Contacts of the helix formed by residues 113 - 128 (chain B) in PDB entry 2A1H
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 ASP 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B SER* 2.9 26.1 + - - +
5B PHE* 5.3 0.2 - - - -
112B PHE* 1.3 78.4 - - - +
114B LYS* 1.3 66.6 + - - +
115B LEU* 3.1 33.1 + - - +
116B GLU* 3.2 31.2 + - + +
117B LEU* 3.2 9.9 + - - +
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Residues in contact with LYS 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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97B MET* 3.8 34.0 - - + +
98B ASP* 2.8 40.5 + - - +
101B LEU* 3.6 33.3 - - + +
112B PHE* 3.6 9.9 + - + +
113B ASP* 1.3 74.2 + - - +
115B LEU* 1.3 65.9 + - + +
117B LEU* 3.5 0.5 + - - +
118B LEU* 3.1 26.6 + - - +
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Residues in contact with LEU 115 (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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94B TRP* 3.9 30.5 - - + +
113B ASP* 3.1 11.7 + - - +
114B LYS* 1.3 83.4 - - + +
116B GLU* 1.3 62.2 + - + +
118B LEU* 3.7 11.5 - - + +
119B GLU* 3.1 27.9 + - - +
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Residues in contact with GLU 116 (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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4B SER* 4.4 1.8 - - - +
5B PHE* 3.4 28.3 - - + +
6B LYS* 3.5 15.3 - - + +
7B ALA* 2.8 40.4 + - - +
8B ALA 4.5 0.9 + - - -
113B ASP* 3.2 28.6 + - + +
115B LEU* 1.3 75.6 - - + +
117B LEU* 1.3 64.5 + - - +
119B GLU* 3.5 1.3 + - - -
120B CYS* 3.1 27.4 + - - -
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Residues in contact with LEU 117 (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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5B PHE* 3.8 23.4 - - + -
39B LEU* 3.9 19.1 - - + -
97B MET* 3.7 14.8 - - + -
100B MET* 3.7 27.1 - - + -
112B PHE* 3.5 27.8 - - + -
113B ASP 3.2 10.5 + - - +
114B LYS 3.9 6.7 - - - +
116B GLU* 1.3 74.1 - - - +
118B LEU* 1.3 60.1 + - - +
120B CYS* 3.1 4.4 + - - +
121B ILE* 2.9 38.6 + - + +
144B PRO* 5.1 0.9 - - + -
163B LEU* 3.7 24.5 - - + -
165B VAL* 4.7 0.4 - - + -
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Residues in contact with LEU 118 (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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78B MET* 5.8 0.2 - - - -
90B LEU* 4.2 8.7 - - + -
93B PRO* 3.6 33.4 - - + -
94B TRP* 3.6 37.0 - - + +
97B MET* 4.1 15.9 - - + -
114B LYS 3.1 18.0 + - - +
115B LEU* 3.7 13.5 - - + +
116B GLU 3.3 0.2 - - - -
117B LEU* 1.3 77.3 - - - +
119B GLU* 1.3 56.8 + - - +
121B ILE* 3.3 6.6 + - + +
122B ARG* 2.9 26.4 + - - +
363B PHE* 3.9 31.0 - - + -
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Residues in contact with GLU 119 (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 ALA* 3.7 25.6 - - + -
115B LEU 3.1 18.7 + - - +
116B GLU* 4.8 0.4 - - - +
117B LEU 3.3 0.2 - - - -
118B LEU* 1.3 74.0 - - - +
120B CYS* 1.3 59.6 + - - +
122B ARG* 2.9 49.1 + - - +
123B ARG* 3.0 41.0 + - + +
363B PHE* 4.9 5.2 - - + -
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Residues in contact with CYS 120 (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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5B PHE* 4.0 9.9 - - - -
7B ALA* 3.9 22.0 - - - -
10B LEU* 4.5 12.3 - - + -
39B LEU* 3.7 28.0 - - + +
51B PRO* 3.9 27.6 - - - -
53B ILE* 4.4 1.2 - - - +
116B GLU 3.1 20.3 + - - +
117B LEU* 3.1 11.5 + - + +
119B GLU* 1.3 76.5 - - - +
121B ILE* 1.3 58.0 + - - +
123B ARG* 3.5 3.5 + - - +
124B LEU* 3.1 26.0 + - - +
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Residues in contact with ILE 121 (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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39B LEU* 4.7 1.3 - - + -
