Contacts of the helix formed by residues 659 - 664 (chain A) in PDB entry 2C11
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 659 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A ARG* 2.6 57.0 + - - +
626A SER* 3.2 10.4 + - - -
656A PRO* 4.3 15.1 + - + +
657A THR 4.2 0.4 - - - -
658A VAL* 1.3 70.4 - - - +
660A PHE* 1.3 66.7 + - - +
661A SER 3.4 4.6 + - - -
662A ASP* 2.9 37.2 - - - +
663A PHE* 3.7 12.0 - - - -
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Residues in contact with PHE 660 (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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525A HIS* 3.4 21.3 - + - -
623A ARG 4.8 0.2 + - - -
626A SER* 3.0 15.9 + - - +
627A TRP* 3.3 31.4 - - + +
630A TYR* 3.8 24.5 - + + -
633A ALA* 4.6 5.8 - - + -
635A THR* 5.7 0.4 - - + -
644A SER* 3.6 26.9 - - - +
658A VAL 3.5 3.8 + - - -
659A ASP* 1.3 69.0 - - - +
661A SER* 1.3 62.2 + - - +
662A ASP 2.9 5.6 - - - -
663A PHE* 3.0 53.9 + + + +
664A ILE* 4.1 8.0 + - + +
677A TRP* 3.5 39.3 - + + -
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Residues in contact with SER 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ARG* 3.5 31.4 + - - -
626A SER* 3.1 23.9 + - - -
629A ARG* 3.6 19.3 + - - -
630A TYR* 4.0 13.9 + - - -
659A ASP* 3.4 2.3 + - - -
660A PHE* 1.3 76.4 - - - +
662A ASP* 1.3 59.7 + - - +
663A PHE 3.3 0.4 - - - -
664A ILE* 3.4 24.9 + - - +
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Residues in contact with ASP 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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623A ARG* 3.3 9.5 + - - -
641A GLU* 4.0 2.0 - - - +
659A ASP* 2.9 44.7 - - - +
660A PHE 2.9 0.6 - - - -
661A SER* 1.3 76.6 - - - +
663A PHE* 1.3 60.3 + - + +
664A ILE 3.0 7.3 + - - -
665A ASN* 3.0 24.3 + - - +
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Residues in contact with PHE 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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572A GLU* 2.7 22.3 - - - +
635A THR* 3.4 14.3 - - + +
640A GLU 5.0 1.6 - - - -
641A GLU* 3.2 56.7 - - + +
642A PRO* 5.1 0.4 - - + -
643A SER 3.0 32.3 - - - -
658A VAL* 4.1 10.1 - - + -
659A ASP 3.7 20.2 - - - -
660A PHE* 3.0 42.4 + + + +
662A ASP* 1.3 78.9 - - + +
664A ILE* 1.3 54.5 + - + +
665A ASN* 3.7 2.0 - - - -
677A TRP* 4.0 16.2 - + - -
1738A CA 3.0 9.6 - - - -
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Residues in contact with ILE 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 GLU* 3.3 15.7 - - + +
573A GLU* 3.2 28.4 - - - +
576A ALA* 4.1 25.4 - - + -
630A TYR* 3.2 46.2 - - + +
633A ALA* 4.4 7.0 - - + -
635A THR* 4.6 9.0 - - + -
660A PHE* 4.2 13.9 - - + +
661A SER* 3.4 15.3 + - - +
662A ASP* 3.0 2.9 - - - -
663A PHE* 1.3 83.7 - - + +
665A ASN* 1.3 58.6 + - - +
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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