Contacts of the helix formed by residues 656 - 663 (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 PRO 656 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643B PHE* 4.0 17.5 - - + -
647B LEU* 3.6 27.3 - - + -
655B LEU* 1.4 88.1 - - + +
657B GLN* 1.3 55.4 + - - +
658B VAL* 3.0 6.1 - - + +
659B LEU* 2.8 39.2 + - + +
660B LYS 3.0 9.2 + - - -
704B ALA 4.3 9.4 - - - +
706B PHE* 3.6 37.2 - - + +
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Residues in contact with GLN 657 (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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647B LEU* 5.7 1.7 - - + +
655B LEU 3.6 2.6 + - - +
656B PRO* 1.3 69.9 - - - +
658B VAL* 1.3 62.8 + - + +
660B LYS* 4.0 11.6 - - + +
661B GLY* 3.8 12.3 + - - -
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Residues in contact with VAL 658 (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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570B ILE* 4.4 14.8 - - + +
656B PRO* 3.0 1.7 - - + -
657B GLN* 1.3 77.9 - - + +
659B LEU* 1.3 61.5 + - - +
661B GLY* 3.4 8.1 + - - -
662B MET* 3.2 23.8 + - - +
706B PHE* 3.3 34.5 - - + +
707B GLU* 3.9 11.4 - - - +
708B GLU* 3.6 36.3 - - + +
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Residues in contact with LEU 659 (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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570B ILE* 3.8 35.0 - - + -
634B LEU* 5.4 1.1 - - + +
637B LEU* 4.1 22.2 - - + -
643B PHE* 4.1 2.2 - - + -
655B LEU* 4.2 11.6 - - + +
656B PRO* 2.8 25.6 + - + +
658B VAL* 1.3 76.5 - - - +
660B LYS* 1.3 60.6 + - - +
661B GLY 3.3 0.2 - - - -
662B MET* 3.4 20.2 + - + +
663B THR* 3.4 14.6 - - - +
681B LEU* 4.1 13.3 - - + +
684B LEU* 4.0 10.1 - - + -
706B PHE* 3.8 40.2 - - + -
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Residues in contact with LYS 660 (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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654B MET* 3.9 35.1 - - - +
655B LEU* 3.8 33.2 - - + +
656B PRO 3.0 7.2 + - - +
657B GLN* 4.4 10.8 - - + +
658B VAL 3.3 0.4 - - - -
659B LEU* 1.3 75.1 - - - +
661B GLY* 1.3 64.9 + - - +
662B MET 3.1 0.4 - - - -
663B THR* 2.7 29.3 + - - +
671B LEU* 6.5 1.1 - - - -
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Residues in contact with GLY 661 (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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657B GLN 3.8 8.1 + - - -
658B VAL 3.4 8.3 + - - -
659B LEU 3.3 0.8 - - - -
660B LYS* 1.3 77.4 - - - +
662B MET* 1.3 61.7 + - - +
663B THR 3.6 6.3 + - - +
677B SER* 5.0 0.9 + - - -
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Residues in contact with MET 662 (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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570B ILE* 3.9 24.9 - - + +
571B GLY* 5.1 3.6 - - - -
572B GLN 5.6 0.2 - - - +
658B VAL* 3.2 26.0 - - - +
659B LEU* 3.4 20.4 - - + +
660B LYS 3.1 0.2 - - - -
661B GLY* 1.3 78.8 - - - +
663B THR* 1.3 52.4 + - - +
673B PRO 3.8 0.2 - - - -
674B GLY* 2.7 33.2 + - - -
677B SER* 3.5 32.1 - - - +
680B ALA* 3.4 33.2 - - + -
681B LEU* 3.8 23.3 - - + +
708B GLU* 5.2 12.3 - - - +
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Residues in contact with THR 663 (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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634B LEU* 3.9 26.9 - - + -
655B LEU* 3.9 19.7 - - + -
659B LEU 3.4 14.8 - - - +
660B LYS* 2.7 28.1 + - - +
661B GLY* 3.7 7.8 - - - +
662B MET* 1.3 82.7 - - + +
664B SER* 1.3 66.1 + - - +
671B LEU* 4.4 18.3 - - + +
672B THR 3.8 8.3 - - - -
673B PRO* 4.5 0.7 - - - -
674B GLY* 4.0 4.5 - - - +
681B LEU* 5.1 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