Contacts of the strand formed by residues 37 - 42 (chain J) in PDB entry 5XVO
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 37 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J GLY* 4.0 7.6 - - - -
3J TRP 4.2 1.8 - - - -
4J ARG* 3.8 6.7 - - + +
6J VAL* 4.2 16.8 - - + -
21J LEU* 4.1 17.7 - - + -
32J ILE* 3.7 24.2 - - + -
33J HIS 3.7 11.9 - - - +
34J LEU* 3.0 33.3 + - + +
35J SER 4.5 0.2 - - - +
36J GLU* 1.3 78.8 - - - +
38J ASP* 1.3 61.9 + - - +
39J VAL 3.7 26.9 - - - +
40J LEU* 4.4 4.9 - - + +
57J LEU* 5.2 2.9 - - + -
62J ILE* 3.6 31.0 - - + +
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Residues in contact with ASP 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J GLY 3.5 24.1 - - - +
3J TRP* 3.9 5.8 - - - +
4J ARG 2.8 19.8 + - - +
5J THR* 5.1 1.5 + - - +
37J ILE* 1.3 75.6 - - - +
39J VAL* 1.3 64.3 + - + +
62J ILE* 3.7 3.4 - - - +
63J LEU 3.2 9.2 + - - -
189J ARG* 3.0 51.0 + - - +
248J PHE* 4.8 3.5 - - - +
262J THR* 3.0 33.3 + - - +
102M ARG* 5.3 3.6 + - - -
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Residues in contact with VAL 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J ARG 3.1 3.2 + - - +
5J THR* 3.5 25.5 - - + +
6J VAL 2.8 27.9 + - - -
37J ILE* 3.7 7.1 - - - +
38J ASP* 1.3 101.7 - - + +
40J LEU* 1.3 70.5 + - - +
41J LEU* 4.4 3.6 - - + +
62J ILE* 4.3 0.4 - - - -
63J LEU* 3.4 37.5 - - + +
65J LEU* 4.5 12.6 - - + -
189J ARG* 4.6 2.7 - - - +
248J PHE* 4.4 18.6 - - + -
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Residues in contact with LEU 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 3.7 31.6 - - + +
8J VAL* 4.0 16.2 - - + -
14J LEU* 4.6 9.6 - - + -
21J LEU* 4.6 14.6 - - + -
37J ILE* 4.9 4.5 - - + -
39J VAL* 1.3 74.5 - - - +
41J LEU* 1.3 61.2 + - - +
42J LEU* 3.8 21.0 + - + -
49J LEU* 6.1 0.9 - - + -
53J LEU* 5.3 0.9 - - + -
57J LEU* 3.6 31.4 - - + -
62J ILE* 4.0 12.7 - - + +
63J LEU 2.8 12.2 + - - +
64J VAL* 3.4 10.7 - - + +
65J LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J THR* 5.1 2.7 - - + -
6J VAL 2.8 14.4 + - - +
7J VAL* 4.5 9.4 - - + -
8J VAL* 3.0 28.6 + - - +
39J VAL* 4.0 10.3 - - + -
40J LEU* 1.3 73.3 - - - +
42J LEU* 1.3 67.4 + - - +
43J GLU* 3.5 31.8 + - + +
65J LEU* 4.0 23.6 - - + +
67J CYS* 4.0 13.7 - - - -
73J PRO* 6.5 0.7 - - + -
178J TYR* 3.8 12.8 - - - +
182J LEU* 5.1 3.4 - - + -
245J PHE* 3.7 34.8 - - + -
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I THR* 4.1 9.1 - - + +
8J VAL* 3.9 16.6 - - + -
14J LEU* 3.7 28.0 - - + -
40J LEU* 3.8 21.5 - - + +
41J LEU* 1.3 74.6 - - - +
43J GLU* 1.3 62.3 + - - +
44J THR 3.4 6.3 + - - +
47J ILE* 4.1 12.6 - - + -
49J LEU* 3.6 27.8 - - + -
54J LEU* 6.2 0.2 - - + -
64J VAL* 4.3 9.4 - - + -
65J LEU 2.9 12.3 + - - +
66J PHE* 3.9 26.5 - - + -
67J CYS* 3.2 23.4 + - - +
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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