Contacts of the strand formed by residues 592 - 598 (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 SER 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A LYS* 3.7 15.9 - - - +
591A GLN* 1.3 79.2 - - - +
593A VAL* 1.3 60.5 + - - +
594A PRO* 3.6 9.8 - - - +
608A ASN* 3.4 16.1 + - - +
609A LEU 3.2 4.5 - - - -
610A LYS* 2.5 37.7 + - - -
614A GLU* 4.4 6.5 - - - -
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Residues in contact with VAL 593 (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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587A LEU 3.9 17.7 - - - +
588A LEU* 4.2 13.2 - - + -
590A LYS* 3.5 36.6 - - + +
592A SER* 1.3 73.3 + - - +
594A PRO* 1.3 77.7 - - + +
595A ALA 3.4 1.2 + - - -
608A ASN* 4.1 2.0 - - - -
609A LEU* 2.8 39.9 + - + +
611A MET* 3.7 21.8 - - + -
665A LEU* 4.0 16.6 - - + -
667A ARG* 4.6 9.4 - - - +
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Residues in contact with PRO 594 (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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590A LYS* 4.9 11.4 - - - +
592A SER 3.6 9.0 - - - +
593A VAL* 1.3 93.4 - - + +
595A ALA* 1.3 60.4 + - - +
596A HIS* 5.4 4.6 + - + +
607A ILE 3.6 0.9 - - - +
608A ASN* 3.4 22.9 - - - +
665A LEU* 4.1 10.0 - - - +
666A GLU 5.6 0.2 + - - -
667A ARG* 5.2 5.4 + - - +
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Residues in contact with ALA 595 (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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593A VAL 3.9 0.2 - - - +
594A PRO* 1.3 74.5 - - - +
596A HIS* 1.3 79.5 + - - +
606A ASN* 3.5 1.9 - - - +
607A ILE* 3.0 42.0 + - + +
609A LEU* 3.8 20.0 - - + -
663A VAL* 4.4 2.9 - - + -
664A PHE 3.5 7.2 - - - +
665A LEU* 3.3 25.6 - - + +
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Residues in contact with HIS 596 (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* 5.4 2.9 - - + +
595A ALA* 1.3 85.9 + - - +
597A PHE* 1.3 61.9 + - - +
604A LYS* 3.6 25.3 + - + +
605A LEU 3.1 11.0 + - - +
606A ASN* 2.8 31.6 + - - -
607A ILE* 3.9 5.3 - - - +
663A VAL* 3.3 9.4 - - - +
664A PHE* 3.0 69.3 + + + +
665A LEU* 4.7 5.4 - - - -
666A GLU* 5.0 12.2 + - + +
671A PHE* 5.8 0.4 - + - -
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Residues in contact with PHE 597 (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* 1.3 75.3 - - - +
598A VAL* 1.3 73.7 + - - +
604A LYS* 3.8 1.4 - - - -
605A LEU* 2.8 55.5 + - + +
607A ILE* 3.5 35.0 - - + -
652A GLU* 3.8 14.4 - - + -
653A SER 3.7 5.6 - - - -
654A PRO* 3.5 36.3 - - + -
658A GLU* 3.3 27.4 - - + -
662A ALA 3.7 15.9 - - - +
663A VAL* 4.6 3.6 - - + -
664A PHE* 4.1 3.6 - - - -
677A VAL* 4.2 14.4 - - + -
694A ARG* 3.8 4.9 - - - -
709A HIS* 5.7 0.7 - - - -
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Residues in contact with VAL 598 (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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458A THR* 3.8 35.9 - - + +
460A TRP* 5.2 0.9 - - - +
461A HIS* 3.3 48.4 + - + +
473A ARG* 5.0 1.0 - - - +
597A PHE* 1.3 88.3 - - - +
599A ALA* 1.3 71.2 + - - +
602A GLY* 3.6 22.4 - - - +
603A SER 3.4 5.4 - - - +
604A LYS* 4.6 3.1 - - - -
658A GLU* 3.8 13.2 - - - +
661A GLY* 6.2 0.8 - - - -
662A ALA 4.5 2.6 + - - -
664A PHE* 4.0 12.1 - - + -
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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