Contacts of the helix formed by residues 97 - 116 (chain B) in PDB entry 4H3E
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 LYS 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 5.3 1.8 - - - +
91B VAL* 4.3 20.0 - - + +
94B ASP* 2.9 27.2 + - - +
96B GLU* 1.3 79.6 - - + +
98B LYS* 1.3 64.3 + - - +
99B GLY 3.2 2.9 - - - +
100B LEU* 3.3 16.4 + - + +
101B PHE* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL 5.6 0.2 - - - -
94B ASP 3.5 6.4 + - - +
95B ALA* 4.0 11.8 + - - +
96B GLU 3.8 2.2 - - - -
97B LYS* 1.3 76.1 - - - +
99B GLY* 1.3 52.5 + - - +
101B PHE* 3.1 10.8 + - + +
102B ASN* 2.8 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.6 13.0 - - - -
97B LYS* 3.2 1.2 - - - +
98B LYS* 1.3 77.2 - - - +
100B LEU* 1.3 60.3 + - - +
102B ASN* 3.3 11.7 + - - +
103B GLN* 3.2 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.5 28.0 - - + -
74B LEU* 3.6 36.8 - - + +
75B ALA* 4.1 9.2 - - + +
79B TYR* 3.2 42.4 - - + +
87B ILE* 4.4 11.9 - - + -
91B VAL* 4.3 11.4 - - + -
97B LYS* 3.3 17.0 + - + +
99B GLY* 1.3 70.6 - - - +
101B PHE* 1.3 66.7 + - - +
103B GLN* 3.4 1.9 + - - +
104B ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.6 42.6 - - + -
91B VAL* 3.8 17.6 - - + +
92B ALA* 3.7 26.0 - - + -
97B LYS 3.0 14.1 + - - +
98B LYS* 3.4 11.0 - - + +
100B LEU* 1.3 76.3 - - - +
102B ASN* 1.3 71.8 + - - +
104B ALA* 3.9 2.2 - - - +
105B ALA* 2.8 49.8 + - + +
179B ALA* 4.2 14.8 - - + -
180B GLY* 4.8 3.4 - - - -
181B CYS 4.8 6.3 - - - -
184B THR* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 3.3 49.9 - - + +
98B LYS* 2.8 31.0 + - - +
99B GLY* 3.3 8.7 + - - +
101B PHE* 1.3 85.0 - - - +
103B GLN* 1.3 62.3 + - - +
106B GLN* 3.0 36.2 + - - +
179B ALA* 3.7 13.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
154A PHE* 4.5 10.7 - - - -
66B ALA 4.1 0.3 - - - +
67B TYR* 3.2 46.7 - - - +
70B LYS* 3.3 43.3 - - + +
71B LEU* 3.8 14.8 - - - +
74B LEU* 4.0 7.5 - - + +
99B GLY* 3.2 19.7 + - - +
100B LEU* 4.1 2.9 - - - +
102B ASN* 1.3 82.4 - - - +
104B ALA* 1.3 60.3 + - - +
106B GLN* 3.3 1.2 + - - +
107B HIS* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.9 25.3 - - + +
84B ILE* 3.4 17.8 - - + +
87B ILE* 4.1 17.9 - - + -
88B ILE* 3.7 16.3 - - + +
100B LEU 3.0 18.5 + - - +
101B PHE* 3.9 2.9 - - - +
103B GLN* 1.3 77.2 - - - +
105B ALA* 1.3 64.4 + - - +
107B HIS* 3.4 0.5 + - - +
108B PHE 3.1 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.7 15.4 - - + +
101B PHE* 2.8 32.9 + - + +
104B ALA* 1.3 76.9 - - - +
106B GLN* 1.3 55.9 + - - +
108B PHE* 3.3 2.6 + - - +
109B ASN* 2.8 35.2 + - - +
179B ALA* 3.2 28.5 - - + +
181B CYS* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 4.1 4.0 - - + -
67B TYR* 3.1 52.8 + - + -
102B ASN 3.0 22.3 + - - +
103B GLN 3.9 0.2 - - - +
104B ALA 3.3 0.2 - - - -
105B ALA* 1.3 73.0 - - - +
107B HIS* 1.3 58.3 + - - +
109B ASN* 3.1 15.2 + - - -
110B HIS* 2.7 49.0 + - - +
158B TRP* 2.8 30.1 + - - -
178B ASN 3.5 7.6 - - - +
179B ALA* 3.5 9.4 - - + -
196B TRP* 3.3 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.8 15.4 - - + +
27B LEU 5.4 0.8 + - - -
34B ALA* 4.7 6.6 - - + +
35B GLU 4.1 6.0 + - - -
37B PRO* 3.7 24.9 - - + -
64B HIS* 3.1 22.5 + - - -
67B TYR* 4.3 4.4 - - + +
68B VAL* 3.6 18.6 - - + +
71B LEU* 3.6 28.0 - - + -
84B ILE* 3.7 23.9 - - + +
103B GLN 2.9 18.6 + - - +
104B ALA 3.5 4.7 - - - +
105B ALA 3.3 0.2 - - - -
106B GLN* 1.3 72.1 - - - +
108B PHE* 1.3 62.0 + - - +
111B THR* 2.8 48.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 4.0 17.0 - - - -
