Contacts of the strand formed by residues 203 - 209 (chain B) in PDB entry 3NVN
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 THR 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.9 16.8 - - + +
181B ALA 4.5 0.7 - - - +
183B TYR* 3.4 25.0 + - - +
199B SER 4.8 1.6 - - - +
200B ASP* 2.7 39.0 + - - +
201B HIS 3.5 1.4 - - - +
202B ASP* 1.3 82.9 - - - +
204B ALA* 1.3 60.5 + - - +
205B ILE 5.2 1.1 - - - -
206B ALA* 5.6 1.8 - - - -
222B ARG* 3.4 44.9 - - + +
223B LEU 3.7 4.7 - - - -
224B LYS* 4.3 6.3 - - + +
225B LEU* 3.9 6.6 - - - +
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Residues in contact with ALA 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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179B VAL 3.7 0.9 - - - +
180B ALA* 3.4 2.6 - - - -
181B ALA 3.2 33.2 + - - +
183B TYR* 3.8 5.0 - - - -
202B ASP 3.4 0.6 + - - -
203B THR* 1.3 74.9 - - - +
205B ILE* 1.3 68.5 + - + +
223B LEU 2.9 12.9 + - - +
224B LYS 4.6 0.2 - - - -
225B LEU* 3.4 34.8 - - + +
234B PHE* 4.0 13.2 - - + -
347B PHE* 4.3 9.2 - - + -
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Residues in contact with ILE 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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178B ALA* 5.0 2.2 - - + -
179B VAL 3.2 15.3 - - - +
180B ALA* 4.0 6.5 - - + -
203B THR* 5.2 0.6 - - - -
204B ALA* 1.3 86.1 + - + +
206B ALA* 1.3 62.6 + - - +
207B LEU* 5.5 2.5 - - + -
222B ARG* 3.3 4.5 - - - +
223B LEU* 2.7 64.4 + - + +
234B PHE* 4.1 16.8 - - + -
246B PHE* 3.4 55.9 - - + -
265B ALA* 4.5 7.2 - - + -
267B ILE* 3.9 9.6 - - + -
273B VAL* 4.7 2.2 - - + +
347B PHE* 4.9 1.1 - - + -
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Residues in contact with ALA 206 (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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203A LEU* 4.1 11.2 - - + -
177B LEU 3.6 1.6 - - - +
178B ALA* 3.6 1.0 - - - -
179B VAL* 2.8 35.8 + - - +
183B TYR* 4.5 8.3 + - + +
203B THR* 5.6 2.0 - - - -
205B ILE* 1.3 75.6 - - - +
207B LEU* 1.3 63.5 + - - +
208B LYS* 3.5 30.1 + - - +
217B THR* 4.1 13.0 - - + -
221B GLY 3.6 4.5 - - - -
222B ARG* 4.5 3.6 - - + -
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Residues in contact with LEU 207 (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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167B TYR* 3.3 27.8 - - + +
176B TYR* 5.3 2.5 - - + -
177B LEU 3.4 0.9 - - - -
178B ALA* 3.5 28.9 - - + -
205B ILE* 5.5 4.3 - - + -
206B ALA* 1.3 74.1 - - - +
208B LYS* 1.3 62.2 + - - +
216B ALA 3.8 0.7 - - - +
217B THR* 3.4 24.4 + - - +
218B GLN 4.5 1.6 + - - -
221B GLY* 2.8 18.4 + - - +
244B ILE* 4.6 4.9 - - + -
246B PHE* 6.0 0.2 - - + -
267B ILE* 5.3 8.5 - - + -
268B ALA 5.6 0.7 - - - +
270B SER 3.7 6.7 - - - +
271B THR 3.9 11.0 - - - +
272B GLU 3.7 8.3 - - - +
273B VAL* 3.4 41.7 - - + +
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Residues in contact with LYS 208 (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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202A SER* 3.2 19.1 + - - +
203A LEU* 3.9 6.9 - - - +
152B GLU 3.8 17.0 + - - -
153B VAL* 3.9 27.4 + - + +
176B TYR* 3.2 11.6 - - - -
177B LEU* 2.7 63.3 + - + +
179B VAL* 4.1 8.1 - - + -
183B TYR* 4.2 1.8 + - - -
206B ALA* 3.5 24.2 - - - +
207B LEU* 1.3 74.5 - - - +
209B ASP* 1.3 62.0 + - - +
210B THR* 3.6 0.8 + - + -
215B LEU* 3.3 17.7 - - + +
216B ALA 3.6 3.1 - - - -
217B THR* 3.1 27.4 + - - +
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Residues in contact with ASP 209 (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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174B ARG* 2.4 38.0 + - - -
175B TRP 4.9 0.9 - - - -
176B TYR* 3.3 36.2 + - + -
208B LYS* 1.3 72.7 - - - +
210B THR* 1.3 62.5 + - - +
211B GLU 2.8 7.4 + - - -
212B GLY* 2.6 36.0 + - - +
215B LEU* 3.5 19.6 - - - -
216B ALA* 3.3 15.2 + - + +
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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