Contacts of the helix formed by residues 661 - 669 (chain A) in PDB entry 2Q5I
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 THR 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A LEU* 3.6 3.6 - - - -
660A ILE* 1.3 81.3 - - - +
662A TRP* 1.3 77.0 + - + +
663A ALA* 3.2 24.2 - - + +
664A ASP* 2.7 25.6 + - - -
665A VAL* 3.1 17.8 + - - +
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Residues in contact with TRP 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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614A PHE* 4.9 2.9 - + - -
632A LEU* 3.5 49.6 - - + -
634A ASP* 3.5 38.4 - - + +
637A SER* 4.0 10.3 + - - -
639A ARG* 3.1 36.6 - - - +
640A GLN* 4.2 6.5 - - - -
641A ILE* 4.3 11.4 - - + -
655A LEU* 3.7 24.6 - - + +
661A THR* 1.3 76.2 - - + +
663A ALA* 1.3 63.1 + - - +
665A VAL* 3.0 12.5 + - + +
666A GLU* 2.9 52.0 + - + +
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Residues in contact with ALA 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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661A THR* 3.2 16.4 - - + +
662A TRP* 1.3 79.4 - - - +
664A ASP* 1.3 62.8 + - - +
666A GLU* 3.2 10.7 + - - +
667A ALA* 2.9 23.7 + - - +
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Residues in contact with ASP 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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659A ASN 5.0 0.5 - - - +
660A ILE* 3.7 15.9 - - + +
661A THR* 2.7 41.3 + - - +
663A ALA* 1.3 76.3 - - - +
665A VAL* 1.3 64.7 + - - +
667A ALA* 3.1 12.2 + - - -
668A ARG* 3.1 51.7 + - - +
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Residues in contact with VAL 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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632A LEU* 4.5 0.7 - - + -
641A ILE* 4.0 25.8 - - + -
651A ILE* 4.2 15.3 - - + -
655A LEU* 3.5 29.6 - - + -
660A ILE* 3.7 9.6 - - + +
661A THR 3.4 14.1 - - - +
662A TRP* 3.0 19.5 + - + +
664A ASP* 1.3 75.8 - - - +
666A GLU* 1.3 58.9 + - - +
668A ARG* 3.0 4.9 + - - +
669A TYR* 2.8 50.0 + - + +
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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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639A ARG* 3.1 39.0 + - - +
640A GLN 5.0 3.3 - - - +
641A ILE* 4.3 7.2 - - + -
662A TRP* 2.9 49.7 + - + +
663A ALA* 3.6 10.7 - - - +
664A ASP 3.2 0.2 - - - -
665A VAL* 1.3 75.2 - - - +
667A ALA* 1.3 60.8 + - - +
669A TYR 3.1 17.9 - - - +
671A LEU* 3.7 30.7 - - + +
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Residues in contact with ALA 667 (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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663A ALA 2.9 13.4 + - - +
664A ASP* 3.1 10.3 + - - +
666A GLU* 1.3 76.2 - - - +
668A ARG* 1.3 68.9 + - + +
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Residues in contact with ARG 668 (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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660A ILE* 5.2 11.3 - - - +
664A ASP* 3.1 57.7 + - - +
665A VAL* 3.0 6.1 + - - +
667A ALA* 1.3 87.8 - - + +
669A TYR* 1.3 82.2 + - + +
670A PRO* 4.7 0.9 - - - +
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Residues in contact with TYR 669 (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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641A ILE* 3.0 31.4 - - + +
642A ARG 4.4 0.2 - - - +
643A ALA* 3.7 19.3 - - + -
644A GLU 5.6 0.2 - - - -
647A GLU* 2.9 30.4 + - - +
651A ILE* 3.3 35.6 - - + +
665A VAL* 2.8 34.1 + - + +
666A GLU 3.1 14.6 - - - +
668A ARG* 1.3 97.8 - - + +
670A PRO* 1.3 72.0 - - + +
671A LEU* 3.5 1.7 + - - +
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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