Contacts of the strand formed by residues 77 - 82 (chain B) in PDB entry 3OTC
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 GLU 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 4.2 6.7 - - + -
28B LEU 3.0 16.4 - - - +
29B ASP* 3.2 20.3 - - - +
54B MET* 3.5 6.7 - - - +
72B TYR* 5.0 3.5 - - - +
74B GLN* 2.8 64.4 + - + +
75B SER* 3.3 2.0 + - - +
76B ASP* 1.3 76.6 - - - +
78B TYR* 1.3 78.7 + - - +
79B SER* 4.4 4.5 + - - -
147B ARG* 2.6 49.7 + - - +
150B ASP* 4.8 0.7 - - - +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL 3.7 0.5 - - - +
27B ARG* 4.8 0.2 - - - -
28B LEU* 3.0 29.5 + - + +
51B LEU 5.1 0.2 - - - -
54B MET* 3.7 40.4 - - + -
55B THR* 2.9 33.1 + - - +
58B ALA* 3.4 26.7 - - + -
71B ALA* 4.2 6.5 - - + -
72B TYR 3.4 11.2 - - - -
73B GLY* 3.4 29.2 - - - -
75B SER 5.8 0.2 - - - -
77B GLU* 1.3 87.2 - - - +
79B SER* 1.3 66.5 + - - +
80B PHE* 3.7 22.5 - + + -
104B PHE* 4.3 10.1 - - + -
210B THR* 3.6 13.3 - - - +
212B LEU* 3.8 11.7 - - + +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.2 6.7 - - - -
26B VAL 3.4 7.4 - - - -
27B ARG* 3.9 10.2 - - - +
71B ALA* 3.1 9.0 - - - +
72B TYR* 2.6 43.5 + - - -
77B GLU* 4.4 1.7 + - - -
78B TYR* 1.3 75.0 - - - +
80B PHE* 1.3 62.0 + - - +
81B VAL* 4.2 2.0 - - - -
143B TYR* 3.5 33.8 + - - -
144B LEU* 5.3 5.2 - - - -
147B ARG* 4.2 8.9 - - - +
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Residues in contact with PHE 80 (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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24B VAL 3.6 2.3 - - - +
25B VAL* 3.3 3.6 - - - -
26B VAL* 2.9 39.1 + - + +
28B LEU* 4.0 7.9 - - + -
58B ALA* 3.5 48.0 - - + -
61B VAL* 3.7 23.6 - - + -
62B MET* 4.3 3.4 - - + -
68B ILE* 4.2 13.0 - - + -
70B ILE 4.0 2.7 - - - -
71B ALA* 4.0 15.9 - - + -
78B TYR* 3.7 26.2 - + + -
79B SER* 1.3 75.5 - - - +
81B VAL* 1.3 63.3 + - - +
82B PHE* 3.8 17.5 + - + -
100B VAL* 3.7 26.9 - - + -
104B PHE* 4.0 8.3 - + - -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.7 30.3 - - + -
24B VAL 3.6 5.6 - - - +
25B VAL* 4.0 19.3 - - + -
68B ILE* 3.4 4.7 - - - +
69B VAL* 2.9 33.7 + - + +
70B ILE* 3.0 34.9 + - + +
72B TYR 6.3 0.2 - - - +
79B SER* 5.3 2.0 - - - -
80B PHE* 1.3 74.5 - - - +
82B PHE* 1.3 63.7 + - - +
140B LEU* 3.9 22.9 - - + -
143B TYR* 6.1 0.4 - - + -
144B LEU* 4.8 13.5 - - + -
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Residues in contact with PHE 82 (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 TRP* 3.4 15.6 - - - -
24B VAL* 2.9 38.8 + - + +
26B VAL* 3.7 22.7 - - + -
65B LEU* 4.4 6.1 - - + -
66B GLU 3.4 26.5 - - - -
67B ASP* 3.1 8.7 - - + -
68B ILE* 3.5 27.6 - - + -
69B VAL* 4.7 0.9 - - - -
80B PHE* 3.9 11.7 - - + -
81B VAL* 1.3 75.7 - - - +
83B LYS* 1.3 68.7 + - - +
86B THR* 4.7 4.3 - - + -
88B TRP* 4.3 9.2 - + - -
96B PHE* 3.5 40.8 - + + -
100B VAL* 3.9 17.5 - - + -
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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