Contacts of the strand formed by residues 77 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.2 5.8 - - + -
28A LEU 3.0 17.0 - - - +
29A ASP* 3.3 19.4 - - - +
54A MET* 3.6 6.4 - - - +
72A TYR* 5.0 3.1 - - - +
74A GLN* 2.8 64.2 + - + +
75A SER* 3.3 2.2 + - - +
76A ASP* 1.3 75.5 - - - +
78A TYR* 1.3 77.4 + - - +
79A SER* 4.4 4.2 + - - -
147A ARG* 2.6 50.5 + - - +
150A ASP* 4.8 0.5 - - - +
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Residues in contact with TYR 78 (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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27A ARG* 3.7 0.9 - - - -
28A LEU* 3.0 29.4 + - + +
51A LEU 5.1 0.2 - - - -
54A MET* 3.7 41.5 - - + -
55A THR* 2.9 33.9 + - - +
58A ALA* 3.5 25.4 - - + -
71A ALA* 4.2 6.3 - - + -
72A TYR 3.4 10.1 - - - -
73A GLY* 3.3 29.6 - - - -
77A GLU* 1.3 86.7 - - - +
79A SER* 1.3 68.0 + - - +
80A PHE* 3.7 20.6 - + + -
104A PHE* 4.3 10.8 - + + -
210A THR* 3.5 13.3 - - - +
212A LEU* 3.9 11.3 - - + +
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Residues in contact with SER 79 (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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25A VAL* 4.2 6.3 - - - -
26A VAL 3.4 7.4 - - - -
27A ARG* 3.8 10.5 - - - +
71A ALA* 3.2 8.7 - - - +
72A TYR* 2.7 42.9 + - - -
77A GLU* 4.4 1.7 + - - -
78A TYR* 1.3 75.8 - - - +
80A PHE* 1.3 62.4 + - - +
81A VAL* 4.3 2.2 - - - -
143A TYR* 3.5 33.9 + - - -
144A LEU* 5.3 5.2 - - - -
147A ARG* 4.2 9.6 - - - +
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Residues in contact with PHE 80 (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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24A VAL 3.6 2.1 - - - +
25A VAL* 3.3 4.4 - - - +
26A VAL* 2.9 42.5 + - + +
28A LEU* 4.0 8.1 - - + -
58A ALA* 3.6 48.0 - - + -
61A VAL* 3.7 20.6 - - + -
62A MET* 4.4 2.7 - - + -
68A ILE* 4.3 13.0 - - + -
70A ILE 4.0 2.7 - - - -
71A ALA* 4.0 16.2 - - + -
78A TYR* 3.7 23.8 - + + -
79A SER* 1.3 75.2 - - - +
81A VAL* 1.3 62.2 + - - +
82A PHE* 3.8 16.8 + - + -
100A VAL* 3.7 24.2 - - + -
104A PHE* 4.0 11.0 - + - -
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Residues in contact with VAL 81 (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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23A TRP* 3.7 29.4 - - + -
24A VAL 3.6 5.6 - - - +
25A VAL* 4.0 18.8 - - + -
68A ILE* 3.3 4.9 - - - +
69A VAL* 2.9 34.3 + - + +
70A ILE* 3.0 34.2 + - + +
71A ALA* 5.7 0.2 - - - -
79A SER* 5.4 2.0 - - - -
80A PHE* 1.3 76.1 - - - +
82A PHE* 1.3 61.7 + - - +
140A LEU* 3.9 24.2 - - + -
143A TYR* 6.1 0.2 - - + -
144A LEU* 4.8 12.8 - - + -
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Residues in contact with PHE 82 (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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23A TRP* 3.4 15.0 - - - -
24A VAL* 2.9 37.4 + - + +
26A VAL* 3.8 22.4 - - + -
65A LEU* 4.4 6.1 - - + -
66A GLU 3.4 26.5 - - - -
67A ASP* 3.2 9.0 - - + +
68A ILE* 3.5 26.5 - - + -
69A VAL* 4.7 0.4 - - - -
80A PHE* 3.9 11.4 - - + -
81A VAL* 1.3 75.7 - - - +
83A LYS* 1.3 68.8 + - - +
86A THR* 4.7 4.5 - - + -
88A TRP* 4.3 9.0 - + - -
96A PHE* 3.5 42.0 - + + -
100A VAL* 3.9 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