Contacts of the strand formed by residues 36 - 41 (chain B) in PDB entry 4M83
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 ARG 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 4.5 10.6 + - + +
7B ALA 2.5 15.8 + - - +
8B HIS* 3.2 21.1 - - + +
9B ILE 2.7 31.9 + - - +
34B GLY 3.7 1.4 + - - -
35B HIS* 1.3 71.9 - - - +
37B VAL* 1.3 61.2 + - - +
38B THR* 5.0 5.6 - - + -
55B ARG* 4.8 17.2 - - + +
102B ASP* 4.3 20.8 + - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.2 25.1 - - + +
11B MET* 4.9 6.1 - - + -
27B ILE* 4.2 15.7 - - + -
30B LEU* 4.2 18.6 - - + -
31B VAL* 3.6 28.0 - - + +
35B HIS* 3.6 12.2 + - + +
36B ARG* 1.3 80.4 - - - +
38B THR* 1.3 73.9 + - - +
39B TYR* 5.3 0.2 - - + -
53B GLY 4.7 0.3 - - - +
54B ALA* 3.3 18.3 - - + -
55B ARG* 2.9 24.4 + - - +
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Residues in contact with THR 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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8B HIS* 2.7 35.2 + - + +
9B ILE 2.8 8.1 + - - +
10B ALA* 3.3 5.0 - - - -
11B MET 2.7 29.7 + - - -
36B ARG* 4.0 6.7 + - + -
37B VAL* 1.3 80.6 - - - +
39B TYR* 1.3 58.3 + - - +
55B ARG* 3.3 39.7 - - + +
57B VAL* 3.8 9.4 - - + -
99B TYR* 2.8 25.4 + - + -
102B ASP* 5.2 0.4 - - - +
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Residues in contact with TYR 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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11B MET* 3.1 49.7 - - + +
13B SER* 3.5 29.5 - - - -
19B HIS 4.8 0.2 + - - -
20B VAL* 4.2 16.3 + - + +
23B SER* 4.5 3.3 + - - -
27B ILE* 4.1 30.3 - - + -
38B THR* 1.3 76.1 - - - +
40B ALA* 1.3 71.1 + - - +
41B ILE* 3.3 17.1 + - + +
49B VAL* 3.4 36.1 - - + -
54B ALA* 4.3 10.3 - - + -
55B ARG 2.8 11.8 + - - +
56B PRO* 3.3 5.1 - - + +
57B VAL* 2.8 22.4 + - - +
99B TYR* 4.3 0.4 - - - -
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Residues in contact with ALA 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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11B MET 2.7 9.2 + - - +
12B PHE* 3.4 37.5 - - + -
13B SER 3.3 26.2 + - - +
39B TYR* 1.3 71.1 - - - +
41B ILE* 1.3 59.9 + - - +
57B VAL* 3.1 14.4 - - - +
59B TYR* 3.7 4.4 - - + -
95B LEU* 4.2 13.2 - - + -
99B TYR* 3.8 14.7 + - + +
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Residues in contact with ILE 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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13B SER* 3.8 10.1 - - - +
14B ILE 3.7 19.3 - - - +
20B VAL* 4.8 0.9 - - + -
39B TYR* 3.7 35.0 - - + +
40B ALA* 1.3 71.7 - - - +
42B PRO* 1.3 93.2 - - + +
45B PHE* 3.6 23.1 - - + +
46B ALA* 4.3 6.5 - - + -
49B VAL* 3.7 24.7 - - + -
56B PRO* 4.0 13.2 - - + -
57B VAL 3.1 5.5 + - - +
58B LEU* 3.1 20.8 - - - -
59B TYR* 3.1 7.8 + - - -
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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