Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 4OWW
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 VAL 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG 4.1 0.9 - - - +
29B VAL* 3.6 2.6 - - - +
30B THR* 2.9 60.4 + - - +
31B LYS 5.2 0.2 - - - +
32B THR 5.0 5.8 - - - +
36B HIS 5.0 2.9 - - - +
37B GLU* 1.3 75.5 - - - +
39B ARG* 1.3 70.9 + - - +
53B SER* 4.3 7.4 - - - +
54B VAL 3.4 11.2 - - - +
55B TRP* 4.1 39.7 - - + +
7L T 3.6 26.0 - - + +
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 4.5 10.8 + - - -
27B GLY 3.9 15.7 + - - +
28B ARG 3.8 16.6 - - - +
29B VAL* 3.3 46.3 - - - +
37B GLU* 4.2 4.0 + - - +
38B VAL* 1.3 79.3 - - - +
40B THR* 1.3 63.1 + - - +
41B CYS* 3.9 21.5 + - - -
52B ILE 3.8 0.2 - - - +
53B SER* 3.6 1.7 - - - -
54B VAL* 2.9 32.5 + - + +
56B ASP 4.8 1.8 + - - -
59B GLY* 3.0 35.0 + - - -
60B ASN* 2.7 31.3 + - - +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY* 2.9 29.2 + - - +
28B ARG 4.8 2.5 + - - -
39B ARG* 1.3 72.3 - - - +
41B CYS* 1.3 62.0 + - - +
42B LYS 4.2 0.3 + - - -
51B ASN* 4.1 27.6 - - + +
52B ILE 3.4 8.7 - - - +
53B SER* 3.4 24.5 - - - +
78B PHE* 6.3 2.5 - - + -
83B THR* 4.7 2.7 - - + -
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Residues in contact with CYS 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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23B VAL* 4.5 3.8 - - + -
25B GLU 3.2 8.7 - - - +
26B THR* 3.6 25.8 - - + -
39B ARG* 4.1 17.9 - - - -
40B THR* 1.3 76.9 - - - +
42B LYS* 1.3 60.9 + - - +
43B VAL* 3.7 8.4 + - + -
51B ASN* 3.4 5.8 - - - -
52B ILE* 2.8 47.4 + - + +
54B VAL* 4.3 15.0 - - - -
62B ILE* 3.9 17.0 - - + -
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Residues in contact with LYS 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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23B VAL* 3.6 0.7 - - - -
24B LEU* 2.7 44.6 + - + -
25B GLU* 2.8 51.4 + - + +
40B THR 4.2 0.6 + - - -
41B CYS* 1.3 72.1 - - - +
43B VAL* 1.3 55.1 + - - +
49B SER* 3.4 30.0 + - - -
50B ILE 3.8 3.8 - - - +
51B ASN* 4.4 12.7 + - - +
104B GLU* 3.9 27.2 + - - +
107B ASN* 3.7 25.1 + - - +
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Residues in contact with VAL 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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7B VAL* 5.5 0.2 - - + -
21B PHE* 3.3 50.5 - - + -
22B ILE 3.3 5.4 - - - +
23B VAL* 3.9 17.5 - - + -
24B LEU* 4.6 1.1 - - - -
41B CYS* 4.3 3.1 - - + +
42B LYS* 1.3 78.6 - - - +
44B ALA* 1.3 63.3 + - - +
49B SER* 3.2 5.1 - - - -
50B ILE* 2.9 53.9 + - + +
52B ILE* 3.7 25.1 - - + -
62B ILE* 6.4 0.2 - - + -
84B LEU* 4.9 0.2 - - + -
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Residues in contact with ALA 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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7B VAL* 4.6 2.2 - - - -
21B PHE* 3.4 7.8 - - - +
22B ILE* 2.8 37.2 + - - +
24B LEU* 3.6 22.0 - - + -
43B VAL* 1.3 79.5 - - - +
45B ASP* 1.3 61.3 + - - +
48B GLY 3.4 14.4 - - - +
49B SER* 3.8 2.7 - - - -
100B MET* 4.1 0.3 - - - +
102B TYR* 4.1 9.4 - - + -
103B SER 3.6 15.9 - - - +
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Residues in contact with ASP 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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5B THR 4.8 0.7 - - - +
6B PHE* 3.5 22.9 - - + -
7B VAL* 2.9 32.3 + - + +
19B LEU* 4.9 1.0 - - - +
20B ILE 3.9 10.8 - - - +
44B ALA* 1.3 74.5 - - - +
46B LYS* 1.3 62.7 + - + +
47B THR* 2.6 27.9 + - - -
48B GLY 3.1 11.6 + - - +
100B MET* 3.8 23.6 - - + -
102B TYR* 3.5 8.2 - - - -
103B SER 2.9 17.3 + - - +
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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