Contacts of the strand formed by residues 617 - 621 (chain B) in PDB entry 2O8C
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 LEU 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477B GLY* 3.7 28.7 - - - +
479B LYS* 4.2 14.4 - - + +
518B THR* 3.7 28.5 - - + -
519B LYS* 4.2 25.4 - - + -
592B VAL 3.0 18.2 + - - +
593B GLN* 3.4 11.5 - - + +
594B VAL* 2.8 29.6 + - - +
615B CYS 4.7 3.6 - - - +
616B SER* 1.3 84.7 - - - +
618B GLN* 1.3 64.9 + - - +
619B GLU* 4.5 5.2 - - - +
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Residues in contact with GLN 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B VAL* 3.7 7.0 - - + +
596B PHE* 4.0 14.6 - - + -
609B LEU* 2.7 50.8 + - + +
610B LYS* 3.4 30.3 - - - +
613B LEU* 3.5 9.3 + - - +
614B SER* 4.4 5.4 - - - +
616B SER* 3.5 16.0 - - - +
617B LEU* 1.3 74.5 - - - +
619B GLU* 1.3 70.1 + - - +
620B GLY 4.3 0.2 - - - -
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Residues in contact with GLU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ASP* 4.5 4.9 - - - +
479B LYS* 3.5 29.4 + - - +
593B GLN* 3.0 35.5 + - + +
594B VAL 2.9 14.6 + - - +
595B LEU* 3.5 22.2 - - + -
596B PHE* 3.1 31.0 + - - +
617B LEU* 4.5 5.7 - - - +
618B GLN* 1.3 82.9 - - - +
620B GLY* 1.3 62.1 + - - +
621B LEU* 3.7 6.3 + - + +
690B TYR* 3.9 13.0 + - + +
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Residues in contact with GLY 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ASP* 5.2 5.2 - - - +
596B PHE* 3.7 25.3 - - - -
598B LYS* 3.6 19.4 - - - +
618B GLN 4.3 0.4 - - - -
619B GLU* 1.3 70.9 + - - +
621B LEU* 1.3 65.6 + - - +
622B ILE* 4.1 1.0 + - - +
626B GLN* 4.3 2.6 - - - +
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B LEU* 4.5 14.8 - - + -
596B PHE 2.8 17.8 + - - +
597B GLU* 3.5 4.2 - - - -
598B LYS* 3.0 25.5 + - - -
619B GLU* 4.5 9.0 - - + +
620B GLY* 1.3 79.2 - - - +
622B ILE* 1.3 64.2 + - - +
623B PRO 3.3 0.3 - - - -
626B GLN* 3.5 14.1 - - + +
627B PHE* 3.8 31.4 - - + +
686B GLY* 3.6 27.4 - - - +
689B PHE* 3.9 26.2 - - + -
690B TYR* 4.6 13.7 - - + -
693B LYS* 6.4 0.2 - - + -
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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