Contacts of the helix formed by residues 11 - 23 (chain A) in PDB entry 4I7H
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 1.3 75.9 - - - +
12A ALA* 1.3 55.2 + - - +
13A TYR* 3.3 8.9 + - - +
14A GLU* 2.8 58.5 + - - +
15A ASN* 2.7 33.3 + - - +
98A GLN* 3.7 17.9 - - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 1.3 75.3 - - - +
13A TYR* 1.3 63.1 + - - +
15A ASN* 3.3 2.4 + - - +
16A VAL* 3.1 27.9 + - - +
39A ILE* 3.8 23.8 - - + -
94A PHE* 4.0 18.2 - - + -
96A GLY 4.5 2.5 - - - +
97A HIS 3.7 16.8 - - - +
98A GLN* 3.7 11.2 - - + +
119A MET* 4.7 11.7 - - + -
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 3.3 9.7 + - - +
12A ALA* 1.3 76.0 - - - +
14A GLU* 1.3 75.6 + - + +
16A VAL* 3.1 14.6 + - - +
17A LEU* 3.3 37.1 + - + +
32A LYS* 3.5 54.4 - - + +
35A ILE* 4.1 17.7 - - + -
36A SER* 4.1 19.5 - - - -
39A ILE* 3.3 16.1 - - + +
40A GLN* 6.4 0.2 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 4.3 2.1 - - - +
10A LEU* 3.3 27.4 - - + +
11A ASP* 2.8 46.5 + - - +
13A TYR* 1.3 83.7 - - + +
15A ASN* 1.3 62.4 + - - +
17A LEU* 3.4 8.1 + - - +
18A GLU* 3.0 25.6 + - - +
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 3.4 2.6 + - - -
10A LEU* 4.0 14.0 - - + +
11A ASP 2.7 21.9 + - - +
12A ALA 3.5 4.8 + - - +
14A GLU* 1.3 72.0 - - - +
16A VAL* 1.3 65.9 + - - +
18A GLU* 3.3 1.6 + - - +
19A HIS* 3.0 29.5 + - - -
78A PHE* 3.5 12.5 - - - -
97A HIS* 3.2 45.0 + - - +
98A GLN* 4.5 2.7 - - - -
99A HIS* 3.4 5.0 + - - -
201A NI 2.4 33.8 - - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 3.1 16.3 + - - +
13A TYR 3.1 6.0 + - - +
15A ASN* 1.3 75.4 - - - +
17A LEU* 1.3 59.8 + - - +
19A HIS* 3.2 3.8 + - - +
20A LEU* 2.9 36.2 + - + +
35A ILE* 3.7 36.8 - - + -
73A LEU* 4.3 4.5 - - + -
78A PHE* 3.7 44.4 - - + -
94A PHE* 3.9 22.4 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.3 46.4 + - + +
14A GLU* 3.8 7.6 - - - +
15A ASN 3.3 0.4 - - - -
16A VAL* 1.3 73.8 - - - +
18A GLU* 1.3 65.8 + - - +
20A LEU* 3.4 1.0 + - + -
21A ARG* 2.9 60.8 + - - +
27A ILE* 3.6 32.7 - - + +
32A LYS* 4.4 11.2 - - + -
35A ILE* 3.7 23.1 - - + -
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 4.4 13.5 + - + +
8A GLN* 4.8 11.7 + - - +
10A LEU* 3.5 35.0 - - + -
14A GLU 3.0 11.8 + - - +
15A ASN 3.6 8.1 - - - +
17A LEU* 1.3 77.8 - - - +
19A HIS* 1.3 63.2 + - - +
21A ARG* 3.3 21.4 + - - +
22A GLU* 3.0 45.7 + - - +
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS* 3.5 19.3 - + - -
6A HIS* 3.1 11.8 + + - -
15A ASN* 3.0 28.2 + - - -
16A VAL 3.2 3.3 + - - +
18A GLU* 1.3 78.3 - - - +
20A LEU* 1.3 63.8 + - - +
22A GLU* 3.4 19.6 + - - +
23A LYS* 3.4 15.9 + - - +
78A PHE* 3.4 28.9 - + + -
97A HIS* 3.3 7.4 + + - -
201A NI 2.4 39.4 - - + +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 2.9 34.9 + - + +
17A LEU* 4.8 0.2 - - + -
19A HIS* 1.3 74.3 - - - +
21A ARG* 1.3 65.4 + - - +
23A LYS* 2.9 13.7 + - - +
25A ILE* 3.0 52.0 + - + +
26A ARG 4.9 1.1 - - - +
27A ILE* 3.9 23.8 - - + -
31A ARG* 3.9 28.0 - - - +
35A ILE* 4.2 8.5 - - + -
72A VAL* 5.0 4.3 - - + -
73A LEU* 4.7 6.3 - - + -
76A GLU* 4.0 22.4 - - + +
78A PHE* 4.8 6.3 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 2.9 48.0 + - - +
18A GLU* 3.5 21.5 + - - +
20A LEU* 1.3 75.8 - - - +
22A GLU* 1.3 54.6 + - + +
24A HIS* 2.7 36.1 + - - +
25A ILE 4.8 3.4 - - - +
27A ILE* 3.7 25.5 - - + +
32A LYS* 4.5 14.1 - - - +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 3.0 40.1 + - - +
18A GLU* 3.0 28.1 + - - +
19A HIS* 3.7 13.8 + - - +
20A LEU 3.3 0.2 - - - -
21A ARG* 1.3 74.7 - - + +
23A LYS* 1.3 61.1 + - + +
24A HIS* 3.3 11.3 + - - -
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS 3.4 9.3 + - - +
20A LEU* 2.9 9.7 + - - +
22A GLU* 1.3 79.7 - - + +
24A HIS* 1.3 72.4 + - - +
25A ILE* 3.1 17.0 + - + +
75A ASP 5.7 0.6 + - - -
76A GLU* 3.1 35.8 + - - +
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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