Contacts of the strand formed by residues 31 - 37 (chain B) in PDB entry 3OF6
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 SER 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 3.9 3.3 - - - +
30B VAL* 1.3 86.1 - - - +
32B LEU* 1.3 61.8 + - - +
33B PHE* 3.9 20.6 - - - -
48B TYR* 4.0 17.6 + - - -
49B PHE 3.3 10.0 + - - -
50B GLN* 4.6 2.5 - - - +
69B ARG* 3.7 2.2 + - - -
94B SER* 3.3 26.7 - - - -
95B SER* 3.3 17.0 + - - +
96B LEU 4.4 8.5 + - - -
97B GLY* 5.1 1.9 + - - -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B CYS* 4.5 0.4 - - - -
25B PRO* 3.6 28.3 - - + -
31B SER* 1.3 75.2 - - - +
33B PHE* 1.3 75.5 + - - +
34B TRP* 3.4 33.0 - - + +
48B TYR* 3.8 0.9 - - - -
49B PHE* 2.9 41.1 + - + +
69B ARG* 3.2 26.2 - - - +
75B SER* 3.5 31.6 - - - +
92B CYS* 3.6 14.6 - - - -
93B ALA 3.3 7.0 - - - +
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Residues in contact with PHE 33 (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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31B SER* 3.9 14.4 - - - -
32B LEU* 1.3 74.1 - - - +
34B TRP* 1.3 70.6 + - - +
35B TYR* 3.6 31.9 - + + -
45B PHE* 4.9 7.6 - + + -
47B THR 4.0 9.4 - - - -
48B TYR* 3.3 40.2 - + + -
92B CYS* 3.2 26.5 - - - -
93B ALA* 2.8 24.1 + - + +
95B SER* 3.6 24.5 - - - -
97B GLY 5.8 1.3 - - - -
106B GLN* 3.9 26.5 - - - -
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Residues in contact with TRP 34 (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 GLN* 3.6 27.8 - - - -
21B LEU* 3.8 37.5 - - + -
22B ARG 4.4 0.4 - - - -
23B CYS* 3.6 22.0 - - + -
32B LEU* 3.4 22.1 - - + +
33B PHE* 1.3 84.5 - - - +
35B TYR* 1.3 67.1 + - - +
45B PHE* 5.2 0.3 - - - -
46B LEU* 3.2 32.0 + - + +
47B THR* 3.5 36.6 + - + +
49B PHE* 4.9 4.0 - + - -
67B ALA* 5.1 2.2 - - + +
75B SER* 3.6 15.1 + - - -
77B LEU* 3.9 33.0 - - + +
90B TYR* 4.1 19.1 - - + -
91B LEU 3.1 21.8 - - - -
92B CYS* 3.8 6.3 - - + -
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Residues in contact with TYR 35 (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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33B PHE* 3.6 33.5 - + + -
34B TRP* 1.3 79.5 - - - +
36B GLN* 1.3 61.6 + - - +
43B PRO* 4.1 28.7 - - + -
44B GLU 3.8 15.0 - - - +
45B PHE* 4.1 24.2 - + + -
46B LEU* 3.4 10.2 - - - +
90B TYR* 3.2 8.3 - - - +
91B LEU* 2.8 43.5 + - + -
93B ALA* 4.6 1.1 - - + -
106B GLN* 3.6 22.4 + - - -
108B PHE* 3.7 31.2 - + - -
46F TRP* 4.5 17.4 - + + -
54F ALA* 5.1 6.4 - - + +
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Residues in contact with GLN 36 (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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35B TYR* 1.3 78.6 - - - +
37B GLN* 1.3 69.9 + - - +
38B ALA* 4.1 7.9 + - - +
42B GLY 3.8 2.6 - - - +
43B PRO* 3.7 0.3 - - - +
44B GLU* 3.1 48.2 + - + +
46B LEU* 3.7 27.0 - - + +
61B PRO* 5.0 8.4 - - - +
85B GLU 4.8 10.7 + - - -
86B ASP* 5.0 0.4 + - - +
88B ALA* 3.9 25.5 - - + +
89B VAL 3.7 2.2 - - - -
90B TYR* 4.1 20.0 + - + -
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Residues in contact with GLN 37 (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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36B GLN* 1.3 79.7 - - - +
38B ALA* 1.3 59.8 + - - +
40B GLY* 5.3 1.6 - - - -
41B GLN 4.1 12.1 + - - +
42B GLY* 5.2 0.2 - - - -
43B PRO* 3.3 39.3 - - + +
88B ALA* 3.5 1.3 - - - +
89B VAL* 2.9 50.7 + - + +
91B LEU* 3.9 26.1 - - + +
44F PRO* 3.8 18.2 - - - +
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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