Contacts of the helix formed by residues 661 - 666 (chain A) in PDB entry 5A7R
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 PHE 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A LEU* 4.3 11.4 - - + -
637A ALA* 2.9 32.8 + - + +
638A PHE* 3.7 33.7 - + - +
640A CYS* 3.8 3.2 - - - -
659A ILE 3.2 18.6 - - - -
660A ASN* 1.3 69.4 - - - +
662A ASN* 1.3 64.0 + - - +
663A ARG 3.2 3.4 - - - -
664A LEU* 2.9 41.1 + - + +
665A PHE* 3.9 10.9 - + + -
679A LEU* 4.2 18.8 - - + -
683A PHE* 4.3 18.2 - + - -
748A THR* 4.1 13.9 - - + -
766A ILE* 4.0 35.2 - - + -
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Residues in contact with ASN 662 (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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568A TRP* 3.3 65.7 - - + +
569A ASP 4.1 5.5 + - - +
570A PHE* 5.6 0.7 - - + -
640A CYS* 3.5 9.3 - - - -
646A ASN* 4.3 2.1 - - - +
660A ASN* 3.3 19.3 - - - +
661A PHE* 1.3 76.3 - - - +
663A ARG* 1.3 72.2 + - - +
665A PHE* 3.1 34.7 + - + +
666A GLU* 3.9 5.7 + - - +
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Residues in contact with ARG 663 (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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658A ASP* 4.3 20.2 + - - +
660A ASN 4.8 1.4 + - - +
661A PHE 3.2 1.0 - - - -
662A ASN* 1.3 87.9 - - - +
664A LEU* 1.3 62.7 + - - +
665A PHE 3.1 0.9 + - - -
666A GLU* 3.1 50.4 + - - +
672A LYS* 3.5 10.4 + - - -
748A THR* 3.4 17.2 + - - +
749A SER* 3.5 29.4 + - - -
750A ALA* 5.3 2.0 - - - +
1965A AR6 2.9 43.9 + - - -
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Residues in contact with LEU 664 (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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572A ALA* 4.0 4.9 - - - +
661A PHE* 2.9 39.2 + - + +
663A ARG* 1.3 76.2 - - - +
665A PHE* 1.3 69.6 + - + +
666A GLU 3.4 0.4 - - - -
672A LYS* 3.4 23.9 - - + +
675A LYS* 4.0 21.8 - - + -
676A LEU* 4.6 17.5 - - + +
679A LEU* 3.5 30.1 - - + -
747A VAL 3.7 20.2 - - - +
748A THR* 3.2 23.4 + - + +
749A SER 4.0 9.0 - - - +
760A LEU* 5.8 0.2 - - + -
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Residues in contact with PHE 665 (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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557A ILE* 4.3 15.5 - - + -
569A ASP 3.3 8.3 - - - +
570A PHE* 2.9 41.0 - + + -
572A ALA* 2.8 28.1 + - - -
573A LEU* 4.1 30.7 - - + +
638A PHE* 3.6 57.2 - + - -
640A CYS* 4.3 3.4 - - - -
661A PHE* 3.9 15.3 - - + -
662A ASN* 3.1 23.8 + - + +
664A LEU* 1.3 90.6 - - + +
666A GLU* 1.3 56.6 + - - +
676A LEU* 4.5 9.0 - - + -
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Residues in contact with GLU 666 (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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568A TRP* 5.8 0.7 - - - -
569A ASP* 3.4 32.6 + - + +
572A ALA* 3.6 8.0 - - - +
662A ASN* 3.9 4.4 + - - +
663A ARG* 3.1 61.7 + - - +
664A LEU 3.4 0.6 - - - -
665A PHE* 1.3 78.3 - - - +
667A GLY* 1.4 66.7 - - - +
669A SER 5.2 0.2 + - - -
672A LYS* 3.8 19.0 + - - +
749A SER* 5.2 0.5 - - - -
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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