Contacts of the strand formed by residues 707 - 711 (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 ASP 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A LEU 3.9 0.2 - - - +
645A CYS* 3.4 5.7 - - - -
646A SER* 2.8 36.5 + - - +
647A GLY* 3.4 14.6 - - - -
652A GLU 3.9 1.9 - - - +
653A SER* 2.6 35.1 + - - -
654A PRO* 3.4 24.8 - - + +
679A TRP 3.5 6.6 - - - +
680A GLY* 3.9 8.1 - - - -
681A LEU 4.6 0.2 + - - -
682A TYR 4.4 5.4 - - - +
706A ARG* 1.3 81.9 + - - +
708A PHE* 1.3 64.6 + - - +
709A HIS* 3.7 20.2 - - - +
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Residues in contact with PHE 708 (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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619A ALA* 4.0 7.6 - - - -
622A VAL* 3.7 23.3 - - + -
639A VAL* 3.8 27.1 - - + -
643A PHE* 3.9 10.1 - - + -
644A LEU 3.3 8.7 - - - -
645A CYS* 3.4 24.7 - - + -
678A SER* 3.3 7.4 + - - -
679A TRP* 2.7 89.7 + + + +
681A LEU* 4.3 2.9 - - + -
706A ARG* 3.9 33.4 - - + -
707A ASP* 1.3 77.8 - - - +
709A HIS* 1.3 62.9 + - - +
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Residues in contact with HIS 709 (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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597A PHE* 5.7 0.2 - - - -
607A ILE* 3.8 15.5 - - + +
609A LEU* 4.0 14.8 - - - +
643A PHE* 3.2 5.2 - - - -
644A LEU* 2.7 48.1 + - + +
646A SER* 2.8 32.8 + - - -
654A PRO* 4.2 11.9 - - + +
663A VAL* 3.7 25.7 - - + +
676A LEU 3.2 14.8 - - - +
677A VAL* 4.0 15.0 - - + -
678A SER 4.6 0.7 - - - -
679A TRP 5.3 0.7 - - - -
707A ASP* 3.7 22.3 - - + +
708A PHE* 1.3 79.3 - - - +
710A ILE* 1.3 64.9 + - - +
711A ASN 3.1 0.2 + - - -
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Residues in contact with ILE 710 (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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538A TYR 4.0 1.1 - - - +
540A ASP* 4.4 1.3 - - - +
541A ASP* 3.4 43.5 - - + +
542A ILE* 4.4 12.1 - - + -
642A GLN* 3.5 21.8 - - + +
643A PHE* 3.6 25.9 - - + -
644A LEU* 5.0 0.2 - - - -
675A GLY* 2.9 27.4 - - - -
676A LEU* 3.0 25.4 + - + -
678A SER* 4.0 9.0 - - - -
709A HIS* 1.3 68.8 - - - +
711A ASN* 1.3 62.4 + - - +
712A LEU* 3.7 1.2 + - + +
715A MET* 3.6 31.2 - - + -
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Residues in contact with ASN 711 (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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584A GLU* 5.0 0.3 - - - +
588A LEU* 5.0 1.6 - - - +
641A ASP 4.8 1.9 - - - +
642A GLN 2.7 22.9 + - - +
643A PHE 4.3 1.6 - - - +
644A LEU* 3.5 34.1 + - + +
674A VAL 3.7 6.7 + - - -
709A HIS 3.1 1.7 + - - -
710A ILE* 1.3 69.8 - - - +
712A LEU* 1.3 59.8 + - - +
713A PHE* 3.0 34.6 - - - +
714A ARG* 2.9 50.9 + - + +
715A MET* 3.2 13.8 - - - +
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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