Contacts of the helix formed by residues 2 - 13 (chain F) 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 LEU 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLY 4.0 2.5 - - - +
31E TRP* 3.3 51.7 - - + +
32E GLY 2.6 12.1 + - - +
69E LYS* 6.1 4.7 - - - +
1F ASN* 1.3 76.1 - - - +
3F PHE* 1.3 66.0 + - - +
4F GLN 3.1 2.2 - - - -
5F PHE* 3.3 24.6 + - + +
6F ALA* 3.2 17.0 + - - +
48F HIS* 5.2 2.7 - - + -
52F TYR* 4.3 18.2 - - + +
69F LYS* 3.6 37.0 - - + +
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Residues in contact with PHE 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLY 4.4 4.7 - - - -
27E CYS* 3.5 25.6 - - - -
31E TRP 3.3 16.7 + - - -
32E GLY* 3.7 7.2 + - - -
33E GLY 3.9 1.8 - - - -
34E GLN* 3.2 51.6 - - + +
121E ALA* 3.1 46.7 - - + +
126E CYS* 3.7 19.1 - - + -
1F ASN* 2.7 19.1 + - - +
2F LEU* 1.3 75.8 - - - +
4F GLN* 1.3 59.9 + - + +
6F ALA* 3.4 8.0 - - - +
7F ARG* 3.3 39.0 + - - +
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Residues in contact with GLN 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 5.3 1.6 - - - +
1F ASN* 3.1 21.4 + - - +
2F LEU 3.1 0.2 - - - -
3F PHE* 1.3 76.7 - - + +
5F PHE* 1.3 62.1 + - - +
7F ARG* 3.4 17.6 + - - +
8F LEU* 2.9 31.9 + - - +
72F GLU* 3.1 38.5 + - + +
73F TYR* 3.0 60.3 + - + +
75F TYR* 3.7 15.8 - - - +
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Residues in contact with PHE 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TRP* 3.9 17.7 - + + -
1F ASN 4.2 0.6 + - - -
2F LEU* 3.3 23.6 + - + +
4F GLN* 1.3 74.0 - - - +
6F ALA* 1.3 69.2 + - - +
8F LEU* 2.8 14.1 + - + -
9F ILE* 2.9 34.7 + - + +
45F CYS* 6.0 2.2 - - - -
48F HIS* 3.2 44.0 - + - -
73F TYR* 3.5 2.1 + - - -
99F ASP* 3.2 49.0 + - + +
102F ALA* 3.9 4.0 - - + -
103F ALA* 3.9 5.6 - - - -
106F PHE* 3.6 25.1 - + - -
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Residues in contact with ALA 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TRP* 3.5 29.0 - - + -
2F LEU 3.2 4.6 + - - +
3F PHE* 3.4 13.0 - - - +
5F PHE* 1.3 79.5 - - - +
7F ARG* 1.3 57.3 + - + +
9F ILE* 3.5 1.2 + - - +
10F ASP* 2.4 36.7 + - - +
19F PHE* 3.7 28.5 - - + -
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Residues in contact with ARG 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ALA 4.2 4.0 + - - -
122E ILE* 3.7 34.2 - - - +
124E SER 3.9 7.1 - - - +
3F PHE* 3.3 30.1 + - - +
4F GLN* 3.7 17.2 - - - +
5F PHE 3.0 1.0 - - - -
6F ALA* 1.3 77.5 - - + +
8F LEU* 1.3 56.2 + - - +
10F ASP* 3.7 5.8 - - - +
11F ALA* 2.5 37.7 + - - +
75F TYR* 4.2 16.6 - - - +
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Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F GLN 2.9 26.7 - - - +
5F PHE* 2.8 11.0 + - + +
7F ARG* 1.3 70.3 - - - +
9F ILE* 1.3 69.8 + - - +
11F ALA* 3.6 3.1 - - + +
12F LYS* 3.0 23.4 + - - +
73F TYR* 3.4 19.7 - - + +
75F TYR* 3.5 36.1 - - + +
82F ILE* 3.5 26.0 - - + -
96F CYS* 4.5 3.4 - - - +
99F ASP* 3.9 4.0 - - + +
100F ARG* 3.5 34.5 - - + +
103F ALA* 3.4 13.5 - - + +
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Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TRP* 3.5 34.5 - - + -
5F PHE* 2.9 38.3 + - + +
6F ALA 3.5 6.1 - - - +
8F LEU* 1.3 81.2 - - - +
10F ASP* 1.3 59.5 + - - +
12F LYS* 2.8 16.3 + - - +
13F GLN* 3.0 17.4 + - - +
18F SER* 4.1 6.5 - - - -
19F PHE* 3.8 17.0 - - + +
22F TYR* 3.5 38.4 - - + -
103F ALA* 3.6 9.1 - - - +
106F PHE* 3.7 12.6 - - + -
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Residues in contact with ASP 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ALA 2.4 26.2 + - - +
7F ARG* 3.7 6.1 - - - +
9F ILE* 1.3 80.2 - - - +
11F ALA* 1.3 64.6 + - - +
13F GLN 2.7 25.0 + - - +
14F GLU* 2.8 18.6 + - - +
16F ALA* 3.1 4.5 - - - +
17F PHE* 2.4 34.2 + - - -
18F SER* 3.7 3.1 - - - -
19F PHE* 3.3 26.1 + - - -
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Residues in contact with ALA 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ARG 2.5 23.2 + - - +
8F LEU* 3.6 10.3 - - + +
10F ASP* 1.3 72.7 - - - +
12F LYS* 1.3 59.7 + - - +
13F GLN 4.6 1.7 - - - +
75F TYR* 6.3 1.8 - - + -
77F TYR* 3.0 49.9 + - + -
80F GLY 5.7 0.2 - - - +
82F ILE* 4.8 7.4 - - + -
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Residues in contact with LYS 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU 3.0 11.8 + - - +
9F ILE 2.8 12.1 + - - +
11F ALA* 1.3 81.9 - - - +
13F GLN* 1.3 59.1 + - - +
77F TYR* 6.2 0.7 - - + -
80F GLY 3.3 25.2 + - - +
81F LYS* 4.7 8.3 - - - +
82F ILE* 4.7 18.6 - - + +
103F ALA* 4.0 18.2 - - + +
104F ILE* 3.7 24.3 - - - +
107F ARG* 3.3 66.9 - - + +
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Residues in contact with GLN 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 3.0 9.7 + - - +
10F ASP 2.7 12.0 + - - +
11F ALA 4.6 1.9 - - - +
12F LYS* 1.3 78.1 - - - +
14F GLU* 1.3 65.4 + - + +
18F SER* 3.1 20.2 + - - +
21F LYS* 3.5 8.8 + - - -
22F TYR* 2.5 33.5 + - - -
106F PHE* 3.9 16.6 - - - +
107F ARG* 4.0 14.4 - - + +
110F MET* 2.8 43.2 - - - +
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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