Contacts of the helix formed by residues 665 - 670 (chain B) in PDB entry 5OA1
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 665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527B PHE* 3.4 6.0 - - - -
625B GLU* 3.5 18.8 - - - +
649B MET 3.3 8.5 - - - -
650B LEU* 4.7 1.3 - - - +
664B VAL* 1.3 72.6 - - - +
666B PRO* 1.4 74.7 - - - +
667B PHE 3.3 2.9 - - - -
668B GLU* 3.1 13.0 + - - +
669B GLN* 3.3 24.4 + - - +
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Residues in contact with PRO 666 (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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210B ARG* 3.5 20.6 - - - +
397B THR* 3.4 38.8 - - + +
398B GLN* 3.4 14.9 - - - +
400B GLN 4.4 1.1 - - - +
523B GLU* 4.1 7.1 - - - +
527B PHE* 3.5 21.9 - - + -
649B MET* 3.4 35.9 - - + +
665B GLY* 1.4 81.2 - - - +
667B PHE* 1.4 61.8 + - - +
669B GLN* 3.9 6.5 + - + +
670B VAL* 3.5 10.0 - - - +
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Residues in contact with PHE 667 (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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210B ARG* 4.1 14.8 - - - +
213B HIS* 3.4 39.0 - + - -
398B GLN* 3.5 32.8 - - - +
399B HIS* 3.8 21.3 - + - -
625B GLU* 3.3 14.0 + - - +
627B GLY* 3.9 20.0 - - - -
629B VAL* 4.0 11.7 - - + -
636B GLN* 3.9 14.8 - - - -
641B TYR* 3.9 23.6 - + + -
643B PHE* 4.2 9.2 - + + -
665B GLY 3.3 0.8 - - - -
666B PRO* 1.4 83.2 - - - +
668B GLU* 1.3 63.0 + - - +
669B GLN 3.5 0.2 + - - -
670B VAL* 3.7 15.4 + - - +
671B TYR* 4.6 6.3 - + - -
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Residues in contact with GLU 668 (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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609B ARG* 2.8 42.5 + - - +
624B LEU 4.3 0.2 - - - +
625B GLU* 3.3 23.5 + - + +
626B ILE 3.4 26.1 + - - +
627B GLY* 3.8 13.2 - - - -
628B TYR 4.9 5.2 + - - +
650B LEU* 6.0 0.2 - - - +
663B ILE 3.7 4.5 - - - +
664B VAL* 3.4 15.7 - - + -
665B GLY 3.1 30.6 + - - +
667B PHE* 1.3 77.4 - - - +
669B GLN* 1.4 65.5 + - - +
670B VAL 3.3 0.7 + - - -
671B TYR* 3.6 11.7 + - - +
672B MET* 3.4 20.3 + - - +
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Residues in contact with GLN 669 (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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960A MET* 5.1 3.7 - - + +
967A PRO* 3.9 15.9 - - + +
522B PRO 4.6 2.0 + - - -
523B GLU* 4.3 7.1 + - - +
525B TRP* 3.0 35.4 + - - +
527B PHE* 3.3 15.3 - - - -
651B ARG* 2.8 37.2 + - - -
664B VAL* 3.9 5.6 - - + +
665B GLY 3.3 16.5 + - - +
666B PRO 4.0 6.7 - - - +
667B PHE 3.4 0.6 - - - -
668B GLU* 1.4 75.8 - - - +
670B VAL* 1.3 58.1 + - + +
672B MET* 2.9 38.5 + - - +
674B ILE* 3.8 16.9 - - + +
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Residues in contact with VAL 670 (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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960A MET* 3.8 38.3 - - + +
961A VAL* 4.9 1.3 - - + +
962A SER* 2.7 43.2 + - - +
964A LYS* 3.2 13.7 - - - +
967A PRO* 5.8 0.5 - - - +
398B GLN* 3.4 36.8 - - + +
523B GLU* 4.2 3.6 - - + -
636B GLN* 5.1 0.4 - - - +
666B PRO 3.5 17.5 - - - +
667B PHE 3.7 7.9 - - - +
668B GLU 3.3 0.2 - - - -
669B GLN* 1.3 74.8 - - - +
671B TYR* 1.3 69.6 + - + +
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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