Contacts of the helix formed by residues 564 - 571 (chain A) in PDB entry 5COX
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 ILE 564 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 5.0 5.2 - - + -
201A PHE* 3.8 19.3 - - + -
301A TYR* 4.0 9.4 - - + +
343A ILE* 3.7 8.5 - - + +
347A ASP* 3.2 18.8 + - + +
563A SER* 1.3 72.0 - - - +
565A GLN* 1.3 64.8 + - + +
567A LEU* 3.5 8.2 + - + -
568A ILE* 3.4 37.5 + - + +
578A THR* 4.2 6.8 + - - -
579A SER* 4.6 15.5 - - - +
580A PHE* 3.2 53.4 - - + -
267D LYS* 5.3 3.4 - - - +
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Residues in contact with GLN 565 (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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563A SER* 3.0 7.7 - - - +
564A ILE* 1.3 83.0 - - + +
566A SER* 1.3 58.3 + - - +
568A ILE* 3.5 1.4 + - - -
569A CYS* 2.9 38.6 + - - +
575A CYS 4.3 1.4 + - - -
576A PRO 3.1 22.8 + - - -
577A PHE* 3.2 18.6 - - - +
578A THR* 2.9 32.4 + - - +
265D THR* 4.7 1.7 + - - -
267D LYS* 4.2 16.2 + - + +
268D ASP* 3.2 40.8 - - + +
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Residues in contact with SER 566 (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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339A GLU* 6.2 0.2 - - - -
561A THR 4.9 5.2 + - - -
562A ALA* 5.4 1.3 - - - -
563A SER* 3.1 27.9 + - - -
565A GLN* 1.3 76.6 - - - +
567A LEU* 1.3 64.5 + - - +
569A CYS* 3.8 6.8 - - - +
570A ASN* 2.9 43.6 + - - -
268D ASP* 3.9 10.8 + - - -
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Residues in contact with LEU 567 (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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201A PHE* 5.1 1.1 - - + -
301A TYR* 5.1 4.5 - - + -
304A ILE* 3.8 22.3 - - + +
305A TRP* 3.6 60.1 - - + +
308A GLU* 4.1 16.2 - - + -
339A GLU* 4.2 9.6 - - - +
343A ILE* 4.2 11.0 - - + -
563A SER 2.8 14.8 + - - +
564A ILE* 3.7 21.3 - - + +
566A SER* 1.3 77.1 - - - +
568A ILE* 1.3 64.5 + - + +
570A ASN* 5.0 0.4 - - - +
571A ASN* 2.8 32.9 + - - +
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Residues in contact with ILE 568 (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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197A MET* 5.0 4.5 - - - -
301A TYR* 4.4 6.7 - - + -
304A ILE* 3.8 23.6 - - + -
423A VAL* 3.8 21.5 - - + -
564A ILE* 3.4 30.9 + - + +
565A GLN 4.1 0.4 - - - +
566A SER 3.2 0.2 - - - -
567A LEU* 1.3 82.7 - - + +
569A CYS* 1.3 59.9 + - - +
572A VAL* 2.5 61.9 + - + +
576A PRO* 3.5 29.1 - - + +
578A THR* 3.6 17.7 - - + +
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Residues in contact with CYS 569 (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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565A GLN* 2.9 30.0 + - - +
566A SER* 3.2 11.2 + - - +
568A ILE* 1.3 80.7 - - - +
570A ASN* 1.3 65.0 + - - +
571A ASN 3.4 0.2 + - - -
572A VAL 3.5 11.8 - - - +
575A CYS* 2.0 63.5 + - - +
253D LYS* 5.9 3.6 - - - -
268D ASP* 4.2 20.6 - - - +
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Residues in contact with ASN 570 (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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308A GLU* 5.2 0.6 + - - -
311A ARG* 3.8 47.8 + - - +
566A SER* 2.9 35.0 + - - +
567A LEU* 5.0 0.6 - - - +
569A CYS* 1.3 83.0 - - - +
571A ASN* 1.3 68.5 + - - +
572A VAL 5.1 0.2 - - - -
575A CYS* 5.8 0.3 - - - -
246D LEU* 5.8 2.9 - - - +
248D LYS* 4.9 10.4 + - - +
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Residues in contact with ASN 571 (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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304A ILE* 3.7 27.2 + - + +
307A ARG* 3.1 57.1 + - + +
308A GLU* 3.1 36.7 + - - +
311A ARG* 4.1 5.0 - - - +
419A LEU* 5.9 0.3 - - - +
567A LEU* 2.8 26.5 + - - +
568A ILE 3.3 1.8 + - - -
569A CYS 3.3 0.2 - - - -
570A ASN* 1.3 87.9 - - - +
572A VAL* 1.3 62.1 + - - +
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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