Contacts of the helix formed by residues 1 - 13 (chain B) in PDB entry 2H4C
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 ASN 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.4 2.9 - - - +
33A GLY 3.2 11.2 - - - +
34A GLN* 2.6 32.2 - - - +
2B LEU* 1.3 62.2 + - - +
3B PHE* 2.8 28.0 + - - +
4B GLN* 3.1 26.2 + - - +
5B PHE* 3.2 8.7 + - - +
52B TYR* 5.7 2.9 - - - -
68B PRO 3.4 15.1 + - - -
69B LYS 2.8 29.6 - - - +
71B VAL 2.6 26.5 + - - -
72B GLU* 2.7 28.6 + - - +
73B TYR* 4.4 6.6 + - - -
95B VAL* 5.0 0.4 - - - +
99B ASP* 4.9 1.4 - - - +
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Residues in contact with LEU 2 (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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30A GLY 4.2 7.0 - - - +
31A TRP* 3.8 40.2 - - + +
32A GLY 3.0 22.1 + - - +
69A LYS* 5.6 7.4 - - - +
1B ASN* 1.3 68.9 - - - +
3B PHE* 1.3 65.2 + - - +
5B PHE* 3.4 36.1 - - + +
6B ALA* 2.9 22.2 + - - +
48B HIS* 4.9 5.8 - - + -
52B TYR* 4.7 13.0 - - + +
69B LYS* 4.0 19.9 + - + +
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Residues in contact with PHE 3 (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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24A ILE* 6.0 0.9 - - + -
26A GLY 5.1 1.8 - - - -
27A CYS* 3.7 11.7 - - - -
31A TRP 3.6 9.9 - - - -
32A GLY* 3.3 26.2 + - - -
33A GLY 3.2 4.7 - - - -
34A GLN* 3.2 51.4 - - + +
120A TYR* 4.6 10.1 - - + -
121A ALA 3.3 28.7 - - - -
122A ILE* 3.5 25.6 - - + -
126A CYS* 4.0 21.3 - - + -
1B ASN* 2.8 8.0 + - - +
2B LEU* 1.3 75.5 - - - +
4B GLN* 1.3 65.9 + - - +
6B ALA* 2.9 18.3 + - - +
7B ARG* 3.0 16.4 + - - +
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Residues in contact with GLN 4 (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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34A GLN* 4.4 6.4 - - - +
122A ILE* 5.3 2.9 - - + +
1B ASN* 3.2 24.4 + - - +
3B PHE* 1.3 77.2 - - + +
5B PHE* 1.3 54.8 + - - +
7B ARG* 3.1 11.3 + - - +
8B LEU* 2.8 33.1 + - - +
72B GLU* 3.5 17.3 - - - +
73B TYR* 2.9 87.5 + - + +
75B TYR* 4.1 14.8 - - + +
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Residues in contact with PHE 5 (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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31A TRP* 3.6 21.5 - + - -
1B ASN 3.2 6.9 + - - +
2B LEU* 3.5 36.8 - - + +
3B PHE 3.1 1.0 - - - -
4B GLN* 1.3 73.6 - - - +
6B ALA* 1.3 58.3 + - - +
8B LEU 4.5 0.2 - - - +
9B ILE* 2.7 65.6 + - + +
22B TYR* 6.3 0.2 - - + -
45B CYS* 6.3 1.6 - - - -
48B HIS* 4.1 24.7 - + - -
52B TYR* 4.9 0.2 - - - +
73B TYR* 4.2 0.4 + - - -
99B ASP* 2.9 52.9 - - + +
102B ALA* 4.1 9.4 - - + -
103B ALA 4.6 0.7 - - - -
106B PHE* 4.1 19.5 - + - -
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Residues in contact with ALA 6 (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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31A TRP* 4.2 6.0 - - + +
2B LEU 2.9 11.9 + - - +
3B PHE* 2.9 12.4 + - - +
5B PHE* 1.3 77.3 - - - +
7B ARG* 1.3 59.9 + - + +
9B ILE* 3.6 2.6 + - - +
10B ASP* 2.4 34.7 + - - +
19B PHE* 3.6 45.8 - - + -
