Contacts of the helix formed by residues 99 - 114 (chain B) in PDB entry 6GHM
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 GLN 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.1 2.3 - - - +
67B GLY 3.0 13.8 + - - +
68B GLN* 5.8 0.2 - - - +
69B TYR* 3.7 22.4 - - + +
70B TYR* 3.2 50.9 + - - +
98B LYS* 1.3 88.3 - - + +
100B SER* 1.3 58.5 + - - +
101B LEU 3.2 2.5 - - - -
102B GLU* 3.3 31.9 - - - +
103B THR* 2.8 30.3 + - - -
139B GLU* 3.7 0.9 - - - -
143B ARG* 4.9 1.6 - - - +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 3.6 15.2 - - - -
94B VAL* 3.4 11.4 - - - +
95B ASP* 3.0 28.9 + - - -
97B GLY 4.2 3.1 + - - -
99B GLN* 1.3 75.6 - - - +
101B LEU* 1.3 56.8 + - - +
103B THR* 3.4 2.5 + - - -
104B ILE* 2.9 32.9 + - - +
135B GLY 5.7 0.3 - - - -
136B PHE* 3.7 24.2 - - - +
139B GLU* 3.0 17.6 + - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 5.0 2.7 - - + -
100B SER* 1.3 74.4 - - - +
102B GLU* 1.3 67.6 + - - +
104B ILE* 4.1 1.8 - - - -
105B CYS* 3.0 36.0 + - - +
136B PHE* 3.9 16.8 - - + -
139B GLU* 2.9 36.3 + - + +
140B CYS* 4.1 7.0 - - - -
143B ARG* 3.8 27.1 - - - +
144B TYR* 4.1 31.2 - - + -
148B LEU* 5.1 0.4 - - + -
152B PHE* 3.6 34.5 - - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.2 18.4 - - + +
19B VAL* 4.7 12.0 - - + +
69B TYR* 3.5 45.3 - - + -
99B GLN* 3.3 29.3 - - - +
100B SER 3.5 0.2 - - - -
101B LEU* 1.3 73.4 - - - +
103B THR* 1.3 63.4 + - - +
105B CYS* 3.9 0.7 - - - +
106B LEU* 3.0 20.3 + - - +
143B ARG* 2.4 46.0 + - - -
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.7 20.9 - - + -
67B GLY* 3.4 10.2 - - - -
69B TYR* 3.5 23.4 - - - -
72B LEU* 4.1 6.6 - - + +
93B TYR* 3.6 23.3 - - + +
99B GLN 2.8 21.1 + - - -
100B SER 3.5 5.2 - - - -
101B LEU 3.2 0.2 - - - -
102B GLU* 1.3 78.9 - - - +
104B ILE* 1.3 63.7 + - - +
106B LEU* 3.3 2.3 + - - +
107B LEU* 3.1 42.3 + - + +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 4.0 27.4 - - + -
94B VAL* 4.2 14.8 - - + -
100B SER 2.9 25.0 + - - +
101B LEU* 3.7 7.2 - - - +
103B THR* 1.3 76.4 - - - +
105B CYS* 1.3 60.1 + - - +
107B LEU* 4.4 8.3 - - + -
108B LEU* 2.8 59.9 + - + +
120B LEU* 5.2 2.2 - - + -
136B PHE* 4.4 3.1 - - + -
152B PHE* 3.5 26.5 - - + -
156B PHE* 3.9 29.8 - - + -
159B LEU* 6.2 1.1 - - + -
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.8 7.4 - - + -
30B LEU* 4.0 25.8 - - + -
35B ILE* 4.0 23.8 - - - -
38B LEU* 3.8 20.8 - - + +
101B LEU* 3.0 28.5 + - - +
102B GLU 3.9 2.0 - - - +
104B ILE* 1.3 79.1 - - - +
106B LEU* 1.3 57.6 + - - +
108B LEU* 3.8 3.3 - - - -
109B ALA* 2.8 30.0 + - - +
152B PHE* 4.2 17.5 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.5 12.3 - - + -
16B LEU* 3.5 22.8 - - + +
17B LEU* 3.9 22.2 - - + -
69B TYR* 3.6 27.8 - - + +
72B LEU* 4.3 4.0 - - + -
73B LEU* 3.9 9.0 - - + -
76B PHE* 4.1 13.7 - - + -
102B GLU 3.0 17.6 + - - +
103B THR 3.8 2.5 - - - +
105B CYS* 1.3 77.7 - - - +
107B LEU* 1.3 57.0 + - - +
109B ALA* 3.2 2.8 + - - +
110B TYR* 2.9 62.5 + - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 5.2 1.3 - - + -
