Contacts of the strand formed by residues 261 - 265 (chain B) in PDB entry 4NDH
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 LEU 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B TRP 3.7 0.2 - - - +
203B LEU* 3.3 6.4 - - - +
204B VAL* 2.8 49.7 + - + +
227B MET* 3.3 46.1 - - + +
228B HIS* 4.0 8.3 - - - +
248B LEU* 3.9 13.9 - - + -
249B GLY* 3.4 35.2 - - - +
250B TYR* 3.6 29.7 - - + +
260B HIS* 1.3 72.3 - - - +
262B HIS* 1.3 66.2 + - - +
263B VAL* 3.9 1.5 + - + -
290B SER* 3.8 9.4 - - - +
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Residues in contact with HIS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS* 2.9 26.1 + - + +
202B TRP 3.6 2.9 - - - -
203B LEU* 3.4 18.7 - - + +
247B ARG 3.6 1.2 - - - +
248B LEU* 3.2 6.4 - - - -
249B GLY 2.8 40.1 + - - +
251B HIS* 3.5 24.7 + + - -
260B HIS* 3.8 12.9 + - - +
261B LEU* 1.3 74.5 - - - +
263B VAL* 1.3 61.1 + - - +
264B ILE* 3.9 2.7 - - + -
282B PHE* 3.8 9.9 - + + -
287B PHE* 4.1 11.8 - + + -
401B AMP 2.7 56.2 + - - -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TYR 3.8 0.9 - - - +
201B HIS* 3.3 3.7 - - - -
202B TRP* 2.9 60.2 + - + +
204B VAL* 4.0 17.7 - - + -
231B GLY* 3.8 28.5 - - - +
234B VAL* 5.7 0.9 - - + -
235B ILE* 3.6 37.7 - - + -
246B PHE* 4.0 3.1 - - + -
247B ARG 3.6 3.1 - - - -
248B LEU* 4.2 12.3 - - + -
261B LEU* 4.5 2.9 - - + -
262B HIS* 1.3 75.0 - - - +
264B ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 264 (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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197B LYS* 3.9 15.7 - - + -
198B ALA* 3.7 10.1 - - + -
200B TYR 3.4 4.5 - - - +
201B HIS* 3.8 28.9 - - + +
246B PHE* 3.5 4.5 - - - -
247B ARG 2.9 40.4 + - - +
262B HIS* 4.8 2.0 - - + -
263B VAL* 1.3 78.2 - - - +
265B SER* 1.3 71.5 + - - +
266B GLN* 3.1 20.6 + - - +
268B PHE* 3.8 21.1 - - + -
282B PHE* 3.9 28.5 - - + -
287B PHE* 4.4 11.0 - - + -
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Residues in contact with SER 265 (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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198B ALA* 3.1 22.2 - - - +
199B ARG 3.9 0.2 - - - -
200B TYR* 2.9 30.8 + - - -
244B LEU* 3.9 12.6 - - - -
245B ARG 3.3 10.8 - - - -
246B PHE* 3.5 23.7 - - - -
264B ILE* 1.3 79.9 - - - +
266B GLN* 1.3 60.3 + - - +
267B ASP* 2.6 26.4 + - - -
268B PHE* 3.9 2.8 + - - -
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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