Contacts of the strand formed by residues 186 - 194 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B VAL* 3.5 26.5 - - + -
182B THR 3.5 9.2 - - - -
183B LYS 3.0 18.3 + - - +
184B ASN* 4.0 0.9 - - - +
185B THR* 1.3 88.5 - - + +
187B ARG* 1.3 66.3 + - - +
188B GLN* 4.1 16.8 + - - +
203B CYS* 4.5 13.2 - - + -
204B GLN 3.2 16.2 - - - +
205B VAL* 4.1 26.5 - - + -
206B ARG* 3.8 9.5 - - - -
251B TYR* 3.9 15.0 - + - -
253B TYR* 3.1 43.3 - + - -
262B VAL* 3.8 20.4 - - + -
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Residues in contact with ARG 187 (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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25B GLY* 2.9 26.2 + - - -
26B LYS 3.8 0.6 - - - -
27B SER* 3.3 20.0 - - - +
186B PHE* 1.3 72.9 - - - +
188B GLN* 1.3 62.1 + - - +
189B TYR* 3.8 26.2 + - + +
203B CYS* 3.3 7.1 - - - +
204B GLN* 2.8 63.9 + - - +
205B VAL 4.5 1.6 + - - -
206B ARG* 3.5 24.3 + - + +
578B SO4 2.7 38.5 + - - +
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Residues in contact with GLN 188 (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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183B LYS* 5.5 12.7 + - + +
186B PHE* 4.3 18.1 - - + +
187B ARG* 1.3 73.0 - - - +
189B TYR* 1.3 69.9 + - - +
201B CYS* 3.4 11.4 - - - -
202B ALA 4.2 2.0 - - - -
203B CYS* 4.3 6.2 - - - +
214B CYS* 4.2 9.3 - - - +
216B LYS* 3.0 35.6 + - - +
253B TYR* 3.4 24.7 + - - -
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Residues in contact with TYR 189 (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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11B VAL* 4.4 25.1 - - + -
12B LEU* 4.7 9.9 - - + -
15B ALA* 4.0 16.0 - - + +
187B ARG* 3.8 32.0 + - + +
188B GLN* 1.3 86.3 - - - +
190B ARG* 1.3 74.5 + - + +
191B VAL* 3.7 1.6 + - - +
201B CYS* 3.5 13.0 - - - +
202B ALA* 3.0 20.6 + - + +
203B CYS* 4.1 8.5 - - - -
204B GLN* 2.7 33.1 + - + +
211B MET* 3.6 32.1 - - + -
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Residues in contact with ARG 190 (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 ALA* 3.7 38.0 + - + +
9B ASN* 3.1 29.6 + - - +
11B VAL* 6.2 0.4 - - - +
12B LEU* 3.8 30.6 - - + +
189B TYR* 1.3 83.4 - - + +
191B VAL* 1.3 87.8 + - - +
192B LEU* 3.9 5.9 - - - +
202B ALA* 3.2 19.6 + - + -
472B ILE* 4.8 7.5 - - - +
474B CYS* 3.5 27.5 - - - -
475B LYS 3.1 20.0 + - - -
476B ASP* 3.6 1.6 - - - +
477B VAL* 3.5 28.5 - - + +
480B ILE* 5.0 2.2 - - - +
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Residues in contact with VAL 191 (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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189B TYR 5.0 1.3 - - - +
190B ARG* 1.3 104.8 + - - +
192B LEU* 1.3 54.1 + - - +
193B GLY 4.4 5.2 - - - +
199B GLU* 3.3 44.4 - - + +
200B VAL 4.2 3.8 - - - +
201B CYS* 3.6 13.0 - - + -
477B VAL* 4.8 17.6 - - + +
480B ILE* 3.8 29.4 - - + +
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Residues in contact with LEU 192 (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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12B LEU* 4.5 16.8 - - + -
16B ARG* 6.1 1.3 - - - +
190B ARG* 3.9 13.2 - - - +
191B VAL* 1.3 75.2 - - - +
193B GLY* 1.3 54.4 + - - +
200B VAL 2.7 14.6 + - - +
201B CYS 3.9 4.5 - - - -
202B ALA* 3.4 35.4 - - + +
213B ALA* 5.1 1.8 - - + -
265B LEU* 4.1 15.0 - - + -
266B MET 6.1 0.2 - - - +
472B ILE* 4.9 5.6 - - + -
474B CYS* 3.8 34.7 - - - +
480B ILE* 4.4 6.0 - - - +
577B SGV 4.0 39.4 + - + +
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Residues in contact with GLY 193 (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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191B VAL* 3.6 5.1 - - - +
192B LEU* 1.3 80.5 - - - +
194B LYS* 1.3 60.3 + - - -
195B GLY 3.8 0.9 - - - -
199B GLU* 3.5 4.7 - - - +
200B VAL 2.8 28.4 + - - -
480B ILE* 4.3 14.8 - - - +
577B SGV 3.8 17.0 - - - -
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Residues in contact with LYS 194 (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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193B GLY* 1.3 69.7 - - - -
195B GLY* 1.3 78.1 + - - +
196B GLY* 4.7 4.5 - - - -
198B GLY 3.7 9.9 - - - +
199B GLU* 4.6 2.9 - - + +
221B ARG* 3.9 22.9 - - - +
225B ARG* 5.6 5.4 - - - +
480B ILE* 4.8 7.3 - - + +
481B GLU* 3.9 48.6 + - + +
482B GLN* 5.1 1.6 - - - +
483B PHE* 4.2 23.9 - - - +
577B SGV 4.1 9.8 - - - -
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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