Contacts of the strand formed by residues 187 - 193 (chain A) in PDB entry 2C6V
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 CYS 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.7 26.9 - - - -
185A PRO* 3.6 20.8 - - - +
186A ASN* 1.3 82.7 - - - +
188A TYR* 1.3 62.3 + - - +
202A ILE* 3.4 21.8 - - + -
203A PHE 3.2 5.4 - - - +
205A LYS* 4.7 2.2 - - - -
208A ILE* 4.2 1.8 - - - -
214A LEU* 3.8 37.7 - - - -
215A PHE 3.1 12.5 + - - +
216A PHE* 3.7 12.1 - - + +
217A ASP 4.5 0.9 + - - -
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Residues in contact with TYR 188 (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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79A LEU* 3.3 11.1 - - + +
185A PRO* 6.3 1.1 - - + -
187A CYS* 1.3 77.1 - - - +
189A ALA* 1.3 85.3 + - - +
190A LYS* 3.6 3.8 + - + +
201A GLY 3.3 3.1 - - - +
202A ILE* 3.3 5.2 - - - -
203A PHE* 2.8 35.6 + - + +
205A LYS* 4.9 16.4 - - + +
216A PHE* 5.3 3.1 - - + -
217A ASP 4.1 16.2 - - - -
218A TYR* 3.2 27.1 - + - -
219A ARG 2.8 20.2 + - - -
221A SER* 2.8 44.5 + - - -
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Residues in contact with ALA 189 (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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79A LEU* 4.5 2.3 - - - +
159A PHE* 4.6 2.9 - - + -
188A TYR* 1.3 107.8 + - - +
190A LYS* 1.3 56.4 + - - +
191A VAL* 4.1 2.6 + - + +
200A ILE* 3.6 31.9 - - + -
201A GLY 3.1 7.0 - - - -
202A ILE* 5.0 1.1 - - + +
216A PHE* 5.8 1.8 - - - +
218A TYR* 3.4 32.1 - - + -
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Residues in contact with LYS 190 (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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66A CYS* 3.7 10.3 - - - +
67A TYR* 3.9 6.7 - - - -
73A CYS* 3.5 27.5 - - + +
77A LEU* 3.6 31.4 - - + +
78A CYS 3.6 5.8 - - - +
79A LEU* 3.2 21.1 - - - +
81A CYS* 3.4 31.0 - - - +
188A TYR* 3.6 4.2 + - + +
189A ALA* 1.3 73.0 - - - +
191A VAL* 1.3 60.7 + - - +
192A MET* 3.0 7.3 + - - +
199A ARG 3.3 0.2 - - - +
200A ILE* 4.9 1.3 - - - -
201A GLY* 2.7 32.7 + - - -
203A PHE* 3.4 33.9 - - + -
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Residues in contact with VAL 191 (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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79A LEU* 2.8 17.9 + - + +
80A THR* 3.1 21.4 - - + -
81A CYS* 2.8 29.7 + - - +
162A ASN* 4.7 11.0 - - - +
189A ALA* 4.2 3.1 + - + +
190A LYS* 1.3 68.0 - - - +
192A MET* 1.3 55.2 + - - +
193A MET* 3.9 6.6 + - + +
198A HIS* 3.5 42.8 - - + +
199A ARG 3.6 4.3 - - - -
200A ILE* 5.2 5.4 - - + +
218A TYR* 4.6 17.3 - - + +
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Residues in contact with MET 192 (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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81A CYS* 3.2 28.5 - - - +
83A ALA* 3.3 36.8 - - + -
84A ALA 5.3 0.7 - - - +
99A ILE* 3.4 34.1 - - + -
100A GLN* 4.3 7.0 - - + +
190A LYS 3.0 4.8 + - - +
191A VAL* 1.3 73.1 - - - +
193A MET* 1.3 85.7 + - - +
194A VAL* 3.6 18.5 + - + +
198A HIS* 3.0 4.8 - - - +
199A ARG* 2.7 62.4 + - + +
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Residues in contact with MET 193 (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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58A GLN* 3.1 37.9 - - - +
80A THR* 5.1 12.1 - - - -
81A CYS 2.9 21.0 + - - +
82A GLY* 3.8 5.7 - - - -
83A ALA 3.5 23.9 + - - +
191A VAL* 4.9 7.2 - - + +
192A MET* 1.3 80.0 - - - +
194A VAL* 1.3 63.6 + - - +
195A ASN* 3.8 35.0 - - - +
198A HIS* 4.0 7.4 - - + +
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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