Contacts of the helix formed by residues 371 - 384 (chain A) in PDB entry 6C90
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 PRO 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A GLY* 1.3 86.0 - - - +
372A SER* 1.3 64.7 + - - +
374A VAL* 2.9 13.3 + - - +
375A PHE 3.2 3.1 + - - -
401A ALA* 6.4 0.9 - - + -
402A TYR* 3.8 12.5 - - + +
405A GLN* 2.8 43.4 + - - +
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Residues in contact with SER 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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370A GLY 3.4 1.0 - - - -
371A PRO* 1.3 80.0 - - - +
373A ASN* 1.3 63.2 + - - +
375A PHE* 3.3 8.9 + - - +
376A LYS* 3.1 23.0 + - - +
405A GLN* 4.7 0.9 - - - +
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Residues in contact with ASN 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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321A PHE* 4.1 17.3 - - + -
323A ALA* 4.0 25.3 - - - +
324A GLY* 3.9 17.4 + - - +
325A GLY 5.3 0.2 - - - +
370A GLY* 3.1 16.7 + - - +
372A SER* 1.3 77.4 - - - +
374A VAL* 1.3 63.1 + - - +
376A LYS* 3.4 10.6 + - - +
377A ILE* 3.1 25.5 + - - +
538A MET* 3.8 18.0 - - + +
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLY 3.0 15.9 + - - +
371A PRO 2.9 9.4 + - - +
373A ASN* 1.3 78.1 - - - +
375A PHE* 1.3 62.6 + - - +
377A ILE* 3.0 9.6 - - + +
378A VAL* 3.0 35.4 + - + +
391A ILE* 5.1 0.2 - - + -
402A TYR* 3.6 48.2 - - + +
406A MET* 3.8 16.4 - - + -
480A PHE* 4.3 3.8 - - + -
497A LEU* 5.4 0.4 - - + -
499A THR* 3.9 20.4 - - + +
538A MET* 4.0 12.6 - - + -
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Residues in contact with PHE 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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371A PRO 3.2 8.8 + - - +
372A SER* 3.3 10.3 + - - +
374A VAL* 1.3 77.4 - - - +
376A LYS* 1.3 66.7 + - - +
378A VAL* 3.4 0.9 + - - +
379A LYS* 2.9 42.2 + - + +
405A GLN* 3.1 34.5 - - + +
406A MET* 3.6 21.5 - - + +
408A LYS* 3.8 36.6 - - + -
409A LEU* 3.9 36.6 - - + -
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Residues in contact with LYS 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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321A PHE* 4.1 13.7 - - + -
325A GLY 3.6 22.4 - - - +
326A ASP* 3.9 31.0 + - - +
372A SER 3.1 13.2 + - - +
373A ASN* 3.7 15.9 - - - +
374A VAL 3.3 0.2 - - - -
375A PHE* 1.3 84.1 - - + +
377A ILE* 1.3 63.5 - - - +
379A LYS* 3.3 4.4 + - - +
380A MET* 3.0 38.9 + - + +
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Residues in contact with ILE 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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321A PHE* 4.0 22.4 - - + -
328A LEU* 3.6 31.6 - - + -
373A ASN 3.1 15.0 + - - +
374A VAL* 3.0 24.9 - - - +
376A LYS* 1.3 76.2 - - - +
378A VAL* 1.3 63.3 + - - +
380A MET* 3.2 16.0 + - + -
381A ILE* 2.9 25.9 + - + +
497A LEU* 3.8 34.1 - - + -
536A ILE* 4.2 12.3 - - + -
538A MET* 4.0 10.1 - - - -
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Residues in contact with VAL 378 (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 VAL* 3.0 28.1 + - + +
375A PHE 3.8 2.7 - - - +
377A ILE* 1.3 76.1 - - - +
379A LYS* 1.3 65.0 + - - +
381A ILE* 2.9 20.3 + - + +
382A MET* 3.0 33.1 + - + +
389A VAL* 5.3 2.2 - - + -
391A ILE* 4.3 12.6 - - + -
406A MET* 3.7 33.4 - - + -
409A LEU* 4.9 0.7 - - + -
411A PHE* 4.8 7.6 - - + -
478A ALA* 4.9 6.3 - - + -
480A PHE* 4.4 5.6 - - + -
497A LEU* 4.0 20.2 - - + -
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Residues in contact with LYS 379 (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 PHE* 2.9 44.4 + - + +
376A LYS* 3.6 4.7 - - - +
378A VAL* 1.3 78.8 - - - +
380A MET* 1.3 63.0 + - + +
382A MET* 3.1 10.4 + - + +
383A GLU* 3.0 50.3 + - + +
409A LEU* 4.3 21.3 - - + +
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Residues in contact with MET 380 (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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321A PHE* 4.3 6.5 - - + -
326A ASP 3.5 26.5 - - - +
327A GLY* 4.3 10.3 - - - -
328A LEU* 4.3 20.0 - - + -
376A LYS* 3.0 41.3 + - + +
377A ILE* 3.4 19.1 - - + +
379A LYS* 1.3 75.8 - - + +
381A ILE* 1.3 63.1 + - + +
383A GLU* 3.3 6.8 + - - +
384A ARG* 3.1 67.0 + - - +
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Residues in contact with ILE 381 (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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328A LEU* 6.0 0.2 - - + -
377A ILE* 2.9 28.4 + - + +
378A VAL* 2.9 12.5 + - + +
380A MET* 1.3 75.5 - - - +
382A MET* 1.3 73.1 + - - +
384A ARG 3.5 0.2 + - - -
385A ASN 3.4 2.3 + - - -
386A PHE* 2.9 63.4 + - + +
387A GLN* 3.3 1.1 - - - +
389A VAL* 4.0 33.0 - - + -
495A THR* 4.1 3.8 - - + +
497A LEU* 4.3 13.7 - - + -
536A ILE* 4.0 30.5 - - + -
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Residues in contact with MET 382 (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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378A VAL* 3.0 31.6 + - + +
379A LYS* 3.1 7.6 + - - +
381A ILE* 1.3 90.5 - - - +
383A GLU* 1.3 65.7 + - + +
385A ASN* 3.2 9.7 + - - -
387A GLN* 3.3 48.9 + - + +
389A VAL* 4.3 5.4 - - - -
409A LEU* 5.1 1.1 - - + -
411A PHE* 3.3 50.5 - - + -
477A LYS* 4.0 13.2 - - + +
478A ALA* 4.6 1.3 - - + -
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Residues in contact with GLU 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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379A LYS* 3.0 55.8 + - + +
380A MET* 3.3 7.0 + - - +
382A MET* 1.3 77.2 - - + +
384A ARG* 1.3 76.2 + - + +
385A ASN* 3.2 2.4 + - - +
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Residues in contact with ARG 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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326A ASP 5.5 1.0 + - - -
328A LEU* 5.5 5.3 - - - +
380A MET* 3.1 67.8 + - - +
381A ILE 4.1 0.2 - - - +
382A MET 3.2 0.4 - - - -
383A GLU* 1.3 89.0 + - - +
385A ASN* 1.3 70.8 + - - +
386A PHE* 3.1 45.9 + - + -
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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