Contacts of the strand formed by residues 371 - 374 (chain O) in PDB entry 6NR8
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 371 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196O GLY 3.3 14.6 - - - +
198O LYS* 3.8 22.0 - - + +
209O GLN 3.7 1.7 - - - +
210O LEU* 3.9 0.9 - - - -
211O VAL* 3.1 46.8 + - - +
213O GLY 3.8 8.5 + - - -
215O ALA* 3.8 23.7 + - + -
321O ARG* 3.0 29.0 + - - +
369O THR* 3.9 1.6 - - - +
370O CYS* 1.3 72.7 - - - +
372O PHE* 1.3 68.0 + - - +
373O ILE* 4.0 3.3 + - + +
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Residues in contact with PHE 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178O MET* 3.2 48.2 - - + -
179O VAL* 4.2 10.8 - - + -
182O ALA* 3.7 13.9 - - + -
195O ILE* 4.2 9.0 - - - -
196O GLY 3.4 4.8 + - - -
197O ILE* 3.3 32.4 - - + +
198O LYS* 2.5 37.1 + - - +
208O SER* 3.8 15.3 - - - +
209O GLN 3.3 16.6 - - - -
210O LEU* 3.6 17.7 - - + -
370O CYS* 5.3 2.2 - - + -
371O THR* 1.3 76.3 - - - +
373O ILE* 1.3 58.6 + - - +
389O LEU* 5.0 11.4 - - + -
393O ILE* 4.3 18.6 - - + -
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Residues in contact with ILE 373 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198O LYS* 3.4 17.7 - - + -
200O VAL* 4.1 9.4 - - + -
208O SER* 3.5 9.1 + - - -
209O GLN* 3.3 33.8 + - + +
211O VAL* 5.3 3.6 - - + -
215O ALA* 4.1 15.5 - - + -
353O ILE* 4.4 5.4 - - + -
358O TYR* 3.6 52.9 - - + +
360O PHE* 4.2 8.3 - - + -
371O THR* 4.2 4.7 - - + +
372O PHE* 1.3 71.7 - - - +
374O LEU* 1.3 57.4 + - - +
375O ARG* 2.4 44.0 + - - +
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Residues in contact with LEU 374 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O PHE* 4.4 5.4 - - + -
197O ILE* 3.7 12.1 - - + -
198O LYS 2.5 18.2 + - - +
199O LYS* 3.5 1.7 - - + -
200O VAL 3.0 27.4 + - - +
208O SER* 3.8 22.0 - - - +
373O ILE* 1.3 72.4 - - - +
375O ARG* 1.3 73.9 + - - +
382O MET* 3.3 28.9 - - + +
385O THR* 3.9 22.7 - - + -
386O GLU* 3.6 38.4 - - + +
389O LEU* 4.0 11.9 - - + -
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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