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Residues in contact with ARG 7 (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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122A ILE* 4.9 21.8 - - + +
3B PHE 3.0 14.2 + - - +
4B GLN* 3.2 10.5 - - - +
6B ALA* 1.3 77.9 - - + +
8B LEU* 1.3 64.0 + - - +
10B ASP* 3.3 22.6 + - - +
11B ALA* 3.5 6.8 + - - +
75B TYR* 3.3 21.9 + - + +
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Residues in contact with LEU 8 (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 GLN 2.8 17.7 + - - +
5B PHE 4.4 1.1 - - - +
7B ARG* 1.3 70.9 - - - +
9B ILE* 1.3 67.9 + - - +
11B ALA* 3.3 21.2 + - + +
12B LYS 4.5 0.9 + - - -
73B TYR* 3.0 33.9 - - + +
75B TYR* 3.1 33.9 - - + -
77B TYR* 5.7 3.6 - - + -
82B ILE* 3.5 45.5 - - + +
96B CYS* 4.3 5.4 - - - +
99B ASP* 3.5 19.5 - - + -
103B ALA* 3.3 15.6 - - + +
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Residues in contact with ILE 9 (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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31A TRP* 3.7 25.6 - - + -
5B PHE* 2.7 58.6 + - + +
6B ALA 3.7 3.8 - - - +
7B ARG 3.3 0.2 - - - -
8B LEU* 1.3 76.5 - - - +
10B ASP* 1.3 64.0 + - - +
11B ALA 3.4 0.3 + - - -
12B LYS 3.9 2.4 + - - -
13B GLN* 3.2 35.6 + - - +
18B SER 3.5 19.5 - - - +
19B PHE* 4.0 9.6 - - + -
22B TYR* 4.1 16.2 - - + -
103B ALA* 3.6 12.9 - - + +
106B PHE* 4.6 7.6 - - + -
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Residues in contact with ASP 10 (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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6B ALA 2.4 27.4 - - - +
7B ARG* 3.5 13.7 - - - +
9B ILE* 1.3 79.8 - - - +
11B ALA* 1.3 56.2 + - - +
13B GLN* 2.5 33.8 - - - +
14B GLU 3.5 14.9 + - - +
16B ALA* 3.4 7.2 - - - +
17B PHE* 2.4 33.9 + - - -
18B SER* 3.8 9.8 + - - +
19B PHE* 4.0 7.2 - - - +
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Residues in contact with ALA 11 (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 ARG 3.5 6.3 + - - +
8B LEU* 3.3 19.1 + - + +
10B ASP* 1.3 77.7 - - - +
12B LYS* 1.3 59.3 + - - +
13B GLN 3.9 1.9 - - - +
77B TYR* 3.4 53.7 + - + -
82B ILE* 4.9 6.7 - - + -
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Residues in contact with LYS 12 (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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8B LEU 4.5 1.4 + - - +
9B ILE 3.9 3.0 + - - +
10B ASP 3.4 0.4 - - - -
11B ALA* 1.3 75.3 - - - +
13B GLN* 1.3 73.0 - - + +
77B TYR* 5.2 1.8 - - - -
103B ALA* 4.5 4.7 - - + +
107B ARG* 2.9 78.6 - - + +
108B GLU* 4.4 11.9 - - - +
110B MET* 6.5 0.2 - - - -
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Residues in contact with GLN 13 (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 ILE* 3.2 34.2 + - - +
10B ASP 2.5 20.5 + - - +
11B ALA 3.9 2.9 - - - +
12B LYS* 1.3 95.1 - - + +
14B GLU* 1.3 65.5 + - - +
18B SER* 3.8 15.1 - - - +
22B TYR* 3.3 17.8 + - - -
103B ALA 3.5 20.0 + - - -
106B PHE* 3.6 5.7 - - - +
107B ARG* 3.5 19.3 - - - +
110B MET* 3.2 36.9 - - + +
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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