72B LEU* 3.9 19.1 - - + -
76B PHE* 4.3 3.6 - - + -
89B PHE* 4.0 21.3 - - + -
93B TYR* 3.3 46.2 - - + -
103B THR* 3.1 27.1 + - + +
104B ILE* 3.8 5.2 - - + +
106B LEU* 1.3 75.8 - - - +
108B LEU* 1.3 57.9 + - - +
110B TYR 3.3 0.5 + - - -
111B LYS* 2.9 27.5 + - - +
118B PHE* 3.3 32.0 - - + -
120B LEU* 3.9 16.8 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.3 16.2 - - + +
39B CYS* 4.2 14.4 - - - -
42B SER* 3.4 30.1 - - - +
46B PHE* 4.0 20.2 - - + -
104B ILE* 2.8 44.4 + - + +
105B CYS* 3.8 4.5 - - - +
107B LEU* 1.3 71.8 - - - +
109B ALA* 1.3 63.7 + - - +
111B LYS* 3.1 5.5 + - - +
112B ILE* 2.9 29.7 + - - +
120B LEU* 4.3 4.5 - - + -
152B PHE* 4.0 26.2 - - + -
155B CYS* 4.1 8.1 - - - -
156B PHE* 5.8 1.6 - - + -
159B LEU* 5.7 1.1 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.9 10.0 - - + +
12B ILE* 4.5 7.6 - - + -
13B ILE* 3.7 26.9 - - + +
16B LEU* 4.7 0.4 - - + -
38B LEU* 4.0 21.4 - - + +
105B CYS 2.8 19.1 + - - +
106B LEU* 3.5 7.2 - - - +
108B LEU* 1.3 76.4 - - - +
110B TYR* 1.3 58.0 + - - +
112B ILE* 3.2 4.0 + - - +
113B LYS* 2.9 28.8 + - - +
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.1 24.2 - - + +
17B LEU* 3.8 17.2 - - - +
76B PHE* 3.9 19.7 - + - -
81B PHE* 3.4 23.2 - - - +
82B PRO* 3.9 28.8 + - + -
106B LEU* 2.9 44.1 + - + +
109B ALA* 1.3 74.5 - - - +
111B LYS* 1.3 60.9 + - - +
113B LYS* 4.4 0.7 - - - +
114B TYR* 2.9 57.2 + + + +
118B PHE* 3.6 30.5 - + + +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 4.8 6.5 - - - -
45B ILE* 3.8 19.1 - - + +
46B PHE* 3.6 36.8 - - + -
49B GLN* 2.8 29.2 + - - -
107B LEU 2.9 14.4 + - - +
108B LEU* 3.4 12.8 - - - +
110B TYR* 1.3 77.7 - - - +
112B ILE* 1.3 61.1 + - - +
115B PRO* 3.0 42.7 + - + +
118B PHE* 2.9 36.5 + - + +
119B PHE* 3.4 13.7 - - - +
120B LEU* 4.2 6.7 - - + +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 6.1 4.3 - - + -
9B LEU* 3.8 20.0 - - + +
37B GLY 5.2 0.2 - - - -
38B LEU* 3.6 49.4 - - + +
41B LYS* 3.6 36.6 - - + -
42B SER* 3.9 15.9 - - - +
45B ILE* 3.8 11.5 - - + +
108B LEU 2.9 15.6 + - - +
109B ALA 3.7 4.9 - - - +
111B LYS* 1.3 78.0 - - - +
113B LYS* 1.3 61.3 + - - +
114B TYR 3.6 0.2 + - - -
115B PRO* 3.6 10.4 - - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.6 16.6 - - + +
10B ASP* 3.0 31.6 + - - +
13B ILE* 3.8 20.4 - - + -
109B ALA 2.9 16.9 + - - +
110B TYR* 4.6 1.1 - - - -
112B ILE* 1.3 79.4 - - - +
114B TYR* 1.3 100.4 + - + +
115B PRO* 3.5 6.4 - - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO* 3.8 30.6 + - + -
83B PRO* 3.6 38.7 - - + +
110B TYR* 2.9 32.4 + + - +
111B LYS 3.5 2.7 - - - -
113B LYS* 1.3 123.5 - - + +
115B PRO* 1.3 65.3 - - - +
116B GLU 3.2 2.9 - - - -
117B ASN* 3.0 28.5 + - + +
118B PHE* 3.1 18.3 + - + +
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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) + - + + + + + -
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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