Contacts of the helix formed by residues 360 - 370 (chain B) in PDB entry 1CZY
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 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B SER* 1.3 80.4 - - - +
361B PHE* 1.3 65.3 + - - +
362B PRO 3.3 2.5 - - - -
363B ARG* 2.7 48.3 + - + +
364B LYS* 3.1 21.3 + - - +
488B ASP* 3.0 21.0 + - - +
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Residues in contact with PHE 361 (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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358B ILE* 4.3 6.5 - - + +
359B SER 3.0 4.5 - - - -
360B ASP* 1.3 76.9 - - - +
362B PRO* 1.3 58.1 - - + +
364B LYS* 4.7 3.1 - - - +
365B ARG* 2.7 68.0 + - + +
396B LEU* 4.2 17.5 - - + -
478B MET* 3.2 35.4 - - + -
479B GLU* 4.0 15.3 - - + -
485B VAL* 3.5 30.1 - - + -
488B ASP* 3.2 22.8 + - - +
489B ALA* 4.1 6.3 - - - +
490B ILE* 3.9 24.5 - - + -
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Residues in contact with PRO 362 (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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361B PHE* 1.3 78.3 - - + +
363B ARG* 1.3 57.8 + - - +
365B ARG* 3.3 6.9 + - + +
366B GLN* 3.0 29.3 + - - +
488B ASP* 2.9 23.7 - - - +
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Residues in contact with ARG 363 (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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360B ASP* 2.7 47.7 + - + +
362B PRO* 1.3 76.6 - - - +
364B LYS* 1.3 82.4 - - - +
366B GLN* 3.0 7.4 + - - +
367B GLU* 2.9 59.2 + - + +
488B ASP* 5.2 0.2 + - - -
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Residues in contact with LYS 364 (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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358B ILE* 4.0 18.1 - - + +
359B SER* 2.9 37.7 + - - +
360B ASP* 3.1 8.6 + - - +
361B PHE 4.0 1.6 - - - +
363B ARG* 1.3 105.7 - - - +
365B ARG* 1.3 61.2 + - - +
367B GLU* 3.3 15.2 + - - +
368B ALA* 3.1 22.7 + - - +
373B ILE 4.8 1.2 - - - +
376B ILE* 4.0 22.1 - - + +
396B LEU* 3.8 16.8 - - + +
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Residues in contact with ARG 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PHE* 2.7 50.0 + - + +
362B PRO* 3.4 7.9 - - + +
364B LYS* 1.3 79.0 - - - +
366B GLN* 1.3 57.3 + - - +
368B ALA* 3.3 3.5 + - - +
369B VAL* 3.1 52.7 + - - +
396B LEU* 3.1 29.8 + - + +
397B ASN* 2.9 23.4 + - - -
475B VAL* 2.9 46.4 - - - +
478B MET* 5.9 0.8 - - - -
479B GLU* 4.6 7.4 - - + +
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Residues in contact with GLN 366 (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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362B PRO 3.0 13.6 + - - +
363B ARG* 3.0 9.2 + - - +
365B ARG* 1.3 75.3 - - - +
367B GLU* 1.3 60.4 + - + +
368B ALA 3.0 2.2 + - - -
369B VAL* 3.1 26.5 + - - +
370B ALA* 2.8 39.9 + - - +
372B ARG* 5.2 1.8 - - - +
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Residues in contact with GLU 367 (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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363B ARG* 2.9 50.3 + - + +
364B LYS* 3.6 17.3 - - - +
366B GLN* 1.3 77.6 - - + +
368B ALA* 1.3 57.7 + - - +
370B ALA* 4.1 0.4 - - - -
371B GLY 3.4 1.0 + - - -
372B ARG* 3.0 51.5 + - - +
373B ILE* 3.0 57.9 + - + +
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Residues in contact with ALA 368 (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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364B LYS 3.1 11.6 + - - +
365B ARG 3.5 8.7 - - - +
366B GLN 3.0 0.4 - - - -
367B GLU* 1.3 75.1 - - - +
369B VAL* 1.3 61.2 + - - +
370B ALA 3.1 1.3 - - - -
371B GLY* 2.8 21.1 + - - -
373B ILE 3.3 18.1 + - - +
374B PRO* 4.3 12.2 - - + +
396B LEU* 4.0 16.6 - - + -
397B ASN* 3.9 24.9 + - + +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ARG* 3.1 51.1 + - - +
366B GLN* 3.1 27.8 + - - +
368B ALA* 1.3 77.2 - - - +
370B ALA* 1.3 61.0 + - - +
371B GLY* 3.4 0.7 + - - -
397B ASN* 3.8 22.7 + - - +
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Residues in contact with ALA 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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366B GLN* 2.8 25.4 + - - +
367B GLU 4.1 0.9 - - - +
369B VAL* 1.3 77.4 - - - +
371B GLY* 1.3 60.8 + - - +
372B ARG* 3.3 26.4 + - + +
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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