Contacts of the helix formed by residues 1 - 13 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E PHE* 1.3 66.9 + - - +
3E PHE* 3.6 2.3 + - - +
4E GLN* 2.5 61.1 + - - +
5E PHE* 3.4 15.9 + - - +
52E TYR* 4.4 5.3 + - - -
68E PRO 3.9 9.1 + - - -
69E LYS 3.6 18.2 - - - +
70E MET 4.3 0.2 - - - +
71E ALA 2.4 31.0 + - - +
72E THR* 3.2 16.8 + - - +
73E TYR* 3.7 8.2 - - - -
99E ASP* 3.9 8.3 - - - +
32F GLY 3.3 13.0 - - - +
33F GLY 3.2 10.1 + - - +
34F GLN* 3.1 41.7 + - - +
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Residues in contact with PHE 2 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN* 1.3 78.0 - - - +
3E PHE* 1.3 65.0 + - - -
4E GLN 2.7 2.6 + - - -
5E PHE* 2.8 20.5 + + + +
6E ALA* 2.9 15.7 + - - +
52E TYR* 4.9 13.7 - + - -
69E LYS* 3.1 63.9 - - + -
30F GLY 3.5 19.3 - - - -
31F TRP* 3.6 22.5 - + + -
32F GLY 2.8 29.2 + - - +
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Residues in contact with PHE 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN* 3.6 4.9 + - - +
2E PHE* 1.3 77.0 - - - +
4E GLN* 1.3 57.2 + - + +
6E ALA* 3.8 6.6 + - - +
7E GLU* 3.1 29.1 + - - +
24F SER* 5.3 3.4 - - - -
26F GLY 4.3 6.7 - - - -
27F CYS* 3.3 28.9 - - - -
31F TRP* 3.3 22.4 - - + -
32F GLY* 3.3 29.3 + - - -
34F GLN* 3.2 44.2 - - + +
120F TYR 5.4 5.6 - - - -
122F ILE* 3.4 38.9 - - + +
126F CYS* 3.7 12.8 - - + -
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Residues in contact with GLN 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN* 2.5 46.9 + - - +
2E PHE 2.7 1.2 + - - -
3E PHE* 1.3 76.9 - - + +
5E PHE* 1.3 57.8 + - - +
7E GLU* 3.3 10.2 + - - +
8E MET* 2.8 34.5 + - - +
72E THR* 3.1 21.0 - - + +
73E TYR* 3.0 66.3 + - + +
75E TYR* 4.6 11.1 + - + -
34F GLN* 4.7 4.0 + - - +
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Residues in contact with PHE 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 3.4 7.2 + - - +
2E PHE* 2.8 16.0 + + - +
4E GLN* 1.3 71.0 - - - +
6E ALA* 1.3 58.3 + - - +
7E GLU 3.0 4.7 - - - -
8E MET* 3.0 2.6 + - + -
9E ILE* 2.8 67.3 + - + +
45E CYS* 6.5 1.3 - - - -
48E HIS* 3.4 23.8 - + + -
52E TYR* 4.8 2.9 - - - +
73E TYR* 3.4 1.0 + - - -
99E ASP* 3.0 40.6 - - + +
102E ALA* 3.4 34.3 - - + -
103E ALA 4.1 0.4 - - - -
106E LEU* 4.5 6.7 - - + -
31F TRP* 4.2 13.9 - + + -
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Residues in contact with ALA 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E PHE 2.9 10.1 + - - +
3E PHE* 3.9 6.5 - - - +
5E PHE* 1.3 78.2 - - - +
7E GLU* 1.3 56.6 + - - +
9E ILE* 4.3 4.5 - - - -
10E VAL* 2.8 32.6 + - - +
19E VAL* 3.1 29.6 - - + +
31F TRP* 3.3 31.2 - - + -
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Residues in contact with GLU 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E PHE 3.1 15.1 + - - +
4E GLN* 3.5 10.8 - - - +
5E PHE 3.0 0.4 - - - -
6E ALA* 1.3 79.8 - - - +
8E MET* 1.3 56.4 + - - +
10E VAL* 3.8 5.7 - - + +
11E LYS* 2.9 47.0 + - - +
75E TYR* 3.3 20.0 + - - +
122F ILE* 3.0 31.1 - - + +
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Residues in contact with MET 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLN 2.8 19.7 + - - +
5E PHE* 3.0 4.2 + - - +
7E GLU* 1.3 75.1 - - - +
9E ILE* 1.3 67.4 + - - +
10E VAL 3.2 0.9 - - - -
11E LYS* 3.1 15.5 + - - +
12E MET* 3.2 10.0 + - - +
73E TYR* 2.6 33.2 - - + -
75E TYR* 4.1 21.5 - - + -
82E ILE* 3.2 43.9 - - + +
96E CYS* 3.9 27.1 - - - +
99E ASP* 3.3 17.3 - - + +
100E ARG 4.4 1.3 - - - +
103E ALA* 3.3 18.5 - - + +
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Residues in contact with ILE 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 2.8 65.4 + - + +
6E ALA* 4.3 4.9 - - - +
8E MET* 1.3 78.1 - - - +
10E VAL* 1.3 57.1 + - - +
11E LYS 3.1 0.3 + - - -
12E MET* 3.2 3.3 + - - +
13E THR* 2.7 32.5 + - + +
18E ALA* 3.2 24.5 - - + -
19E VAL* 4.4 3.1 - - - +
22E TYR* 4.2 20.4 - - + -
103E ALA* 3.5 14.2 - - + +
106E LEU* 4.0 19.1 - - + -
31F TRP* 4.4 15.5 - - + -
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ALA 2.8 26.2 - - - +
7E GLU* 3.8 7.6 - - + +
9E ILE* 1.3 80.8 - - - +
11E LYS* 1.3 61.6 + - + +
13E THR* 3.3 5.4 - - - +
14E GLY* 3.0 29.5 + - - +
16E LYS* 2.9 29.1 + - - +
17E GLU* 3.8 3.4 - - - -
18E ALA 3.1 22.7 - - - +
19E VAL* 3.6 14.8 - - + +
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLU* 2.9 38.3 + - - +
8E MET* 3.1 8.0 + - - +
9E ILE 3.1 1.2 - - - -
10E VAL* 1.3 77.7 - - + +
12E MET* 1.3 61.3 + - + +
13E THR 3.0 12.7 + - - +
75E TYR* 2.7 42.1 + - + +
77E PHE* 3.8 57.9 - - + +
82E ILE* 5.8 2.0 - - + -
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Residues in contact with MET 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET 3.2 6.0 + - - +
9E ILE 4.1 0.2 - - - +
11E LYS* 1.3 79.8 - - - +
13E THR* 1.3 58.7 + - - +
77E PHE* 3.9 8.7 - - + -
80E GLY* 3.1 42.8 - - - +
82E ILE* 3.7 28.9 - - + -
103E ALA 2.9 28.9 - - - +
104E ILE* 3.9 21.1 - - + -
107E GLY* 5.4 4.4 - - - -
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Residues in contact with THR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 2.7 28.5 - - + +
10E VAL* 3.3 5.6 - - - +
11E LYS 3.0 6.2 - - - +
12E MET* 1.3 81.0 - - - +
14E GLY* 1.3 71.9 + - - +
18E ALA* 3.2 27.5 - - + +
22E TYR* 6.2 0.4 - - + -
103E ALA 5.6 0.9 - - - +
107E GLY* 4.9 14.1 - - - -
110E VAL* 4.8 11.7 - - - +
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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