Contacts of the helix formed by residues 715 - 724 (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 MET 715 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A SER* 5.7 0.2 - - - +
540A ASP* 4.2 15.0 - - + +
542A ILE* 3.6 40.8 - - + -
642A GLN* 3.6 33.9 - - - +
710A ILE* 3.6 23.3 - - + -
711A ASN 3.2 18.2 - - - +
712A LEU* 3.1 10.1 + - - +
714A ARG* 1.3 86.9 - - - +
716A GLN* 1.3 63.8 + - - +
717A PRO* 3.5 3.8 - - - -
718A TRP* 3.4 11.8 + - + +
719A LEU* 3.0 31.9 + - + +
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Residues in contact with GLN 716 (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 PRO* 4.4 12.7 + - - +
564A CYS* 3.5 11.0 - - - +
580A CYS* 3.8 23.8 - - - -
712A LEU* 3.0 28.8 + - - +
713A PHE* 3.8 12.6 - - - +
714A ARG 3.5 0.8 - - - -
715A MET* 1.3 77.9 - - - +
717A PRO* 1.4 63.0 - - + +
719A LEU* 3.7 14.8 - - - +
720A ARG* 2.7 75.3 + - - +
729A PHE* 3.8 13.5 - - - -
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Residues in contact with PRO 717 (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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714A ARG 4.6 5.6 - - - +
715A MET* 3.6 4.5 - - - -
716A GLN* 1.4 95.0 - - + +
718A TRP* 1.3 55.1 + - - +
720A ARG* 3.8 7.6 - - + +
721A GLN* 2.9 29.6 + - - +
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Residues in contact with TRP 718 (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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519A VAL* 3.6 32.1 - - + +
521A SER* 3.8 35.5 - - - +
522A PRO* 4.1 9.3 - - + +
542A ILE* 3.7 32.5 - - + -
543A ALA* 3.8 7.0 - - - -
544A LEU* 3.7 36.3 - - + -
715A MET* 3.4 15.1 + - + +
716A GLN 3.3 0.2 - - - -
717A PRO* 1.3 74.7 - - - +
719A LEU* 1.3 82.5 + - + +
721A GLN* 3.2 20.6 + - - +
722A HIS* 3.2 48.4 + + - +
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Residues in contact with LEU 719 (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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483A LEU* 4.1 14.6 - - + -
542A ILE* 4.0 9.6 - - + -
562A LEU* 5.2 7.2 - - + -
712A LEU* 4.1 20.4 - - + +
715A MET* 3.0 32.1 + - + +
716A GLN* 3.7 24.5 - - - +
718A TRP* 1.3 105.2 - - + +
720A ARG* 1.3 57.4 + - - +
722A HIS* 3.3 1.0 + - - -
723A LEU* 2.8 55.0 + - + +
729A PHE* 4.1 15.7 - - + -
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Residues in contact with ARG 720 (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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564A CYS* 4.1 9.1 + - - +
580A CYS* 4.4 8.7 - - - +
716A GLN* 2.7 67.2 + - - +
717A PRO* 3.8 7.0 - - + +
719A LEU* 1.3 72.4 - - - +
721A GLN* 1.3 64.0 + - - +
724A GLY* 3.2 21.7 + - - -
729A PHE* 3.7 45.0 - - + +
730A LEU* 2.4 34.6 + - - +
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Residues in contact with GLN 721 (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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717A PRO 2.9 17.0 + - - +
718A TRP* 3.2 18.0 + - - +
720A ARG* 1.3 76.9 - - - +
722A HIS* 1.3 88.0 + - + +
724A GLY 4.9 0.5 + - - -
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Residues in contact with HIS 722 (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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481A TRP* 4.8 10.7 - + + -
519A VAL* 3.4 34.1 - - + +
522A PRO* 5.9 1.6 - - + -
544A LEU* 3.7 22.0 - - + -
718A TRP* 3.2 50.4 + + - +
719A LEU 4.2 0.2 - - - +
720A ARG 3.1 0.2 - - - -
721A GLN* 1.3 110.7 + - + +
723A LEU* 1.3 63.2 + - - +
724A GLY 3.6 1.7 + - - -
725A ASP 5.4 0.3 + - - -
726A VAL* 4.6 6.1 - - - +
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Residues in contact with LEU 723 (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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477A ILE* 3.5 33.4 - - + -
481A TRP* 4.2 15.9 - - + -
544A LEU* 3.8 28.0 - - + -
562A LEU* 4.7 1.3 - - + -
719A LEU* 2.8 36.0 + - + +
722A HIS* 1.3 82.9 - - - +
724A GLY* 1.3 59.5 + - - +
725A ASP 3.1 3.1 - - - -
726A VAL* 2.8 22.7 + - + -
727A LEU* 2.8 44.4 + - + +
729A PHE* 3.6 13.6 - - + -
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Residues in contact with GLY 724 (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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720A ARG* 3.2 18.7 + - - -
721A GLN 4.8 1.0 + - - -
722A HIS 3.6 1.8 - - - -
723A LEU* 1.3 78.4 - - - +
725A ASP* 1.3 64.5 + - - +
727A LEU 3.2 13.5 - - - +
728A ASN* 5.6 0.2 - - - +
729A PHE* 4.2 12.4 + - - -
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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