Contacts of the helix formed by residues 369 - 378 (chain B) in PDB entry 6HYI
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 ASP 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B TYR* 5.1 5.0 - - - -
367B GLY 3.8 1.8 + - - -
368B LEU* 1.3 76.5 - - - +
370B SER* 1.3 65.0 + - - +
371B TYR* 3.1 11.5 + - - +
372B GLU* 2.8 55.6 + - - +
373B LYS* 2.9 25.0 + - - +
601B NOS 5.1 6.4 + - - +
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Residues in contact with SER 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ILE* 4.9 7.4 - - - +
369B ASP* 1.3 75.1 - - - +
371B TYR* 1.3 64.5 + - - +
373B LYS* 3.1 12.0 + - - +
374B LEU* 2.9 43.0 + - - +
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B TYR* 4.5 6.1 - + - -
302B LYS* 2.7 24.6 + - - -
310B GLU* 2.5 30.3 + - - -
311B LEU* 4.7 10.8 - - + -
352B ARG* 5.3 4.1 + - - -
369B ASP* 3.1 9.9 + - - +
370B SER* 1.3 79.7 - - - +
372B GLU* 1.3 67.9 + - + +
374B LEU* 3.3 10.8 + - + +
375B GLN* 3.0 48.2 + - + +
601B NOS 3.3 65.1 + + - +
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Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B TYR* 3.7 32.6 + - + +
367B GLY 4.3 2.3 - - - +
368B LEU* 3.3 33.1 - - + +
369B ASP* 2.8 47.7 + - - +
371B TYR* 1.3 71.9 - - + +
373B LYS* 1.3 65.6 + - - +
375B GLN* 3.3 13.3 + - - +
376B LEU* 3.1 20.6 + - - +
466B CYS 4.7 5.1 - - - +
469B PRO* 3.6 21.7 - - + +
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Residues in contact with LYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ILE* 3.6 19.1 - - + -
359B LEU* 3.5 41.2 - - + +
360B ALA* 3.9 21.8 - - + +
365B LEU* 3.5 20.2 - - + +
366B GLY* 5.0 5.3 + - - -
368B LEU* 2.5 44.5 + - + -
369B ASP* 2.9 21.2 + - - +
370B SER* 3.1 5.0 + - - +
372B GLU* 1.3 76.4 - - - +
374B LEU* 1.3 57.6 + - - +
376B LEU* 3.2 7.4 + - - +
377B ALA* 2.9 22.3 + - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B TYR* 4.9 4.7 - - + +
352B ARG* 3.5 51.1 + - + +
356B ILE* 3.7 33.9 - - + -
370B SER* 2.9 35.3 + - - +
371B TYR* 3.7 10.1 - - + +
373B LYS* 1.3 73.4 - - - +
375B GLN* 1.3 65.8 + - - +
377B ALA* 3.1 5.6 + - + +
378B ASP* 3.0 26.5 + - - +
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B VAL* 3.4 32.9 - - + +
300B TYR* 3.9 14.7 + - - -
302B LYS* 4.3 6.9 - - - +
306B THR* 6.1 1.6 - - - +
352B ARG* 4.2 2.6 - - - +
371B TYR* 3.0 41.6 + - + +
372B GLU* 3.5 14.9 - - - +
374B LEU* 1.3 77.0 - - - +
376B LEU* 1.3 62.2 + - - +
378B ASP* 3.3 25.0 + - - +
465B MET* 3.6 41.2 - - + +
466B CYS* 4.7 4.7 - - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LEU* 3.9 13.5 - - + -
365B LEU* 3.4 42.0 - - + -
368B LEU* 4.8 3.8 - - + -
372B GLU 3.1 12.5 + - - +
373B LYS* 3.5 8.1 - - - +
374B LEU 3.2 0.2 - - - -
375B GLN* 1.3 74.7 - - - +
377B ALA* 1.3 66.8 + - - +
379B ALA* 3.0 14.2 + - - +
380B LEU* 3.4 27.0 + - + +
403B ILE* 4.5 7.4 - - + -
458B LEU* 4.1 20.2 - - + -
466B CYS* 3.8 32.5 - - + +
467B LEU* 4.2 9.0 - - + -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ARG* 3.4 16.9 - - - +
352B ARG* 4.1 23.1 - - - +
355B TYR* 4.1 13.3 - - + -
356B ILE* 5.0 1.8 - - - +
359B LEU* 4.0 10.7 - - + +
373B LYS 2.9 14.8 + - - +
374B LEU* 3.1 13.7 + - + +
376B LEU* 1.3 78.3 - - - +
378B ASP* 1.3 61.5 + - - +
379B ALA 3.0 1.4 + - - -
380B LEU* 3.1 24.1 + - - +
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B VAL* 3.6 32.4 - - + +
244B LEU* 4.2 14.4 - - - +
246B SER* 3.7 1.7 + - - -
247B PHE* 3.4 17.3 - - - -
314B MET* 4.4 4.7 - - - +
348B ALA* 4.6 6.6 - - - +
351B ARG* 3.5 15.4 + - - +
352B ARG* 2.8 46.5 + - - +
374B LEU 3.0 14.4 + - - +
375B GLN* 3.4 15.6 - - - +
376B LEU 3.1 0.2 - - - -
377B ALA* 1.3 76.1 - - - +
379B ALA* 1.3 56.6 + - - +
380B LEU 3.5 0.2 - - - -
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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