Contacts of the strand formed by residues 604 - 610 (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 LYS 604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A ASN 5.3 2.6 + - - -
448A MET* 5.6 2.8 - - - +
457A ARG* 3.4 53.5 + - - +
458A THR* 4.7 11.8 - - + +
596A HIS* 3.6 43.9 + - + +
597A PHE 3.8 3.4 - - - +
598A VAL* 4.6 3.4 - - + -
602A GLY 3.6 2.6 + - - -
603A SER* 1.3 71.6 - - - +
605A LEU* 1.3 65.9 + - - +
606A ASN* 4.4 4.5 - - - +
664A PHE* 3.8 17.9 - - + -
666A GLU* 4.9 5.3 + - - -
671A PHE* 4.2 24.0 - - - -
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Residues in contact with LEU 605 (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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596A HIS* 3.1 29.3 + - - +
597A PHE* 2.8 36.1 + - + +
599A ALA* 3.7 11.9 - - + -
603A SER* 3.9 24.9 - - - +
604A LYS* 1.3 79.4 - - - +
606A ASN* 1.3 64.6 + - - +
652A GLU* 3.9 22.7 - - + -
694A ARG* 3.5 38.1 - - - +
807A NAG 4.2 14.4 - - - -
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Residues in contact with ASN 606 (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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595A ALA 3.5 4.5 - - - +
596A HIS* 2.8 34.9 + - - -
604A LYS* 4.4 4.4 - - - +
605A LEU* 1.3 76.7 - - - +
607A ILE* 1.3 65.9 + - - +
651A ASP* 3.9 3.2 - - - -
652A GLU* 3.2 30.6 + - + +
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Residues in contact with ILE 607 (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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594A PRO* 3.6 0.5 - - - +
595A ALA* 3.0 44.8 + - + +
596A HIS* 3.9 7.4 - - - +
597A PHE* 3.5 22.7 - - + -
606A ASN* 1.3 82.4 - - - +
608A ASN* 1.3 71.7 + - - +
609A LEU* 3.8 14.4 - - + -
646A SER* 3.5 22.4 - - - +
651A ASP* 3.6 12.8 - - - +
652A GLU 3.3 22.2 - - - +
654A PRO* 5.5 0.9 - - + -
663A VAL* 3.9 15.9 - - + -
709A HIS* 3.8 16.8 - - + +
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Residues in contact with ASN 608 (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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592A SER* 3.4 22.1 + - - +
593A VAL 3.5 2.4 - - - +
594A PRO* 3.4 36.8 - - - +
607A ILE* 1.3 75.3 + - - +
609A LEU* 1.3 61.8 + - - +
610A LYS* 3.5 18.3 + - - +
646A SER* 3.3 18.2 - - - -
648A THR* 5.1 0.4 + - - +
651A ASP* 2.9 28.0 + - - +
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Residues in contact with LEU 609 (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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588A LEU* 4.1 4.7 - - + -
591A GLN 3.7 0.2 - - - +
592A SER* 3.2 4.7 - - - -
593A VAL* 2.8 43.5 + - + +
595A ALA* 3.8 20.9 - - + -
607A ILE* 3.8 23.1 - - + -
608A ASN* 1.3 70.5 - - - +
610A LYS* 1.3 61.0 + - - +
611A MET* 3.1 29.4 - - + +
644A LEU* 4.2 15.7 - - + -
645A CYS 3.4 9.6 - - - +
646A SER* 4.3 0.9 - - - -
663A VAL* 4.1 4.9 - - + -
665A LEU* 3.9 5.6 - - + -
674A VAL* 3.9 25.6 - - + -
709A HIS* 4.0 17.5 - - - +
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Residues in contact with LYS 610 (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 3.4 1.6 - - - +
592A SER* 2.5 39.0 + - - +
608A ASN* 3.7 20.7 + - - +
609A LEU* 1.3 74.6 - - - +
611A MET* 1.3 64.4 + - - +
614A GLU* 3.6 43.8 + - + +
615A TRP* 3.3 27.3 - - - +
618A CYS* 3.9 25.4 - - + -
645A CYS 3.0 8.5 + - - +
646A SER* 5.0 0.2 - - - -
648A THR* 3.4 27.8 + - + -
649A GLN* 4.7 10.5 + - - -
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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