Contacts of the helix formed by residues 11 - 23 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 1.3 76.7 - - - +
12B ALA* 1.3 58.8 + - - +
13B TYR* 3.3 11.1 + - - +
14B GLU* 2.7 43.8 + - - +
15B ASN* 2.8 28.6 + - - +
98B GLN* 3.9 13.0 - - - +
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Residues in contact with ALA 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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11B ASP* 1.3 73.1 - - - +
13B TYR* 1.3 59.7 + - - +
15B ASN* 3.4 1.7 - - - +
16B VAL* 3.0 31.4 + - - +
39B ILE* 3.9 19.3 - - + -
94B PHE* 3.9 15.3 - - + -
96B GLY 4.2 3.1 - - - +
97B HIS 3.7 19.0 - - - +
98B GLN* 3.7 11.7 + - + +
119B MET* 4.0 16.4 - - + -
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Residues in contact with TYR 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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11B ASP* 3.2 12.1 + - - +
12B ALA* 1.3 75.0 - - - +
14B GLU* 1.3 88.8 + - + +
16B VAL* 3.3 14.0 + - - +
17B LEU* 3.3 39.5 + - + +
32B LYS* 3.5 50.8 - - + +
35B ILE* 3.9 18.2 - - + -
36B SER* 4.2 16.8 - - - -
39B ILE* 3.5 15.7 - - + +
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Residues in contact with GLU 14 (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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10B LEU* 4.3 19.5 - - + -
11B ASP* 2.7 29.1 + - - +
13B TYR* 1.3 97.2 - - + +
15B ASN* 1.3 62.4 + - - +
17B LEU* 3.4 15.3 + - - +
18B GLU* 3.0 28.6 + - + +
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Residues in contact with ASN 15 (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 HIS* 3.5 2.9 + - - -
10B LEU* 4.2 12.4 - - + +
11B ASP 2.8 20.2 + - - +
12B ALA 3.4 4.7 + - - +
14B GLU* 1.3 78.2 - - - +
16B VAL* 1.3 62.1 + - - +
18B GLU* 3.3 2.9 + - - +
19B HIS* 3.0 27.9 + - - -
78B PHE* 3.7 10.1 - - - -
97B HIS* 2.9 49.1 + - - +
98B GLN* 4.5 1.6 - - - -
99B HIS* 3.2 6.9 - - - -
202B NI 2.4 32.7 - - - +
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Residues in contact with VAL 16 (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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12B ALA 3.0 17.7 + - - +
13B TYR 3.3 4.4 + - - +
15B ASN* 1.3 76.5 - - - +
17B LEU* 1.3 58.7 + - - +
19B HIS* 3.2 1.7 + - - +
20B LEU* 2.8 54.3 + - + +
35B ILE* 4.0 22.0 - - + -
73B LEU* 4.4 5.8 - - + -
78B PHE* 3.7 35.9 - - + -
94B PHE* 3.3 30.3 - - + -
96B GLY* 5.5 0.2 - - - -
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Residues in contact with LEU 17 (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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13B TYR* 3.3 49.0 + - + +
14B GLU* 3.7 18.8 - - - +
15B ASN 3.3 0.6 - - - -
16B VAL* 1.3 78.9 - - - +
18B GLU* 1.3 62.0 + - + +
20B LEU* 3.5 1.5 + - + -
21B ARG* 3.0 55.7 + - - +
27B ILE* 3.7 27.6 - - + +
32B LYS* 4.4 12.8 - - + -
35B ILE* 4.1 22.4 - - + -
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Residues in contact with GLU 18 (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 HIS* 3.0 36.8 + - + +
8B GLN* 5.6 3.8 + - - -
10B LEU* 4.0 17.5 - - + -
14B GLU* 3.0 17.0 + - + +
15B ASN 3.5 8.7 - - - +
16B VAL 3.2 0.2 - - - -
17B LEU* 1.3 76.5 - - - +
19B HIS* 1.3 57.8 + - - +
21B ARG* 3.3 13.1 + - - +
22B GLU* 2.9 30.6 + - - +
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Residues in contact with HIS 19 (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 HIS* 3.4 22.0 - + - -
6B HIS* 3.5 7.5 + + - -
15B ASN* 3.0 28.6 + - - +
16B VAL 3.6 3.4 - - - +
18B GLU* 1.3 77.1 - - - +
20B LEU* 1.3 62.9 + - - +
22B GLU* 3.4 18.7 + - - +
23B LYS* 3.1 28.4 + - + +
78B PHE* 3.4 28.7 - + + -
97B HIS* 3.2 8.1 + + - -
202B NI 2.5 39.4 - - + +
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Residues in contact with LEU 20 (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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16B VAL* 2.8 41.4 + - + +
17B LEU* 3.9 4.5 - - - +
19B HIS* 1.3 72.2 - - - +
21B ARG* 1.3 63.5 + - - +
23B LYS* 3.1 4.5 + - + -
24B HIS 3.0 4.2 + - - -
25B ILE* 2.8 58.2 + - + +
27B ILE* 4.0 24.9 - - + -
31B ARG* 4.4 19.3 - - + -
35B ILE* 4.4 9.2 - - + -
72B VAL* 5.3 2.5 - - + -
73B LEU* 4.5 7.4 - - + -
76B GLU* 4.2 19.1 - - + +
78B PHE* 4.7 8.1 - - + -
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Residues in contact with ARG 21 (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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17B LEU* 3.0 42.2 + - - +
18B GLU* 3.7 12.6 - - - +
20B LEU* 1.3 75.2 - - - +
22B GLU* 1.3 59.6 + - - +
24B HIS* 2.9 27.7 + - - +
25B ILE 4.7 4.5 - - - +
27B ILE* 3.6 27.8 - - + +
32B LYS* 4.2 16.8 - - - +
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Residues in contact with GLU 22 (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 HIS* 5.0 13.0 + - - -
18B GLU 2.9 13.6 + - - +
19B HIS* 3.4 25.3 + - - +
21B ARG* 1.3 75.6 - - - +
23B LYS* 1.3 62.4 + - + +
24B HIS* 3.3 18.2 + - - -
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Residues in contact with LYS 23 (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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19B HIS* 3.1 19.0 + - - +
20B LEU* 3.1 7.3 + - + +
22B GLU* 1.3 79.0 + - + +
24B HIS* 1.3 74.0 + - - +
25B ILE* 3.2 19.3 + - + +
76B GLU* 3.4 27.6 - - - +
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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