Contacts of the helix formed by residues 36 - 45 (chain B) in PDB entry 7A62
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 TYR 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.9 19.3 - - + -
33B PRO* 2.8 29.5 + - + +
35B PHE* 1.3 97.0 - + + +
37B ASN* 1.3 65.3 + - - +
38B ASP 3.1 3.7 + - - -
39B TRP* 3.1 54.4 + + + +
40B MET* 3.1 11.7 + - - +
65B LEU* 4.3 7.9 - - + -
66B SER 2.7 29.1 + - - -
67B ILE* 3.5 7.8 - - - -
69B HIS* 3.1 38.1 + - + +
70B LEU* 3.6 23.5 + - + -
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Residues in contact with ASN 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 PRO 3.9 1.3 + - - -
34B ASP* 2.9 25.0 + - + +
35B PHE 3.4 1.6 + - - -
36B TYR* 1.3 76.5 - - - +
38B ASP* 1.3 63.2 + - - +
40B MET* 2.9 11.4 + - - +
41B PHE* 2.7 48.7 + - - +
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE 5.0 1.0 + - - -
36B TYR 3.1 1.2 - - - -
37B ASN* 1.3 85.8 - - - +
39B TRP* 1.3 62.1 + - - +
41B PHE* 4.3 3.7 - - - +
42B ILE* 3.2 29.6 + - - +
62B LEU* 3.9 19.0 - - + +
63B ASN* 5.6 5.2 + - - -
65B LEU* 4.6 15.6 - - + +
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Residues in contact with TRP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.6 8.5 - - + -
36B TYR* 3.1 44.5 + + + +
38B ASP* 1.3 76.2 - - - +
40B MET* 1.3 66.8 + - - +
42B ILE* 3.1 5.9 + - - +
43B ALA* 2.9 20.1 + - - +
62B LEU* 4.2 21.1 - - + +
63B ASN 4.8 3.2 + - - -
65B LEU* 3.4 48.8 - - + +
67B ILE* 4.6 7.0 - - + -
70B LEU* 5.2 0.7 - - + -
79B ALA* 4.7 12.3 - - + -
82B VAL* 3.8 16.2 - - + -
83B LEU* 3.6 42.6 - - + -
86B ILE* 3.6 12.0 - - + +
106B ASN 4.8 2.4 + - - -
107B ILE* 4.2 10.5 - - + +
110B PRO* 4.1 16.6 - - + -
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Residues in contact with MET 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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30B GLU 4.5 6.5 - - - +
31B ASN* 4.9 0.4 - - - -
32B LEU* 3.4 51.4 - - + +
36B TYR 3.1 8.3 + - - +
37B ASN* 2.9 15.5 + - - +
39B TRP* 1.3 79.4 - - - +
41B PHE* 1.3 58.3 + - - +
43B ALA* 3.7 1.0 - - - +
44B LYS* 2.9 47.1 + - + +
78B LEU* 4.2 7.0 - - + -
82B VAL* 3.7 14.8 - - + -
152B PHE* 3.9 24.7 - - - -
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Residues in contact with PHE 41 (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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37B ASN* 2.7 34.5 + - - +
38B ASP* 4.3 5.2 - - - +
40B MET* 1.3 74.2 - - - +
42B ILE* 1.3 68.9 + - + +
44B LYS* 4.7 1.8 - - - -
45B HIS* 2.9 66.9 + + + +
49B LEU* 5.1 4.5 - - + -
58B ARG* 3.8 26.9 - - - -
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Residues in contact with ILE 42 (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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38B ASP 3.2 17.9 - - - +
39B TRP* 3.1 7.3 + - - +
41B PHE* 1.3 84.2 - - + +
43B ALA* 1.3 61.8 + - - +
45B HIS 3.2 12.1 + - - -
46B LEU* 3.3 13.9 + - - +
49B LEU* 4.0 13.0 - - + +
55B LEU* 3.7 27.4 - - + -
58B ARG* 4.0 28.5 - - + +
59B VAL* 4.4 6.7 - - + +
62B LEU* 3.9 31.2 - - + -
86B ILE* 4.0 17.9 - - + -
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Residues in contact with ALA 43 (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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39B TRP 2.9 15.9 + - - +
40B MET 3.8 1.8 - - - +
42B ILE* 1.3 77.5 - - - +
44B LYS* 1.3 62.6 + - - +
45B HIS 3.4 0.2 + - - -
46B LEU* 3.4 25.8 + - + +
82B VAL* 3.8 24.9 - - + +
85B CYS* 5.1 1.3 - - + -
86B ILE* 4.1 11.4 - - + -
152B PHE* 3.5 32.4 - - + -
153B SER 4.6 3.5 + - - +
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Residues in contact with LYS 44 (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 GLU* 5.1 8.4 + - - +
40B MET* 2.9 37.1 + - + +
41B PHE* 4.6 1.1 - - - -
43B ALA* 1.3 77.0 - - - +
45B HIS* 1.3 77.3 + - + +
46B LEU 3.6 1.0 + - - -
47B PRO* 4.6 5.8 - - - +
151B LEU* 2.9 36.8 + - - +
152B PHE* 3.6 24.9 - - + -
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Residues in contact with HIS 45 (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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41B PHE* 2.9 59.1 + + + +
42B ILE 3.2 6.6 + - - -
44B LYS* 1.3 91.8 - - + +
46B LEU* 1.3 63.8 + - - +
47B PRO* 3.4 4.0 - - - -
48B ASP* 3.4 23.2 + - + +
49B LEU* 2.9 35.4 + - + +
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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