Contacts of the strand formed by residues 89 - 95 (chain A) 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 VAL 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLN* 4.6 0.4 - - - -
37A GLN* 2.9 46.9 + - + +
88A ALA* 1.3 77.4 - - - +
90A TYR* 1.3 61.1 + - - +
91A LEU* 3.6 27.9 + - + +
110A PRO 5.4 1.6 - - - +
111A GLY* 4.8 1.3 - - - -
112A THR 3.4 16.2 - - - +
113A ARG* 4.0 37.7 - - + +
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 3.3 9.2 + - - -
21A LEU* 4.1 27.1 - - + -
34A TRP* 4.4 10.4 - - + -
35A TYR 3.3 7.9 - - - +
36A GLN* 3.8 28.5 + - + -
46A LEU* 3.8 24.7 - - + -
65A PHE* 3.4 33.4 - + - -
77A LEU* 4.4 6.3 - - + -
79A ILE* 4.1 4.7 - - + -
86A ASP* 2.9 38.1 + - - +
88A ALA 3.7 11.9 - - - -
89A VAL* 1.3 70.5 - - - +
91A LEU* 1.3 60.8 + - - +
112A THR* 3.0 31.6 + - - +
114A LEU* 3.7 16.8 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 3.9 1.6 - - - -
34A TRP* 3.4 13.2 - - - -
35A TYR* 3.1 38.9 + - + -
37A GLN* 3.3 36.3 - - + +
43A PRO* 4.9 5.6 - - + -
89A VAL* 3.6 23.1 + - + +
90A TYR* 1.3 74.0 - - - +
92A CYS* 1.3 61.4 + - - +
108A PHE* 4.5 26.0 - - + -
109A GLY 4.5 8.5 - - - +
110A PRO 4.5 3.1 - - - +
111A GLY* 3.7 24.0 - - - +
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Residues in contact with CYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.0 4.3 - - - +
6A GLN* 2.9 20.0 + - - +
23A CYS* 2.0 51.1 - - + -
25A PRO* 4.8 1.1 - - - -
32A LEU* 3.6 24.2 - - - -
33A PHE 3.4 5.2 - - - +
34A TRP* 4.5 5.2 - - + -
35A TYR* 5.7 0.2 - - - -
91A LEU* 1.3 76.1 - - - +
93A ALA* 1.3 66.4 + - - +
107A TYR 3.7 0.9 - - - +
108A PHE* 3.4 6.8 - - - -
109A GLY 3.3 23.8 + - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 5.3 0.4 - - - -
32A LEU* 3.3 8.8 - - - +
33A PHE* 2.8 43.5 + - + -
35A TYR* 4.6 0.9 - - + -
92A CYS* 1.3 77.2 - - - +
94A SER* 1.3 61.8 + - - +
106A GLN* 3.5 32.3 - - + +
107A TYR 3.3 8.1 - - - +
108A PHE* 3.6 16.8 - - + -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.2 23.8 - - - +
25A PRO* 3.5 27.4 - - - -
26A ILE 3.6 3.8 + - - -
29A HIS* 3.1 22.8 + - - -
31A SER 3.5 11.7 - - - -
33A PHE* 4.6 2.0 - - - -
93A ALA* 1.3 76.3 - - - +
95A SER* 1.3 64.3 + - - +
106A GLN* 3.8 1.0 - - - -
107A TYR* 3.1 26.0 + - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.0 16.8 + - - -
30A VAL 2.9 21.7 + - - -
31A SER* 2.9 15.4 + - - -
33A PHE* 3.4 20.6 - - - -
94A SER* 1.3 72.5 - - - +
96A LEU* 1.3 59.9 + - - +
97A GLY 2.7 26.7 + - - -
100A TYR* 4.1 5.5 + - - -
105A GLU 3.1 26.9 - - - -
106A GLN* 4.6 0.9 - - - -
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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