASN* 3.0 5.9 + - - +
116L GLN* 2.8 69.1 + - + +
148L GLU* 3.4 30.5 + - - +
152L ALA* 4.8 8.1 - - - +
219L GLU* 3.0 56.1 + - + +
220L PRO* 3.9 10.3 - - + +
222L ARG* 4.3 15.0 - - - +
223L PRO* 4.3 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L ILE* 2.9 33.3 + - + +
110L ALA 3.7 5.6 - - - +
112L LYS* 1.3 79.0 - - + +
114L THR* 1.3 63.4 + - - +
116L GLN* 3.1 18.9 + - - +
117L SER* 2.9 22.2 + - - -
132L LEU* 3.6 36.1 - - + +
133L LEU* 5.3 0.2 - - - -
135L MET 5.2 0.2 - - - -
136L ARG* 4.0 14.6 - - + +
139L LEU* 4.2 19.7 - - + -
147L ARG* 4.5 2.7 - - + +
148L GLU* 4.1 21.1 - - - +
151L ALA* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L ALA 2.8 26.8 + - - -
111L GLN* 3.5 11.6 - - - -
113L ILE* 1.3 71.8 - - - +
115L ASN* 1.3 60.5 + - - +
117L SER* 3.1 4.3 + - - -
118L LEU* 2.8 43.9 + - + +
133L LEU* 4.4 19.1 - - + -
136L ARG* 3.4 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L GLN 2.9 18.9 + - - +
112L LYS 3.5 3.8 - - - +
114L THR* 1.3 76.5 - - - +
116L GLN* 1.3 65.6 + - - +
118L LEU* 3.9 9.3 - - - +
119L HIS* 3.0 20.4 + - - +
220L PRO* 3.0 24.7 + - - +
223L PRO* 3.7 17.4 - - + +
286L PHE* 3.0 25.5 + - - +
287L GLY* 3.2 20.5 - - - -
288L ILE* 3.3 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L LYS* 2.8 53.6 + - + +
113L ILE* 3.1 22.0 + - - +
115L ASN* 1.3 73.8 - - - +
117L SER* 1.3 63.1 + - - +
119L HIS 3.3 1.6 + - - -
120L LEU* 3.0 18.0 + - - +
132L LEU* 3.7 6.1 - - + -
148L GLU 4.8 0.3 - - - +
151L ALA* 4.2 13.0 - - - +
152L ALA* 4.2 13.0 + - - +
155L TYR* 3.2 63.3 - - + -
156L PHE* 4.9 3.8 - - - -
222L ARG* 6.2 1.6 - - - +
223L PRO* 3.9 9.6 - - + +
226L ASP* 4.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ILE 2.9 11.4 + - - -
114L THR 3.4 8.1 - - - -
116L GLN* 1.3 76.7 - - - +
118L LEU* 1.3 57.8 + - - +
120L LEU* 2.8 9.9 + - - +
121L ALA* 2.8 26.3 + - - +
129L ALA* 3.1 23.7 + - - +
132L LEU* 2.7 36.7 - - - +
133L LEU* 3.5 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L THR* 2.8 30.9 + - + +
115L ASN* 3.8 24.9 - - - +
117L SER* 1.3 72.0 - - - +
119L HIS* 1.3 56.9 + - - +
121L ALA* 3.4 11.6 + - + +
122L GLN* 2.9 28.7 + - - +
287L GLY* 5.1 3.1 - - - -
288L ILE* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L ASN 3.0 17.7 + - - +
116L GLN 3.4 4.9 - - - +
118L LEU* 1.3 75.5 - - - +
120L LEU* 1.3 64.5 + - - +
122L GLN* 3.2 20.3 - - - +
123L ARG* 3.2 42.2 + - - +
155L TYR* 2.8 28.7 + - - +
159L LEU* 3.7 20.8 - - + +
223L PRO* 4.7 2.2 + - + -
226L ASP* 3.8 6.5 - - - +
227L GLN* 3.6 39.8 + - + +
230L TYR* 4.3 4.6 - - + +
288L ILE* 3.8 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L GLN 3.0 12.6 + - - +
117L SER* 2.8 7.8 + - - +
119L HIS* 1.3 73.6 - - - +
121L ALA* 1.3 66.1 + - - +
123L ARG* 2.9 14.2 + - - +
125L TYR* 3.1 28.3 + - + +
128L LYS* 4.1 18.6 - - + +
129L ALA* 4.1 8.1 - - + -
132L LEU* 3.7 38.6 - - + -
155L TYR* 3.8 15.3 - - + +
158L THR* 3.8 31.0 - - + +
159L LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L SER 2.8 14.4 + - - +
118L LEU* 3.5 17.7 - - + +
120L LEU* 1.3 71.7 - - - +
122L GLN* 1.3 57.9 + - - +
124L ASP* 2.8 26.3 + - - +
125L TYR 4.5 5.8 - - - +
126L GLY* 4.7 4.6 + - - +
129L ALA* 3.9 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L LEU 2.9 13.9 + - - +
119L HIS* 3.2 20.2 - - + +
121L ALA* 1.3 76.6 - - - +
123L ARG* 1.3 91.5 + - - +
124L ASP* 3.3 7.8 + - - +
227L GLN* 2.8 26.3 + - - +
231L GLU* 4.5 4.4 + - - -
288L ILE* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L HIS* 3.2 36.8 + - - +
120L LEU 2.9 4.7 + - - +
122L GLN* 1.3 102.4 + - - +
124L ASP* 1.3 69.7 + - - +
125L TYR* 3.2 32.8 - - + -
159L LEU* 4.2 11.9 - - + -
227L GLN* 3.5 12.3 + - - +
230L TYR* 3.2 35.7 - - + +
231L GLU* 3.1 39.2 + - - +
----------------------------------------------------------
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