Contacts of the strand formed by residues 199 - 205 (chain B) in PDB entry 3NYO
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 GLU 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B VAL* 3.5 35.4 - - + +
193B GLY 3.8 5.8 - - - +
194B LYS* 4.8 2.9 - - + +
198B GLY* 1.3 75.3 - - - +
200B VAL* 1.3 59.8 + - - +
201B CYS* 4.0 2.7 - - + +
214B CYS 3.9 0.5 - - - +
216B LYS* 2.9 52.8 + - + +
218B GLU* 5.5 7.3 - - - +
482B GLN* 5.3 12.7 - - + +
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Residues in contact with VAL 200 (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* 4.5 0.4 - - - -
192B LEU* 2.7 38.5 + - + +
193B GLY 3.0 11.9 + - - +
195B GLY* 4.4 8.3 - - - +
198B GLY 4.4 0.2 - - - +
199B GLU* 1.3 76.9 - - - +
201B CYS* 1.3 54.5 + - - +
213B ALA* 4.6 9.9 - - + -
214B CYS 3.6 11.0 - - - +
215B LYS* 3.9 26.5 - - + +
263B LEU* 5.8 0.2 - - + -
577B AMP 3.6 65.7 - - + +
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Residues in contact with CYS 201 (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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188B GLN* 3.6 25.8 - - - -
189B TYR 3.7 13.7 - - - +
190B ARG 3.2 20.6 - - - +
191B VAL* 3.6 18.2 - - + +
192B LEU* 3.8 3.8 - - - -
199B GLU* 4.0 2.4 - - + -
200B VAL* 1.3 74.5 - - - +
202B ALA* 1.3 63.4 + - - +
213B ALA* 4.6 0.4 - - - -
214B CYS* 2.7 48.9 + - - +
216B LYS* 4.7 11.0 - - - -
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Residues in contact with ALA 202 (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* 3.8 30.7 - - + -
189B TYR* 3.2 29.9 + - + +
190B ARG 3.5 4.0 + - - +
192B LEU* 3.3 21.4 - - + +
201B CYS* 1.3 77.4 - - - +
203B CYS* 1.3 61.5 + - - +
211B MET* 5.8 1.6 - - + -
212B TYR 3.6 5.4 - - - +
265B LEU* 3.9 21.8 - - + -
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Residues in contact with CYS 203 (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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186B PHE* 4.2 21.1 - - + -
187B ARG 3.1 17.7 - - - +
188B GLN* 4.6 9.2 - - - +
189B TYR* 3.6 5.6 - - - -
201B CYS* 5.5 0.2 - - - -
202B ALA* 1.3 76.2 - - - +
204B GLN* 1.3 63.3 + - - +
211B MET* 3.2 11.3 - - - +
212B TYR* 2.7 54.6 + - - -
214B CYS* 3.8 26.7 - - + -
253B TYR* 5.8 0.2 - - - -
262B VAL* 4.5 4.9 - - - -
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Residues in contact with GLN 204 (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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15B ALA* 4.6 10.9 + - - +
24B LYS 5.2 0.2 + - - -
25B GLY* 4.1 15.6 - - - -
186B PHE* 3.1 12.8 - - - +
187B ARG* 2.7 61.2 + - + +
189B TYR* 2.9 21.0 + - + +
203B CYS* 1.3 77.2 - - - +
205B VAL* 1.3 70.7 + - - +
206B ARG 3.4 0.2 + - - -
209B GLY 2.8 29.7 + - - +
210B LYS 3.6 2.7 - - - +
211B MET* 3.6 27.3 - - + +
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Residues in contact with VAL 205 (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 4.6 0.7 - - - +
185B THR* 3.9 15.5 - - + +
186B PHE* 4.0 17.3 - - + -
204B GLN* 1.3 73.9 - - - +
206B ARG* 1.3 65.9 + - - +
207B ALA* 3.9 6.5 - - + +
208B THR* 3.3 30.5 - - + +
209B GLY* 3.0 20.8 + - - -
210B LYS 3.1 7.9 + - - +
212B TYR* 3.6 29.4 - - + -
251B TYR* 4.3 8.5 - - + +
514B GLU* 3.2 20.2 - - - +
515B MET* 6.0 0.4 - - + -
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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