Contacts of the helix formed by residues 1 - 12 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G GLY 3.0 15.9 - - - +
33G GLY* 3.9 3.5 + - - -
34G GLN* 3.5 37.0 + - - +
2H LEU* 1.3 64.7 + - - +
3H PHE* 3.3 8.6 + - - +
4H GLN* 2.8 51.7 + - - +
5H PHE* 2.8 27.6 + - - +
52H TYR* 4.8 2.5 - - - -
68H PRO 3.8 16.3 + - - -
69H LYS 3.3 13.7 - - - +
71H VAL 2.7 31.6 + - - +
72H GLU* 3.8 11.3 - - - +
73H TYR* 3.4 15.2 + - - -
99H ASP* 4.0 1.2 - - - +
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Residues in contact with LEU 2 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G GLY 2.9 27.8 - - - +
31G TRP* 3.2 40.9 - - + +
32G GLY 3.0 2.7 + - - +
69G LYS* 6.2 1.8 - - - +
1H ASN* 1.3 74.2 - - - +
3H PHE* 1.3 63.5 + - - +
5H PHE* 3.7 17.0 - - + -
6H ALA* 3.1 19.8 + - - +
48H HIS* 5.4 0.7 - - + -
52H TYR* 4.2 25.8 - - + +
69H LYS* 3.4 35.9 + - + +
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Residues in contact with PHE 3 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ILE* 4.2 15.0 - - + -
26G GLY 4.0 14.4 - - - -
27G CYS* 3.3 29.8 - - + -
31G TRP 3.3 13.9 + - - -
32G GLY* 3.3 21.5 + - - -
33G GLY 4.1 0.4 - - - -
34G GLN* 4.2 9.0 - - + -
120G TYR 3.2 32.1 - - - -
121G ALA* 4.1 3.6 - - - -
122G ILE* 3.1 39.5 - - + -
126G CYS* 4.4 4.5 - - - -
1H ASN* 3.2 9.1 + - - +
2H LEU* 1.3 79.7 - - - +
4H GLN* 1.3 62.7 + - - +
6H ALA* 3.7 5.4 + - + +
7H ARG* 3.4 32.1 + - - +
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Residues in contact with GLN 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G GLN* 4.7 2.5 - - - +
122G ILE* 5.1 6.6 - - + +
1H ASN* 2.8 35.0 + - - +
2H LEU 3.2 0.2 - - - -
3H PHE* 1.3 78.5 - - + +
5H PHE* 1.3 63.6 + - - +
7H ARG* 2.9 20.1 + - - +
8H LEU* 3.0 13.9 + - - +
72H GLU* 3.0 37.5 + - - +
73H TYR* 3.0 63.9 + - + +
75H TYR* 5.1 12.0 - - + -
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Residues in contact with PHE 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G TRP* 3.6 24.9 - + - -
1H ASN 2.8 12.4 + - - +
2H LEU* 3.8 15.0 - - + +
3H PHE 3.4 0.2 - - - -
4H GLN* 1.3 77.4 - - - +
6H ALA* 1.3 56.6 + - - +
8H LEU* 3.2 2.8 + - + +
9H ILE* 2.8 47.4 + - + +
45H CYS* 6.2 0.7 - - - -
48H HIS* 3.2 42.8 - + + -
52H TYR* 4.3 2.9 - - - +
73H TYR* 3.2 7.4 + - - -
99H ASP* 3.1 32.5 - - + +
102H ALA* 3.6 23.3 - - + -
103H ALA 4.4 0.2 - - - -
106H PHE* 4.1 7.4 - + - -
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Residues in contact with ALA 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G TRP* 3.7 12.5 - - + -
2H LEU 3.1 17.5 + - - +
3H PHE* 3.9 6.3 - - - +
5H PHE* 1.3 76.8 - - - +
7H ARG* 1.3 53.9 + - + +
9H ILE* 3.5 8.3 - - - +
10H ASP* 2.7 39.2 + - - +
19H PHE* 3.2 39.9 - - + +
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Residues in contact with ARG 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ALA* 4.0 12.5 - - - +
122G ILE* 2.9 64.1 + - - +
3H PHE* 3.4 19.4 + - - +
4H GLN* 2.9 13.1 + - - +
6H ALA* 1.3 79.2 - - + +
8H LEU* 1.3 56.8 + - - +
9H ILE 3.2 0.2 - - - -
10H ASP* 3.9 7.0 - - - +
11H ALA* 2.6 34.6 + - - +
75H TYR* 4.3 22.2 + - + +
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Residues in contact with LEU 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H GLN 3.0 12.1 + - - +
5H PHE* 3.8 8.3 - - + +
7H ARG* 1.3 74.8 - - - +
9H ILE* 1.3 69.1 + - - +
11H ALA* 3.5 7.6 - - + +
12H LYS* 3.3 14.7 + - - +
73H TYR* 3.5 30.1 - - + +
75H TYR* 3.8 26.5 - - + -
77H TYR* 5.3 0.2 - - + -
82H ILE* 3.3 50.0 - - + +
96H CYS* 4.2 15.5 - - - +
99H ASP* 4.3 2.0 - - + -
100H ARG* 4.3 10.3 - - - +
103H ALA* 3.2 18.5 - - + +
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G TRP* 3.8 28.0 - - + -
5H PHE* 2.8 46.1 + - + +
6H ALA* 3.5 5.4 - - - +
8H LEU* 1.3 79.6 - - - +
10H ASP* 1.3 65.7 + - - +
12H LYS* 3.3 5.5 + - - +
13H GLN* 3.4 20.0 - - - +
19H PHE* 3.8 28.9 - - + +
22H TYR* 4.1 18.4 - - + -
103H ALA* 3.6 9.1 - - + +
106H PHE* 3.4 31.2 - - + -
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Residues in contact with ASP 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ALA 2.7 27.8 + - - +
7H ARG* 3.9 7.8 - - - +
9H ILE* 1.3 71.3 - - - +
11H ALA* 1.3 54.0 + - - +
12H LYS 2.5 5.9 + - - -
13H GLN 2.4 28.8 + - - -
14H GLU* 2.6 30.8 + - - +
16H ALA* 3.9 4.2 - - - -
17H PHE 3.4 10.0 + - - -
18H SER* 2.5 27.3 + - - -
19H PHE* 2.7 31.8 + - - -
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Residues in contact with ALA 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ARG 2.6 24.4 + - - +
8H LEU* 3.5 18.2 - - + +
10H ASP* 1.3 70.8 - - - +
12H LYS* 1.3 58.9 + - + +
14H GLU* 4.8 0.9 - - - +
75H TYR* 5.9 1.6 - - + +
77H TYR* 3.4 48.4 + - + -
82H ILE* 5.3 0.4 - - + -
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Residues in contact with LYS 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU 3.3 10.9 + - - +
9H ILE 3.3 1.8 + - - +
10H ASP 2.5 8.9 + - - -
11H ALA* 1.3 77.4 - - - +
13H GLN* 1.3 63.7 + - - +
77H TYR* 4.3 6.5 - - + +
80H GLY 3.4 14.3 + - - -
81H LYS* 3.7 28.7 - - - +
82H ILE* 4.1 16.2 - - + +
100H ARG* 4.1 4.4 - - - +
103H ALA 4.3 10.5 - - - +
104H ILE* 3.7 38.4 - - + +
107H ARG* 3.1 62.2 - - - +
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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