78B MET* 4.4 4.5 - - + -
90B LEU* 4.5 11.2 - - + -
97B MET* 3.7 30.7 - - + -
117B LEU* 2.9 30.0 + - + +
118B LEU* 3.6 7.4 - - + +
120B CYS* 1.3 74.6 - - - +
122B ARG* 1.3 58.2 + - - +
124B LEU* 3.2 7.3 + - + +
125B ILE* 3.0 47.5 + - + +
142B VAL* 3.9 15.7 - - + -
144B PRO* 4.0 19.5 - - + -
165B VAL* 4.0 22.2 - - + -
167B LEU* 5.7 0.2 - - + -
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Residues in contact with ARG 122 (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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90B LEU* 5.2 1.5 - - - +
118B LEU 2.9 16.7 + - - +
119B GLU* 2.9 43.2 + - - +
121B ILE* 1.3 78.1 - - - +
123B ARG* 1.3 77.1 + - - +
125B ILE* 3.4 5.0 + - - -
126B GLU* 2.9 52.2 + - - +
363B PHE* 3.8 25.6 - - + -
364B PRO 3.8 15.0 - - - -
365B VAL* 2.8 50.0 + - + +
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Residues in contact with ARG 123 (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 ALA 5.4 2.4 + - - +
10B LEU* 3.7 50.6 + - + +
12B LEU* 4.0 28.1 - - - +
53B ILE* 3.9 7.9 - - + +
119B GLU* 3.0 33.6 + - + +
120B CYS 3.8 1.3 - - - +
121B ILE 3.3 0.2 - - - -
122B ARG* 1.3 93.7 - - - +
124B LEU* 1.3 59.7 + - - +
126B GLU* 3.4 18.1 + - - +
127B VAL* 3.1 34.6 + - - +
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Residues in contact with LEU 124 (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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37B HIS* 3.9 11.0 - - + +
38B MET* 3.8 29.6 - - - +
39B LEU* 3.7 10.1 - - + +
53B ILE* 3.8 24.8 - - + +
120B CYS 3.1 13.7 + - - +
121B ILE* 3.5 10.1 - - + +
123B ARG* 1.3 75.0 - - - +
125B ILE* 1.3 64.3 + - - +
127B VAL* 3.3 5.1 + - + +
128B ASP* 3.1 22.6 + - - +
165B VAL* 3.6 43.5 - - + +
167B LEU* 4.0 19.3 - - + -
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Residues in contact with ILE 125 (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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80B ALA* 4.2 2.7 - - + -
88B VAL* 4.0 25.4 - - + -
90B LEU* 3.9 23.1 - - + -
121B ILE* 3.0 37.6 + - + +
122B ARG 3.9 3.6 - - - +
124B LEU* 1.3 75.2 - - - +
126B GLU* 1.3 52.5 + - - +
128B ASP 3.2 2.9 - - - -
129B LYS* 2.8 33.4 + - + -
132B VAL* 4.3 4.7 - - + -
140B LEU* 4.0 17.5 - - + -
142B VAL* 3.9 19.5 - - + -
167B LEU* 4.1 25.4 - - + -
365B VAL* 4.1 9.0 - - + -
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Residues in contact with GLU 126 (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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122B ARG* 2.9 40.1 + - - +
123B ARG* 3.5 28.8 + - - +
124B LEU 3.2 0.2 - - - -
125B ILE* 1.3 76.6 - - - +
127B VAL* 1.3 62.8 + - + +
129B LYS* 3.3 20.1 - - + +
365B VAL* 3.9 18.3 - - + +
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Residues in contact with VAL 127 (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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12B LEU* 3.9 36.6 - - + -
14B MET* 4.9 6.5 - - + -
37B HIS* 3.6 38.9 - - + +
53B ILE* 4.5 7.4 - - + -
123B ARG* 3.1 19.8 + - - +
124B LEU* 3.3 9.6 + - - +
126B GLU* 1.3 78.3 - - + +
128B ASP* 1.3 59.1 + - - +
129B LYS 3.4 2.0 + - - -
130B ASP 5.3 0.3 + - - -
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Residues in contact with ASP 128 (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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35B THR* 2.9 28.1 + - - -
36B ASP* 3.8 6.5 - - - +
37B HIS* 2.8 50.7 + - - +
124B LEU 3.1 13.5 + - - +
125B ILE* 3.2 4.7 - - - -
127B VAL* 1.3 78.5 - - - +
129B LYS* 1.3 56.5 + - - -
130B ASP* 3.3 3.6 - - - -
131B TRP* 3.0 38.4 + - + +
132B VAL* 4.0 4.7 + - - +
140B LEU* 5.3 1.2 - - - +
167B LEU* 4.0 16.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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