Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 2C5L
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 GLY 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LYS 3.2 5.3 + - - +
6B LEU* 3.5 3.5 - - - -
7B VAL* 2.9 27.0 + - - +
75B GLY 3.6 0.4 - - - -
76B GLU* 1.3 79.0 - - - +
78B PHE* 1.3 67.3 + - - -
110B PRO* 3.2 14.6 - - - -
159B LEU* 3.7 9.1 - - - +
163B ILE* 3.9 14.5 - - - +
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Residues in contact with PHE 78 (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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7B VAL* 3.3 37.2 - - + +
9B VAL* 4.3 7.0 - - + -
71B TYR 4.1 0.7 - - - -
72B MET* 3.6 41.1 - - + -
75B GLY* 3.8 21.8 - - - -
77B GLY* 1.3 77.4 - - - -
79B LEU* 1.3 59.7 + - - +
80B CYS* 3.7 3.8 - - - -
100B ILE* 3.6 40.6 - - + -
104B LYS* 4.0 3.6 - - - -
109B VAL* 3.7 31.2 - - + -
110B PRO 3.1 8.2 + - - +
111B MET* 3.2 12.3 - - + +
112B VAL 3.0 25.3 + - - -
159B LEU* 3.7 6.4 - - - +
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Residues in contact with LEU 79 (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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7B VAL 2.8 13.2 + - - +
8B VAL* 3.6 17.5 - - + -
9B VAL* 2.9 28.1 + - - +
19B LEU* 4.9 6.1 - - + -
78B PHE* 1.3 71.0 - - - +
80B CYS* 1.3 59.7 + - - +
81B VAL* 3.6 8.1 + - + +
112B VAL* 3.7 13.9 - - + -
114B VAL* 3.6 28.9 - - + -
155B ALA* 3.6 28.3 - - + +
156B PHE* 3.7 42.6 - - + +
159B LEU* 3.7 18.0 - - + +
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Residues in contact with CYS 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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9B VAL* 3.6 23.1 - - + -
78B PHE* 4.4 5.6 - - - -
79B LEU* 1.3 69.1 - - - +
81B VAL* 1.3 60.1 + - - +
93B ILE* 3.7 26.9 - - + -
96B TYR* 4.9 5.8 - - + -
97B ARG* 5.2 2.5 - - - -
100B ILE* 4.4 5.8 - - - -
111B MET* 3.6 36.1 - - + -
112B VAL 3.0 12.9 + - - +
113B LEU* 3.5 11.7 - - + +
114B VAL 2.9 24.9 + - - -
139B ILE* 5.7 1.8 - - + -
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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
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8B VAL* 3.9 18.8 - - + -
9B VAL 2.9 14.3 + - - +
10B GLY* 3.5 19.2 - - - -
11B ALA 4.2 0.7 + - - -
14B VAL* 3.6 26.4 - - + +
16B LYS* 4.2 2.9 - - + +
19B LEU* 3.9 21.8 - - + -
79B LEU* 3.8 16.4 - - + +
80B CYS* 1.3 75.1 - - - +
82B PHE* 1.3 72.9 + - - +
89B SER 4.8 0.7 - - - +
93B ILE* 3.6 7.9 - - - +
114B VAL* 3.4 13.9 - - + +
116B ASN* 3.8 20.4 - - + -
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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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14B VAL* 4.0 9.0 - - - -
81B VAL* 1.3 74.1 - - - +
83B ALA* 1.3 71.2 + - - +
84B ILE* 4.0 14.6 - - + -
89B SER* 3.5 29.6 - - - +
90B PHE* 3.7 32.5 - + + +
93B ILE* 4.2 3.1 - - + -
113B LEU* 3.9 22.7 - - + -
114B VAL 3.0 20.1 + - - +
115B GLY* 3.7 5.4 - - - -
116B ASN* 2.8 29.1 + - - +
125B VAL* 3.8 18.4 - - + -
130B ALA* 3.7 14.4 - - + -
141B TYR* 3.7 32.1 - + - -
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Residues in contact with ALA 83 (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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14B VAL* 4.0 23.2 - - + +
82B PHE* 1.3 80.4 - - - +
84B ILE* 1.3 58.7 + - - +
85B ASN* 3.0 21.3 - - - +
86B ASN* 3.0 37.2 + - + +
89B SER* 3.1 7.2 + - - +
116B ASN 3.5 4.9 - - - -
117B LYS* 4.1 17.3 - - + +
125B VAL* 4.4 0.5 - - - +
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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