Contacts of the strand formed by residues 371 - 377 (chain A) in PDB entry 1X8B
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 HIS 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ARG* 3.1 46.6 + - + -
330A SER* 3.1 22.2 - - - +
331A LYS* 4.2 2.2 - - + -
332A LYS* 3.9 7.4 - - - +
367A ALA* 3.3 6.6 - - - +
368A GLU 2.8 36.7 + - - +
369A ASP* 3.1 17.3 + - + +
370A ASP* 1.4 99.8 + - + +
372A MET* 1.3 58.0 + - - +
373A LEU* 3.8 14.4 - - + -
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Residues in contact with MET 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LYS 3.6 0.9 - - - +
329A ARG* 3.5 2.3 - - - -
330A SER* 2.9 43.3 + - - +
331A LYS 5.1 0.9 - - - +
332A LYS* 4.2 8.6 - - + +
333A PRO* 3.3 33.0 - - + -
340A GLU* 5.6 2.7 - - + -
343A ALA* 3.5 25.6 - - + +
344A LEU* 4.4 19.7 - - + -
347A VAL* 4.6 15.3 - - - -
365A ALA* 6.4 0.9 - - + -
366A TRP 3.6 10.5 - - - +
367A ALA* 4.5 10.8 - - + -
371A HIS* 1.3 71.8 - - - +
373A LEU* 1.3 67.9 + - - +
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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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295A TYR* 3.5 35.2 - - + -
327A ILE* 4.0 7.4 - - + -
328A LYS 3.2 5.2 - - - +
329A ARG* 3.6 28.9 - - + +
365A ALA* 3.2 6.7 - - - +
366A TRP* 2.8 69.1 + - + +
368A GLU* 4.0 11.7 - - + -
371A HIS* 3.8 24.7 - - + +
372A MET* 1.3 85.5 - - - +
374A ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 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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326A ALA 3.7 1.7 - - - +
327A ILE* 3.2 5.7 - - - -
328A LYS* 2.9 69.1 + - + +
346A GLU* 4.8 5.8 - - + +
347A VAL* 4.7 13.5 - - + +
350A HIS* 3.8 19.1 - - + -
362A TYR* 3.3 37.7 - - + -
364A SER 3.5 2.9 - - - +
365A ALA* 4.1 7.0 - - + -
366A TRP* 5.1 0.2 - - - -
373A LEU* 1.3 74.1 - - - +
375A GLN* 1.3 59.2 + - - +
376A ASN* 3.5 21.7 + - - +
901A 824 4.4 6.2 - - + -
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Residues in contact with GLN 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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294A ARG* 4.4 2.4 + - - -
299A PHE* 3.6 23.2 - - + -
318A LYS* 4.3 6.1 - - - +
325A TYR* 3.4 53.9 - - + -
326A ALA 3.7 3.8 - - - -
327A ILE* 4.0 12.6 - - + -
363A PHE* 2.9 37.9 + - + +
364A SER* 2.8 35.9 + - - +
366A TRP* 3.9 14.3 - - + -
374A ILE* 1.3 71.8 - - - +
376A ASN* 1.3 64.4 + - - +
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Residues in contact with ASN 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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325A TYR* 3.3 9.7 - - - +
326A ALA 2.8 36.8 + - - +
350A HIS* 3.3 29.6 + - - -
360A VAL* 3.8 3.3 - - + +
361A ARG 3.3 9.6 - - - +
362A TYR* 3.4 14.9 - - - +
363A PHE* 3.8 6.7 - - - -
374A ILE* 3.5 18.1 + - - +
375A GLN* 1.3 81.2 - - - +
377A GLU* 1.3 61.9 + - - +
463A ASP 6.1 0.2 - - - +
901A 824 3.2 43.8 + - - +
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Residues in contact with GLU 377 (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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325A TYR* 4.7 2.0 - - - -
326A ALA* 3.8 0.2 - - - +
360A VAL* 3.7 8.1 - - + +
361A ARG* 2.8 58.1 + - + +
363A PHE* 3.6 15.5 - - + -
376A ASN* 1.3 73.8 - - - +
378A TYR* 1.3 66.0 + - - +
379A CYS* 4.4 5.4 - - - -
435A SER* 4.8 3.5 + - - -
460A LYS* 3.1 37.1 + - - +
901A 824 2.7 32.6 + - - +
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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