Contacts of the strand formed by residues 77 - 83 (chain X) in PDB entry 2CL0
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5X LYS 3.3 4.9 + - - +
6X LEU* 3.4 4.2 - - - -
7X VAL* 2.9 24.9 + - - +
75X GLY 3.6 0.8 - - - -
76X GLU* 1.3 78.3 - - - +
78X PHE* 1.3 68.7 + - - -
110X PRO 3.2 11.9 - - - -
159X LEU* 3.7 16.8 - - - -
163X ILE* 3.8 10.0 - - - +
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Residues in contact with PHE 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X VAL* 3.2 38.1 - - + +
9X VAL* 4.4 5.6 - - + -
72X MET* 3.5 37.5 - - + -
75X GLY* 4.0 21.3 - - - -
77X GLY* 1.3 78.6 - - - -
79X LEU* 1.3 60.8 + - - +
80X CYS* 3.8 2.6 + - - -
100X ILE* 3.6 39.3 - - + -
103X VAL* 6.2 0.7 - - + -
104X LYS* 4.2 8.7 - - + -
109X VAL* 3.6 31.6 - - + -
110X PRO 3.0 5.7 + - - -
111X MET* 3.2 10.1 - - + +
112X VAL 3.1 24.9 + - - +
159X LEU* 3.7 6.4 - - - +
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Residues in contact with LEU 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LEU* 6.2 0.2 - - + -
7X VAL 2.8 11.3 + - - +
8X VAL* 3.7 13.4 - - + -
9X VAL* 3.0 29.7 + - - +
19X LEU* 5.2 5.2 - - + -
78X PHE* 1.3 71.0 - - - +
80X CYS* 1.3 60.4 + - - +
81X VAL* 3.7 11.1 + - + +
112X VAL* 3.7 11.9 - - + -
114X VAL* 3.8 24.5 - - + -
155X ALA* 3.6 27.1 - - + +
156X PHE* 3.6 43.3 - - + -
159X LEU* 3.8 21.4 - - + +
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Residues in contact with CYS 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X VAL* 3.7 10.3 - - + -
78X PHE* 4.5 3.6 - - - -
79X LEU* 1.3 73.1 - - - +
81X VAL* 1.3 58.5 + - - +
93X ILE* 3.9 20.6 - - + -
96X TYR* 5.2 2.0 - - + -
97X ARG* 5.1 7.6 - - - -
100X ILE* 3.7 25.4 - - - -
111X MET* 3.5 32.1 - - + -
112X VAL 2.9 14.3 + - - +
113X LEU* 3.6 14.4 - - + +
114X VAL 2.9 25.1 + - - +
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Residues in contact with VAL 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X VAL* 3.7 25.4 - - + -
9X VAL 2.9 16.8 + - - +
10X GLY* 3.4 19.2 - - - -
11X ALA 3.9 2.8 + - - -
14X VAL* 3.6 24.7 - - + +
16X LYS* 4.2 4.3 - - + +
19X LEU* 4.0 16.2 - - + -
79X LEU* 3.9 11.9 - - + +
80X CYS* 1.3 75.1 - - - +
82X PHE* 1.3 73.1 + - - +
89X SER 4.9 0.3 - - - +
93X ILE* 3.7 6.6 - - - +
114X VAL* 3.4 14.8 - - + +
116X ASN* 4.0 16.4 - - + -
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Residues in contact with PHE 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X VAL* 3.9 8.7 - - - -
81X VAL* 1.3 78.2 - - - +
83X ALA* 1.3 72.3 + - - +
84X ILE* 4.0 6.7 - - + -
89X SER* 3.4 30.1 - - - +
90X PHE* 3.7 33.2 - + + +
93X ILE* 4.1 3.6 - - + -
113X LEU* 3.9 22.2 - - + -
114X VAL 2.9 28.8 + - - +
115X GLY* 3.6 11.2 - - - -
116X ASN* 2.8 23.6 + - - +
125X VAL* 3.7 24.2 - - + -
130X ALA* 3.8 7.0 - - + -
141X TYR* 3.6 34.1 - + - -
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Residues in contact with ALA 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X VAL* 3.7 15.4 - - + +
82X PHE* 1.3 80.9 - - - +
84X ILE* 1.3 58.2 + - - +
85X ASN* 3.1 20.6 - - - +
86X ASN* 3.0 35.9 + - + +
89X SER* 3.0 6.9 + - - -
116X ASN 3.3 9.4 - - - +
117X LYS* 4.0 18.8 - - + +
125X VAL* 4.3 0.7 - - - +
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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