Contacts of the strand formed by residues 31 - 35 (chain D) in PDB entry 1OJ7
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 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP 3.9 1.5 + - - +
30D ALA* 1.3 70.7 - - - +
32D VAL* 1.3 57.7 + - - +
58D ASP* 2.7 41.5 + - - +
60D LEU* 4.1 26.2 - - + +
84D GLN* 3.1 48.5 + - - -
85D LYS* 3.9 12.8 - - - +
86D VAL* 3.4 20.1 - - + +
87D THR* 3.0 27.7 + - + +
88D PHE 3.4 3.3 + - - -
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 3.7 34.3 - - + -
30D ALA* 4.4 9.0 - - + +
31D ARG* 1.3 74.6 - - - +
33D LEU* 1.3 59.8 + - - +
34D ILE* 4.3 9.4 - - + -
54D LEU* 4.5 8.7 - - + -
57D MET* 4.3 12.6 - - + -
58D ASP 3.0 7.8 + - - +
59D VAL* 3.2 15.8 - - + +
60D LEU* 2.8 34.1 + - - +
86D VAL* 5.2 0.2 - - - -
88D PHE* 3.3 13.9 - - + +
90D LEU* 4.1 26.7 - - + +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ARG 3.8 1.0 + - - -
32D VAL* 1.3 71.7 - - - +
34D ILE* 1.3 60.2 + - - +
35D THR* 3.4 14.5 + - + -
60D LEU* 3.5 17.0 - - + -
61D GLU 3.6 32.1 - - - +
62D PHE* 3.8 10.1 - - + +
77D ALA* 4.6 7.4 - - + +
80D LEU* 4.1 16.2 - - + -
81D VAL* 3.5 29.2 - - + -
86D VAL* 3.8 21.1 - - + -
88D PHE 3.0 7.9 + - - -
89D LEU* 3.6 16.6 - - + +
90D LEU 3.0 20.9 + - - -
104D ILE* 5.3 0.2 - - + -
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Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 4.3 13.2 - - + -
33D LEU* 1.3 70.5 - - - +
35D THR* 1.3 64.9 + - - +
36D TYR* 4.0 4.0 - - + -
47D LEU* 3.8 24.7 - - + -
50D VAL* 3.9 19.7 - - + -
51D LEU* 3.5 30.5 - - + -
54D LEU* 4.3 7.0 - - + -
59D VAL* 4.3 16.8 - - + -
60D LEU 2.9 13.9 + - - +
61D GLU* 3.5 5.4 - - + -
62D PHE 3.0 23.6 + - - +
90D LEU* 3.3 10.8 - - + -
92D VAL* 3.8 22.7 - - + -
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Residues in contact with THR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.4 24.8 + - + +
34D ILE* 1.3 76.3 - - - +
36D TYR* 1.3 63.0 + - - +
62D PHE* 3.3 12.3 - - + +
65D ILE* 4.1 10.5 - - + -
77D ALA* 5.6 0.2 - - + -
89D LEU* 4.2 12.8 - - + -
90D LEU 3.1 5.2 + - - +
91D ALA* 3.3 11.6 - - - -
92D VAL* 3.0 28.4 + - - +
97D VAL* 4.0 1.9 - - - +
101D THR* 2.6 31.3 + - + +
104D ILE* 4.5 13.7 - - + -
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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