Contacts of the helix formed by residues 612 - 621 (chain A) in PDB entry 2ODP
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 GLY 612 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A GLN* 5.3 3.1 - - - -
611A MET* 1.3 68.8 - - - +
613A VAL* 1.3 67.1 + - - -
615A TRP* 3.1 20.8 + - - +
616A THR* 3.5 8.1 + - - -
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Residues in contact with VAL 613 (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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591A GLN* 5.1 13.6 + - - +
611A MET 3.4 1.0 + - - -
612A GLY* 1.3 73.4 - - - -
614A GLU* 1.3 63.5 + - + +
616A THR* 3.3 19.2 + - - -
617A SER* 3.3 12.9 + - - +
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Residues in contact with GLU 614 (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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591A GLN* 3.6 49.9 + - + +
592A SER* 4.4 3.9 - - - -
610A LYS* 3.6 33.3 + - + +
611A MET 3.2 9.4 + - - +
613A VAL* 1.3 76.3 - - + +
615A TRP* 1.3 59.8 + - - +
617A SER* 3.0 11.0 + - - +
618A CYS* 2.9 30.3 + - - +
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Residues in contact with TRP 615 (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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610A LYS 3.3 26.4 + - - +
611A MET* 3.5 7.8 + - - -
612A GLY* 3.1 20.7 + - - +
614A GLU* 1.3 78.6 - - - +
616A THR* 1.3 71.3 + - + +
618A CYS* 3.5 4.0 - - - +
619A ALA* 2.9 38.6 + - + +
635A VAL* 5.6 2.0 - - + -
636A ARG* 3.3 37.2 - - - -
639A VAL* 3.6 29.8 - - + -
640A THR 3.5 19.7 - - - -
641A ASP* 4.6 4.7 - - - -
643A PHE 2.8 24.6 + - - -
644A LEU* 4.6 2.5 - - + -
645A CYS* 4.0 18.6 - - + +
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Residues in contact with THR 616 (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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612A GLY 3.5 9.0 + - - -
613A VAL* 3.3 13.6 + - - -
615A TRP* 1.3 94.6 - - + +
617A SER* 1.3 57.5 + - - +
619A ALA* 3.4 1.7 + - - +
620A GLU* 3.0 32.8 + - + +
635A VAL* 5.7 0.5 - - - +
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Residues in contact with SER 617 (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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613A VAL* 3.3 6.3 + - - +
614A GLU* 3.0 26.9 + - - +
616A THR* 1.3 76.0 - - - +
618A CYS* 1.3 65.7 + - - +
619A ALA 3.4 0.3 + - - -
620A GLU* 3.5 16.0 + - - +
621A VAL* 4.3 2.6 + - - +
706A ARG* 3.5 10.7 + - - -
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Residues in contact with CYS 618 (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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610A LYS* 3.9 11.9 - - + -
614A GLU 2.9 18.6 + - - +
615A TRP 3.5 4.0 - - - +
617A SER* 1.3 79.0 + - - +
619A ALA* 1.3 58.5 + - - +
621A VAL* 3.8 1.9 - - - +
645A CYS* 2.1 56.8 - - + -
646A SER* 3.7 5.8 - - - -
648A THR* 3.9 22.9 - - + -
706A ARG* 2.8 39.8 + - - +
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Residues in contact with ALA 619 (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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615A TRP* 2.9 28.9 + - + +
616A THR 4.1 2.5 - - - +
618A CYS* 1.3 73.9 - - - +
620A GLU* 1.3 65.5 + - - +
621A VAL 3.0 4.9 + - - -
622A VAL* 3.1 26.3 + - - +
635A VAL* 4.2 10.1 - - + -
639A VAL* 3.9 30.1 - - + -
645A CYS* 4.6 1.8 - - - -
708A PHE* 4.0 13.1 - - + -
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Residues in contact with GLU 620 (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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616A THR* 3.0 20.2 + - + +
617A SER* 3.9 9.9 - - - +
618A CYS 3.4 1.2 - - - -
619A ALA* 1.3 76.0 - - - +
621A VAL* 1.3 71.9 + - - +
622A VAL 3.1 0.2 - - - -
623A SER* 2.9 42.0 + - - +
624A GLN* 5.1 2.9 + - - +
635A VAL* 3.8 18.5 - - + +
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Residues in contact with VAL 621 (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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617A SER 4.4 2.2 - - - +
618A CYS 3.8 4.3 - - - +
619A ALA 3.0 1.3 + - - +
620A GLU* 1.3 84.1 - - - +
622A VAL* 1.3 66.8 + - + +
623A SER* 3.0 3.4 - - - -
624A GLN* 3.0 40.9 + - - +
681A LEU* 3.9 7.4 - - + -
703A PRO* 3.7 6.2 - - - +
704A PRO* 4.3 13.2 - - + -
706A ARG* 3.2 64.8 - - + +
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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