Contacts of the strand formed by residues 371 - 376 (chain A) in PDB entry 2I91
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 PHE 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A THR* 3.7 10.5 - - + -
369A LYS* 3.4 30.7 - - + -
370A ARG* 1.3 73.9 - - - +
372A LEU* 1.3 59.0 + - - +
373A LEU* 3.9 15.3 - - + -
403A VAL* 4.7 3.6 - - + -
407A GLU* 3.3 52.3 - - + -
409A ASP 3.0 8.1 + - - -
410A SER* 3.2 11.0 - - - -
411A HIS* 3.1 25.5 + - - +
461A ALA* 4.6 2.9 - - - -
463A ILE* 3.5 27.4 - - + +
465A ILE* 4.6 11.2 - - + -
530A ILE* 4.5 11.7 - - + -
534A THR* 3.8 21.8 - - + -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PHE* 1.3 73.4 - - - +
373A LEU* 1.3 66.8 + - - +
374A ALA* 4.0 9.2 - - + -
411A HIS* 3.4 24.5 - - + +
413A VAL* 3.7 25.4 - - + -
450A PRO* 4.4 13.5 - - + +
453A TRP* 3.8 30.5 - - + -
454A ALA* 5.1 3.6 - - + -
459A THR* 5.1 5.6 - - + -
461A ALA* 4.1 5.1 - - + +
463A ILE 2.9 6.5 + - - -
464A PHE* 3.5 33.6 - - + -
465A ILE 2.9 25.9 + - - +
466A VAL* 6.3 0.2 - - + -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PHE* 3.9 16.4 - - + -
372A LEU* 1.3 80.4 - - - +
374A ALA* 1.3 54.5 + - - +
375A ILE 4.1 0.2 + - - -
400A CYS* 3.7 38.7 - - - +
403A VAL* 3.3 37.2 - - + -
404A ALA* 3.8 16.8 - - + +
410A SER* 4.2 8.3 - - - -
411A HIS 3.0 10.8 + - - +
412A MET* 3.3 5.7 - - + +
413A VAL* 2.8 32.6 + - - +
465A ILE* 3.5 25.8 - - + +
467A PHE* 4.6 4.3 - - + -
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.9 3.3 + - + -
373A LEU* 1.3 72.1 - - - +
375A ILE* 1.3 62.4 + - - +
376A ASP 3.8 0.7 + - - -
413A VAL* 3.1 18.2 - - + -
415A PHE* 3.8 6.7 - - + -
450A PRO* 3.5 35.7 - - + -
465A ILE 2.8 13.5 + - - +
466A VAL* 3.4 7.1 - - + +
467A PHE* 2.8 30.0 + - - -
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ALA* 1.3 73.6 - - - +
376A ASP* 1.3 72.0 + - - +
377A VAL* 3.1 3.9 + - + +
393A SER* 4.2 2.5 - - - +
396A ALA* 4.0 20.9 - - + +
397A ALA* 3.4 31.2 - - + -
400A CYS* 3.7 29.6 - - + -
412A MET* 5.7 0.2 - - + -
413A VAL 2.7 16.3 + - - +
414A ALA* 3.3 7.8 - - + -
415A PHE* 3.0 27.8 + - - -
422A CYS* 5.5 4.5 - - - -
424A ILE* 4.1 13.2 - - + -
437A MET* 3.9 22.9 - - + -
467A PHE* 4.2 5.4 - - + -
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ILE* 1.3 73.8 - - - +
377A VAL* 1.3 59.2 + - - +
378A SER* 2.7 28.3 + - - -
381A MET* 3.0 33.0 - - + +
393A SER* 4.3 2.3 + - - -
415A PHE* 3.5 23.4 - - + +
445A THR* 3.5 17.2 - - - +
447A CYS* 3.9 1.4 - - - -
467A PHE 3.0 23.5 + - - +
468A THR* 2.7 31.1 + - - -
469A ASP* 4.2 3.6 - - - +
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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