Contacts of the strand formed by residues 570 - 575 (chain J) in PDB entry 2A07
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 570 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564J ARG* 5.1 1.8 - - - -
566J GLU* 3.3 10.3 - - - +
567J ASN* 2.9 30.9 + - - +
568J VAL 3.4 2.0 + - - -
569J LYS* 1.3 79.8 - - - +
571J ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 571 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B A 3.7 12.0 + - - +
526J THR* 3.8 20.3 - - - +
527J LEU 4.8 1.0 + - - -
564J ARG* 3.6 40.8 - - + +
565J VAL 3.4 12.6 - - - +
566J GLU* 4.0 2.2 - - - -
567J ASN* 3.7 3.6 + - - -
569J LYS 4.3 0.4 + - - -
570J GLY* 1.3 76.0 - - - +
572J VAL* 1.3 68.5 + - - +
573J TRP* 5.3 1.1 - - - -
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Residues in contact with VAL 572 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524J GLN* 3.6 45.5 - - + +
525J LEU 3.5 12.3 - - - +
526J THR* 4.2 15.3 - - + +
529J GLU* 5.5 0.7 - - - +
564J ARG* 3.6 2.9 - - - -
565J VAL* 2.8 52.0 + - + +
567J ASN* 3.4 21.3 - - - +
571J ALA* 1.3 78.1 - - - +
573J TRP* 1.3 62.9 + - - +
574J THR* 4.3 3.1 - - + -
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Residues in contact with TRP 573 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B A 2.8 47.8 + - + -
10B T 3.4 23.6 - - - -
517J ILE* 3.8 9.2 - - + +
524J GLN* 3.4 6.6 - - - -
525J LEU 2.7 39.3 + - - +
526J THR* 4.9 0.2 - - - -
527J LEU* 4.0 13.8 - - - +
530J ILE* 3.9 13.9 - - + -
556J LEU* 3.5 66.8 - - + +
557J SER* 4.4 0.4 - - - -
562J PHE 3.8 10.1 - - - -
563J VAL 3.7 5.6 - - - -
564J ARG* 3.7 41.3 - - + -
571J ALA 5.3 0.7 - - - -
572J VAL* 1.3 77.0 - - - +
574J THR* 1.3 60.5 + - - +
605J MG 4.2 1.1 - - - -
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Residues in contact with THR 574 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517J ILE* 4.1 7.6 - - - +
523J ARG* 4.0 13.7 - - - +
524J GLN* 4.2 11.4 - - + +
562J PHE* 3.4 8.1 - - - +
563J VAL* 2.9 48.4 + - - +
565J VAL* 3.7 24.5 - - + +
572J VAL* 4.3 4.7 - - + -
573J TRP* 1.3 80.5 - - - +
575J VAL* 1.3 68.8 + - - +
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Residues in contact with VAL 575 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514J ARG* 4.0 20.0 - - + +
517J ILE* 3.5 41.0 - - + +
518J MET* 5.0 4.7 - - + -
523J ARG* 3.2 25.6 + - - +
561J CYS 3.3 6.5 - - - +
562J PHE* 4.0 17.9 - - + -
574J THR* 1.3 77.8 - - - +
576J ASP* 1.3 63.6 + - - +
577J GLU* 3.1 30.5 + - - +
580J TYR* 4.3 10.1 - - + -
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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