23B LEU* 3.9 22.2 - - + +
26B LEU* 4.1 13.9 - - + -
84B ILE* 4.2 4.7 - - + -
85B GLU* 3.6 39.3 - - + -
88B ILE* 3.8 20.2 - - + -
104B ALA 3.1 4.0 + - - +
105B ALA 3.6 6.1 - - - +
107B HIS* 1.3 81.2 - - - +
109B ASN* 1.3 77.9 + - - +
111B THR* 3.6 1.0 - - - -
112B PHE* 2.9 38.5 + + + +
160B TRP* 4.4 5.4 - + - -
181B CYS* 3.7 18.4 - - - -
183B LEU* 5.2 2.7 - - + -
189B PRO* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 2.8 21.3 + - - +
106B GLN* 3.1 21.5 + - - +
108B PHE* 1.3 83.9 - - - +
110B HIS* 1.3 57.6 + - - +
112B PHE* 3.4 2.9 + - - +
113B TYR* 2.9 29.5 + - - +
158B TRP* 3.4 33.7 - - + +
160B TRP* 3.2 27.7 - - + -
179B ALA 3.3 21.4 + - - -
180B GLY 3.6 5.5 + - - -
181B CYS* 3.5 8.3 - - - -
192B ALA* 4.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B HIS* 3.3 20.3 + + - -
63B HIS* 4.9 0.8 - - - +
64B HIS* 3.6 32.5 - + + +
67B TYR* 3.3 29.8 - + - -
106B GLN* 2.7 39.4 + - - +
109B ASN* 1.3 68.8 - - - +
111B THR* 1.3 66.4 + - - +
113B TYR* 3.7 3.1 - + - +
114B PHE* 2.9 39.9 + + + -
158B TRP* 3.5 23.6 - + - -
194B ASP* 3.5 0.2 + - - -
198B HIS* 3.7 2.2 + - - -
301B FE2 2.1 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.9 11.9 - - + -
26B LEU* 3.9 12.1 - - + +
37B PRO* 3.4 21.5 - - + +
64B HIS* 3.3 16.5 - - - -
107B HIS* 2.8 28.8 + - - -
108B PHE 3.6 3.4 - - - -
110B HIS* 1.3 76.1 - - - +
112B PHE* 1.3 64.8 + - - +
114B PHE* 3.7 4.0 + - - +
115B ARG* 3.4 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.5 31.6 - - + -
23B LEU* 4.3 10.7 - - + +
108B PHE* 2.9 35.2 + + + +
109B ASN* 3.6 4.5 - - - +
111B THR* 1.3 75.3 - - - +
113B TYR* 1.3 65.2 + - - +
115B ARG* 3.0 16.9 + - - +
116B CYS* 3.1 35.7 + - - -
160B TRP* 4.2 4.7 - + + -
189B PRO* 3.5 26.7 - - + -
190B VAL 3.6 21.8 - - - -
191B LEU* 3.7 6.5 - - - -
192B ALA* 3.8 14.4 - - + -
223B PHE* 3.8 10.7 - + - -
227B MET* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.9 13.0 - - - -
56B MET* 5.4 1.5 - - + +
59B HIS* 3.5 29.5 + + - -
109B ASN 2.9 20.7 + - - +
110B HIS* 3.7 5.2 - + - +
112B PHE* 1.3 73.7 - - - +
114B PHE* 1.3 81.6 + + - +
116B CYS* 2.9 26.4 + - - +
117B ILE* 3.6 17.5 + - + +
158B TRP* 3.7 13.7 - + + -
192B ALA* 3.3 30.1 - - + +
193B VAL* 4.0 4.5 - - - -
194B ASP* 3.5 26.7 - - + -
199B ALA* 4.4 4.0 + - - +
211B TYR* 2.8 23.1 + - - -
215B ILE* 3.8 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.6 32.9 - - + +
41B PHE* 3.8 12.1 - + + -
56B MET* 4.7 10.8 - - - -
59B HIS* 3.7 45.3 - + + -
60B TYR* 3.9 11.4 - + + -
64B HIS* 3.6 34.3 - + + -
110B HIS* 2.9 31.0 + + + +
111B THR* 4.2 4.5 - - - +
113B TYR* 1.3 97.5 - + - +
115B ARG* 1.3 57.9 + - + +
116B CYS 3.2 0.2 - - - -
117B ILE* 3.1 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.5 31.8 - - - +
26B LEU* 4.9 6.5 - - - +
37B PRO* 4.0 16.0 - - - +
38B LYS 5.0 8.8 + - - +
111B THR* 3.4 34.2 + - - +
112B PHE 3.0 10.8 + - - +
114B PHE* 1.3 77.3 - - + +
116B CYS* 1.3 60.8 + - - +
117B ILE 3.2 3.1 + - - +
220B ASP* 3.9 8.8 - - - +
223B PHE* 3.3 51.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.1 41.6 + - - -
113B TYR 2.9 10.5 + - - +
115B ARG* 1.3 77.6 - - - +
117B ILE* 1.3 62.0 + - + +
190B VAL 4.2 1.8 - - - -
191B LEU* 3.9 22.2 - - + -
192B ALA 3.6 22.2 - - - +
219B ILE* 3.3 12.6 - - + +
220B ASP* 2.8 25.2 + - - +
223B PHE* 4.0 12.3 - - - -
224B VAL* 4.5 1.8 - - + -
----------------------------------------------------------
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