Contacts of the helix formed by residues 28 - 40 (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 THR 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.7 45.7 + - + +
27B ILE* 1.3 76.6 - - - +
29B GLU* 1.3 59.9 + - - +
30B THR* 3.5 10.7 + - - +
31B ARG* 2.9 29.1 + - - +
32B LYS* 3.0 30.5 + - - +
69B ASN* 4.7 2.8 + - - -
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Residues in contact with GLU 29 (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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28B THR* 1.3 71.2 - - - +
30B THR* 1.3 60.4 + - - +
32B LYS* 3.3 34.8 + - - +
33B ALA* 2.9 30.0 + - - +
58B PHE* 3.8 16.6 - - + -
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Residues in contact with THR 30 (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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28B THR* 3.2 10.5 + - - -
29B GLU* 1.3 78.7 - - - +
31B ARG* 1.3 62.4 + - - +
33B ALA* 3.2 2.4 + - - +
34B ILE* 3.0 32.3 + - + +
58B PHE* 3.5 26.2 - - - +
61B MET* 3.6 26.4 - - + +
65B THR* 3.9 23.7 - - + +
69B ASN* 4.1 3.4 - - - +
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Residues in contact with ARG 31 (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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20B LEU* 4.4 15.9 - - + -
25B ILE* 3.5 19.2 - - - +
26B ARG* 2.9 33.3 + - - +
27B ILE* 4.5 5.4 - - + +
28B THR* 2.9 27.3 + - - +
30B THR* 1.3 77.6 - - - +
32B LYS* 1.3 61.8 + - - +
34B ILE* 3.3 4.7 + - - +
35B ILE* 2.9 42.5 + - + +
68B ASN 4.8 0.8 + - - -
69B ASN* 2.6 40.2 + - - +
72B VAL* 3.5 34.3 - - - +
73B LEU* 5.0 9.8 - - + +
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Residues in contact with LYS 32 (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* 3.5 28.7 - - - +
17B LEU* 4.4 10.8 - - + -
21B ARG* 4.2 16.5 - - - +
27B ILE* 3.6 32.7 + - + -
28B THR 3.0 18.9 + - - +
29B GLU* 3.3 34.7 + - - +
31B ARG* 1.3 75.7 - - - +
33B ALA* 1.3 58.1 + - - +
35B ILE* 3.3 9.5 + - - +
36B SER* 2.9 31.1 + - - -
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Residues in contact with ALA 33 (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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29B GLU 2.9 18.7 + - - +
30B THR* 3.2 4.5 + - - +
32B LYS* 1.3 75.2 - - - +
34B ILE* 1.3 57.7 + - - +
36B SER* 3.9 5.5 - - - -
37B TYR* 2.9 30.1 + - - +
54B LEU* 3.9 12.8 - - + +
58B PHE* 3.5 30.3 - - + -
61B MET* 6.1 0.2 - - + -
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Residues in contact with ILE 34 (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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30B THR* 3.0 36.3 + - + +
31B ARG* 3.7 4.0 - - - +
33B ALA* 1.3 72.1 - - - +
35B ILE* 1.3 67.5 + - - +
37B TYR* 3.2 2.5 + - - +
38B MET* 2.9 41.1 + - + +
50B ILE* 4.4 12.1 - - + -
54B LEU* 3.7 22.0 - - + -
61B MET* 4.7 4.5 - - + -
66B VAL* 4.3 18.8 - - + -
69B ASN* 3.7 27.8 - - + +
70B LEU* 4.5 14.1 - - + -
73B LEU* 4.4 16.4 - - + -
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Residues in contact with ILE 35 (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* 3.9 13.2 - - + -
16B VAL* 4.0 28.7 - - + -
17B LEU* 4.1 19.1 - - + -
20B LEU* 4.4 2.5 - - + -
31B ARG* 2.9 38.8 + - + +
32B LYS* 3.6 4.3 - - - +
34B ILE* 1.3 78.1 - - - +
36B SER* 1.3 63.1 + - - +
38B MET* 3.2 6.0 + - - +
39B ILE* 3.0 43.2 + - + +
73B LEU* 3.9 25.8 - - + -
94B PHE* 4.2 13.0 - - + -
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Residues in contact with SER 36 (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* 4.2 17.4 - - - -
32B LYS 2.9 17.3 + - - -
33B ALA* 3.9 5.8 - - - -
35B ILE* 1.3 79.0 - - - +
37B TYR* 1.3 61.7 + - - +
39B ILE* 3.5 4.9 + - - +
40B GLN* 3.0 35.0 + - - +
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Residues in contact with TYR 37 (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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33B ALA 2.9 19.2 + - - +
34B ILE 3.6 4.3 - - - +
36B SER* 1.3 77.6 - - - +
38B MET* 1.3 68.1 + - - +
40B GLN* 3.4 4.1 + - - +
41B SER* 3.0 32.4 + - - -
45B PRO* 4.1 14.2 - - + +
49B LYS* 3.3 21.0 - - - +
50B ILE* 3.7 34.1 - - + -
53B ASP* 2.7 42.2 + - + -
54B LEU* 3.9 26.2 - - + -
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Residues in contact with MET 38 (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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34B ILE* 2.9 33.0 + - + +
35B ILE* 3.6 4.9 - - - +
37B TYR* 1.3 78.8 - - + +
39B ILE* 1.3 63.5 + - - +
41B SER* 3.2 17.1 + - - +
43B GLU 5.5 0.3 - - - +
45B PRO* 3.6 14.9 - - + +
50B ILE* 3.4 26.7 - - + -
70B LEU* 4.4 6.7 - - + -
73B LEU* 5.6 1.3 - - + -
79B VAL* 4.8 6.5 - - + -
92B TYR* 3.6 46.4 - - + +
93B ASP 4.0 0.9 - - - +
94B PHE* 3.6 37.5 + - + +
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Residues in contact with ILE 39 (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* 3.9 9.0 - - + -
13B TYR* 3.5 42.2 - - + +
35B ILE* 3.0 31.9 + - + +
36B SER* 3.8 5.4 - - - +
38B MET* 1.3 77.1 - - - +
40B GLN* 1.3 73.9 + - + +
41B SER 3.1 8.1 + - - +
94B PHE* 3.6 25.4 - - + -
119B MET* 3.6 29.9 - - + +
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Residues in contact with GLN 40 (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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36B SER* 3.0 27.3 + - - +
37B TYR* 3.7 4.0 - - - +
39B ILE* 1.3 93.7 - - + +
41B SER* 1.3 61.3 + - - +
42B THR 3.5 2.4 + - - -
132B LYS* 3.6 19.1 - - - +
133B VAL 4.3 10.0 + - - +
134B THR* 3.4 33.8 + - - +
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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