Contacts of the strand formed by residues 602 - 605 (chain G) in PDB entry 5JLH
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 602 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484G ILE* 5.9 1.9 - - - +
583G GLN* 3.4 27.7 + - - +
585G PRO* 5.3 12.7 - - - +
590G ASP* 6.0 0.2 + - - -
595G SER* 3.4 28.4 + - - -
596G VAL 3.4 7.6 - - - +
597G LEU* 3.5 19.9 - - + +
601G GLY* 1.3 70.4 - - - -
603G VAL* 1.3 64.4 + - - +
604G ASP* 3.5 13.1 + - - +
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Residues in contact with VAL 603 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482G PHE* 4.0 20.4 - - + -
483G GLU 5.5 1.1 - - - +
484G ILE* 4.8 15.0 - - + -
488G ASN* 3.3 26.5 - - - +
496G ASN* 4.5 4.3 - - - +
595G SER* 3.1 20.8 - - - -
596G VAL 2.9 15.1 + - - +
598G HIS* 3.6 27.1 - - + -
601G GLY 4.0 5.2 - - - +
602G LYS* 1.3 76.2 - - - +
604G ASP* 1.3 71.4 + - - +
605G TYR* 3.9 21.0 - - + +
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Residues in contact with ASP 604 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486G GLN 5.3 4.7 - - - +
487G LEU 3.7 2.1 - - - +
488G ASN* 3.0 33.6 + - - +
590G ASP* 5.8 0.3 - - - +
592G ALA* 3.4 21.8 - - + +
595G SER* 2.7 28.9 + - - +
602G LYS* 3.5 15.4 - - - +
603G VAL* 1.3 80.4 - - - +
605G TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 605 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488G ASN* 3.6 19.7 - - + -
489G SER 4.1 5.4 - - - -
493G LEU* 3.6 35.1 - - + +
496G ASN* 3.1 23.2 + - - -
592G ALA* 3.7 4.0 - - - -
593G ASP* 2.8 28.9 + - - -
594G PHE* 2.9 47.8 + + + +
596G VAL* 3.5 27.4 - - + -
598G HIS* 2.9 25.6 + - - -
603G VAL* 3.9 17.2 - - + +
604G ASP* 1.3 78.2 - - - +
606G LYS* 1.3 52.9 - - - +
607G ALA 4.1 0.4 + - - -
610G TRP* 4.0 18.6 - + + -
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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