Contacts of the strand formed by residues 372 - 377 (chain N) in PDB entry 6NRB
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 VAL 372 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175N SER* 3.2 27.1 - - - +
178N ALA* 3.9 6.3 - - + -
189N PHE 3.6 1.7 - - - +
190N MET* 3.2 49.0 - - + +
192N GLU* 3.1 19.6 + - - +
206N LEU* 4.3 4.7 - - + -
207N ILE 3.2 11.0 - - - +
208N ARG* 3.6 31.6 - - - -
209N GLY 3.3 5.2 - - - +
371N SER* 1.3 79.0 - - - +
373N THR* 1.3 66.4 + - - +
374N LEU* 5.4 0.9 - - + -
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Residues in contact with THR 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N GLU* 3.5 16.6 - - + +
194N MET* 3.5 34.5 - - + -
205N SER 3.2 1.2 - - - +
206N LEU* 3.4 1.9 - - - +
207N ILE* 2.3 79.0 + - + -
209N GLY 3.2 14.0 + - - -
210N LEU* 4.1 0.3 - - - -
211N VAL* 3.4 20.9 + - + -
360N PHE* 6.2 0.2 - - + -
372N VAL* 1.3 71.1 - - - +
374N LEU* 1.3 68.6 + - - +
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Residues in contact with LEU 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N LEU* 5.1 6.7 - - + -
171N ALA* 4.5 8.5 - - + +
172N VAL* 5.4 0.4 - - + -
175N SER* 4.6 1.8 - - - +
190N MET 4.9 6.5 - - - +
191N ILE* 5.5 1.3 - - - -
192N GLU 2.8 14.3 + - - +
193N ILE* 3.9 3.5 - - + -
194N MET 2.8 29.4 + - - +
204N THR* 3.7 26.5 - - + -
205N SER 3.3 0.7 - - - -
206N LEU* 3.7 37.2 - - + -
373N THR* 1.3 74.1 - - - +
375N LEU* 1.3 59.4 + - - +
376N ILE* 3.7 6.5 + - + +
391N VAL* 3.6 31.6 - - + -
395N LEU* 3.8 24.5 - - + -
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Residues in contact with LEU 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N MET* 3.1 10.1 - - + -
195N GLU* 3.5 11.9 - - - +
196N MET* 3.4 28.0 - - + +
204N THR* 3.3 1.5 - - - -
205N SER* 2.5 47.1 + - - +
207N ILE* 3.7 21.8 - - + -
353N TYR* 6.6 0.4 - - + -
355N LEU* 6.0 4.9 - - + -
360N PHE* 3.5 41.1 - - + -
373N THR 4.0 0.2 - - - -
374N LEU* 1.3 70.9 - - - +
376N ILE* 1.3 62.0 + - - +
377N LYS* 3.1 32.7 + - - +
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Residues in contact with ILE 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N ILE* 4.9 12.3 - - + -
194N MET 2.6 18.7 + - - +
195N GLU* 3.5 16.8 - - + +
196N MET 2.9 25.6 + - - -
203N ASP 3.3 5.6 - - - +
204N THR* 3.3 31.4 - - + +
374N LEU* 4.3 6.1 - - + +
375N LEU* 1.3 74.7 - - - +
377N LYS* 1.3 80.8 + - - +
384N LEU* 3.6 29.2 - - + -
387N ILE* 3.7 19.5 - - + -
388N LYS* 5.3 2.2 - - + +
391N VAL* 4.0 20.6 - - + -
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Residues in contact with LYS 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195N GLU* 5.2 0.4 - - - -
196N MET* 3.4 38.1 - - + +
198N HIS* 3.7 22.0 - - + +
201N GLU 3.7 8.7 - - - +
202N THR* 3.7 15.0 + - - +
203N ASP* 2.7 43.6 + - + +
205N SER* 2.5 30.2 + - - -
355N LEU* 5.9 1.8 - - - -
375N LEU* 3.1 34.2 + - - +
376N ILE* 1.3 81.7 - - - +
378N GLY* 1.3 63.9 + - - +
383N THR* 4.4 4.7 + - - -
384N LEU* 5.6 0.3 + - - -
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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