Contacts of the strand formed by residues 186 - 194 (chain A) in PDB entry 3NYN
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 PHE 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A VAL* 3.6 19.7 - - + -
182A THR 3.6 16.2 - - - -
183A LYS 3.2 14.8 + - - +
184A ASN* 4.3 1.6 - - - +
185A THR* 1.3 94.2 - - + +
187A ARG* 1.3 68.1 + - - +
188A GLN* 4.3 13.1 + - - +
203A CYS* 4.6 12.1 - - + -
204A GLN 3.0 12.8 - - - +
205A VAL* 4.0 21.5 - - + -
206A ARG* 4.1 9.4 - - - -
251A TYR* 4.0 22.9 - + - -
253A TYR* 3.1 45.1 - + - -
262A VAL* 4.0 13.0 - - + -
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Residues in contact with ARG 187 (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 GLY* 2.7 30.3 + - - -
26A LYS 3.8 1.0 + - - -
27A SER* 3.3 19.6 - - - +
186A PHE* 1.3 73.0 - - - +
188A GLN* 1.3 62.7 + - - +
189A TYR* 4.1 12.2 - - + -
203A CYS* 3.1 8.3 - - - +
204A GLN* 2.7 70.8 + - + +
206A ARG* 3.8 23.8 + - + +
578A SO4 2.7 38.7 + - - +
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Residues in contact with GLN 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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183A LYS* 5.6 6.8 + - + +
186A PHE* 4.4 12.7 - - - +
187A ARG* 1.3 76.7 - - - +
189A TYR* 1.3 72.6 + - - +
201A CYS* 3.3 12.0 - - - -
202A ALA 4.1 2.0 - - - -
203A CYS* 4.0 18.4 - - - +
214A CYS* 4.2 7.7 - - - -
216A LYS* 2.8 36.7 + - - +
253A TYR* 3.8 20.4 + - - -
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Residues in contact with TYR 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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11A VAL* 3.4 34.1 - - + -
12A LEU* 4.4 11.4 - - + -
15A ALA* 3.2 22.4 - - + +
187A ARG* 4.1 17.7 - - + -
188A GLN* 1.3 82.3 - - - +
190A ARG* 1.3 73.5 + - + +
191A VAL* 3.7 1.6 + - - +
201A CYS* 3.5 12.3 - - - +
202A ALA* 3.1 26.2 + - + +
203A CYS* 3.8 16.6 - - - -
204A GLN* 2.7 31.0 + - + -
211A MET* 3.7 21.5 - - + -
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Residues in contact with ARG 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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8A ALA* 3.6 35.7 + - + +
9A ASN* 3.2 30.1 + - - +
12A LEU* 3.7 31.3 - - + +
189A TYR* 1.3 80.7 - - + +
191A VAL* 1.3 93.7 + - - +
192A LEU* 3.8 6.5 - - - +
201A CYS* 3.3 7.6 - - - +
202A ALA* 3.4 9.0 + - - +
472A ILE* 4.5 8.2 - - - +
474A CYS* 3.2 28.9 + - - -
475A LYS 2.8 22.6 + - - -
476A ASP* 3.6 11.7 + - - +
477A VAL* 3.9 16.5 - - + +
480A ILE* 5.0 3.2 - - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR 5.0 0.9 - - - +
190A ARG* 1.3 105.8 + - - +
192A LEU* 1.3 54.3 + - - +
193A GLY 4.4 5.8 - - - +
199A GLU* 3.7 41.1 - - + +
200A VAL 4.2 3.8 - - - +
201A CYS* 3.6 13.7 - - + -
477A VAL* 4.7 18.2 - - + +
480A ILE* 4.1 25.9 - - + +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.3 13.9 - - + -
16A ARG* 5.9 2.5 - - - +
190A ARG* 3.8 29.8 - - - +
191A VAL* 1.3 74.8 - - - +
193A GLY* 1.3 54.8 + - - +
200A VAL* 2.6 16.6 + - + +
201A CYS 3.7 5.2 - - - -
202A ALA* 3.2 34.3 - - + +
213A ALA* 5.2 0.7 - - + -
265A LEU* 4.3 15.0 - - + -
472A ILE* 5.2 3.6 - - + -
474A CYS* 3.9 23.0 - - - +
480A ILE* 4.5 5.6 - - - +
577A SGV 3.3 42.3 + - + +
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Residues in contact with GLY 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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191A VAL* 3.7 5.1 - - - +
192A LEU* 1.3 81.5 + - - +
194A LYS* 1.3 60.0 + - - -
195A GLY 4.0 0.7 - - - -
199A GLU* 3.6 6.6 - - - +
200A VAL* 3.1 25.0 + - - -
480A ILE* 4.3 16.6 - - - +
577A SGV 3.7 17.3 - - - -
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Residues in contact with LYS 194 (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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193A GLY* 1.3 71.4 - - - -
195A GLY* 1.3 74.5 + - - +
196A GLY 5.7 0.7 - - - -
198A GLY 3.8 7.4 - - - +
199A GLU* 4.8 1.3 - - + +
221A ARG* 4.1 14.1 - - - +
480A ILE* 4.7 14.8 - - + +
481A GLU* 3.4 45.3 + - + +
482A GLN* 5.1 0.7 - - - -
483A PHE* 3.6 42.2 - - - +
577A SGV 4.5 11.0 + - - -
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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