Contacts of the strand formed by residues 382 - 388 (chain A) in PDB entry 1N1M
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 ARG 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A GLU* 5.6 2.0 + - - -
353A TRP 4.8 0.8 + - - -
355A GLY* 3.8 34.1 - - - +
356A ARG* 3.6 42.3 - - - +
374A ILE* 3.8 20.1 + - + +
375A ILE* 3.6 11.7 - - - +
376A SER* 4.1 19.4 + - - +
381A TYR* 1.3 72.0 - - - +
383A HIS* 1.3 64.2 + - - +
403A GLU* 2.8 28.1 + - - +
404A VAL 2.9 26.1 + - - -
588A ASP* 3.1 35.1 + - - -
591A MET* 3.3 22.9 - - - +
592A HIS* 4.0 4.9 + - - -
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Residues in contact with HIS 383 (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 ILE* 3.4 3.7 - - - -
375A ILE 3.0 31.8 + - - +
377A ASN* 3.2 26.7 - - - -
381A TYR* 3.5 6.6 + - + +
382A ARG* 1.3 77.6 + - - +
384A ILE* 1.3 65.6 + - - +
385A CYS 3.6 0.5 + - - -
396A PHE* 3.7 14.7 - - + -
398A THR* 3.1 31.9 + - - +
399A LYS* 3.4 22.9 + - - -
400A GLY 2.7 27.0 + - - -
402A TRP* 3.1 38.6 + + - -
404A VAL* 3.9 4.9 - - - +
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Residues in contact with ILE 384 (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 TYR* 4.0 18.2 - - + -
373A LYS 3.8 3.8 - - - +
374A ILE* 4.4 2.2 - - + +
383A HIS* 1.3 70.9 - - - +
385A CYS* 1.3 63.3 + - - +
396A PHE* 3.3 4.9 - - - -
397A ILE* 2.9 47.7 + - + +
398A THR* 3.0 13.9 + - + +
404A VAL* 3.8 25.4 - - + -
407A ILE* 3.7 26.2 - - + -
415A LEU* 3.6 28.3 - - + -
417A TYR* 3.7 24.9 - - + -
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Residues in contact with CYS 385 (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 TYR* 3.3 7.9 - - - +
373A LYS 3.0 31.8 + - - +
375A ILE* 3.8 20.4 - - + -
383A HIS 3.6 0.6 + - - -
384A ILE* 1.3 76.5 - - - +
386A TYR* 1.3 59.2 + - - +
387A PHE* 3.6 11.6 - - + -
394A CYS* 2.0 48.5 - - - -
395A THR 3.5 19.5 - - - -
396A PHE* 3.6 15.7 - - + -
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Residues in contact with TYR 386 (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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365A THR* 4.9 2.2 - - + +
370A SER* 3.5 25.5 + - - -
371A PHE 3.6 3.1 - - - -
372A TYR* 3.2 47.3 - + + -
385A CYS* 1.3 72.3 - - - +
387A PHE* 1.3 63.7 + - - +
388A GLN* 3.4 34.1 + - - +
393A ASP 4.6 0.2 - - - +
394A CYS* 2.9 6.4 - - - +
395A THR* 2.7 48.9 + - - +
397A ILE* 3.9 6.7 - - + -
439A TYR* 3.7 15.5 - - - -
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Residues in contact with PHE 387 (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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345A HIS* 3.7 33.4 - + + +
370A SER* 2.9 26.5 - - - -
371A PHE* 2.7 54.1 + + + +
373A LYS* 3.4 31.6 - - + -
375A ILE* 4.3 7.9 - - + -
385A CYS* 3.6 18.4 - - + -
386A TYR* 1.3 79.0 - - - +
388A GLN* 1.3 67.4 + - - +
391A LYS 5.0 1.8 - - - -
392A LYS 5.3 2.2 - - - -
393A ASP 5.1 0.9 - - - -
394A CYS* 3.4 37.9 - - + +
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Residues in contact with GLN 388 (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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345A HIS* 3.6 3.5 + - - -
369A ASN* 3.9 5.6 + - - +
370A SER* 3.4 23.6 + - - -
386A TYR* 3.4 28.2 + - - +
387A PHE* 1.3 76.7 - - - +
389A ILE* 1.3 53.0 + - - +
390A ASP* 2.4 23.8 + - - +
391A LYS* 2.6 68.8 + - + +
393A ASP 5.0 1.0 + - - -
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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