Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 3ITW
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 ILE 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 4.7 0.2 + - - -
58A VAL* 3.4 15.6 - - - +
2B VAL* 4.5 13.8 - - + +
3B VAL* 4.4 3.6 - - - +
26B LEU* 3.7 26.7 - - + -
39B ASP* 3.9 22.4 - - + +
40B LEU 3.1 10.3 - - - +
41B ASP* 4.4 7.4 - - + +
45B GLY* 1.3 77.3 - - - +
47B VAL* 1.3 80.5 + - - +
48B MET* 4.4 6.3 - - + +
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Residues in contact with VAL 47 (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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58A VAL* 3.9 9.6 - - + -
3B VAL* 3.6 32.8 - - + +
5B LEU* 3.9 22.2 - - + -
23B PHE* 4.9 0.2 - - + -
39B ASP* 3.5 4.7 - - - -
40B LEU* 3.0 52.0 + - + +
42B THR* 3.8 22.0 - - + -
46B ILE* 1.3 84.8 - - - +
48B MET* 1.3 58.7 + - - +
49B VAL* 4.0 8.9 + - + -
114B TRP* 4.5 11.0 - - + -
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Residues in contact with MET 48 (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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2B VAL* 3.8 30.5 - - + -
3B VAL 2.9 10.7 + - - +
4B GLU* 3.2 21.7 - - + +
5B LEU* 2.8 28.2 + - - +
37B HIS* 3.5 26.5 - - + +
38B ALA 3.5 4.7 - - - -
39B ASP* 3.5 16.6 - - - +
46B ILE* 4.5 2.2 - - + -
47B VAL* 1.3 73.8 - - - +
49B VAL* 1.3 63.5 + - - +
50B ARG* 5.9 4.5 - - + -
58B VAL* 4.1 21.3 - - + -
60B CYS* 6.3 1.6 - - - -
61B ALA* 4.2 19.1 - - + -
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Residues in contact with VAL 49 (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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5B LEU* 3.4 8.5 - - + +
7B TYR* 4.1 24.2 - - + -
10B PRO* 4.7 10.8 - - + -
14B VAL* 3.7 19.7 - - + +
17B LEU* 4.3 5.2 - - + -
35B ILE* 5.1 0.2 - - - +
37B HIS* 3.5 5.9 + - - -
38B ALA* 2.9 55.4 + - + +
40B LEU* 3.9 26.2 - - + -
47B VAL* 4.3 8.5 - - + -
48B MET* 1.3 78.7 - - - +
50B ARG* 1.3 64.1 + - - +
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Residues in contact with ARG 50 (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 GLU* 3.0 31.0 + - + +
5B LEU 2.8 18.3 + - - +
6B ALA* 3.4 13.0 - - - +
7B TYR* 2.9 27.9 + - - +
10B PRO* 3.8 10.4 - - - +
36B ARG 3.7 14.6 - - - +
37B HIS* 5.0 5.6 - - + +
48B MET* 5.6 3.8 - - + -
49B VAL* 1.3 78.1 - - - +
51B ARG* 1.3 82.7 + - - +
52B THR* 4.3 0.8 - - - +
53B GLY 4.1 3.0 - - - +
56B TYR* 3.1 44.4 + - + -
61B ALA* 4.9 5.8 - - - -
62B GLY* 3.9 17.7 + - - +
64B HIS 4.1 9.1 + - - -
65B THR* 4.2 16.9 - - - +
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Residues in contact with ARG 51 (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 ALA* 4.6 0.2 - - - -
7B TYR 3.5 5.6 - - - -
8B THR* 2.6 27.9 + - - +
9B ASP* 4.0 8.1 - - - +
10B PRO* 3.4 34.3 - - + +
11B ASP* 5.2 1.2 + - - -
34B THR* 4.2 15.8 + - - -
35B ILE 3.6 12.6 - - - +
36B ARG* 3.8 16.4 + - + +
50B ARG* 1.3 97.2 + - - +
52B THR* 1.3 60.6 + - - +
53B GLY 3.0 9.0 + - - +
54B GLU* 3.5 43.7 + - + -
56B TYR* 4.0 1.4 - - - -
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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