Contacts of the helix formed by residues 676 - 683 (chain C) in PDB entry 4O64
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 GLU 676 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674C VAL* 4.9 1.0 - - - +
675C GLU* 1.3 79.0 - - - +
677C GLU* 1.3 67.1 + - - +
678C GLU* 4.4 5.2 - - + +
679C GLY* 2.9 22.2 + - - +
680C LYS* 2.9 15.9 + - - +
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Residues in contact with GLU 677 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675C GLU 3.6 2.4 + - - -
676C GLU* 1.3 71.7 - - - +
678C GLU* 1.3 66.2 + - + +
680C LYS* 3.5 14.9 + - - +
681C PHE* 3.4 19.4 + - - +
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Residues in contact with GLU 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C GLU* 3.2 4.9 - - + +
677C GLU* 1.3 82.9 - - + +
679C GLY* 1.3 62.7 + - - +
681C PHE* 3.4 7.8 + - + +
682C ASN* 3.3 42.6 + - - +
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Residues in contact with GLY 679 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674C VAL* 3.9 16.6 - - - +
676C GLU* 2.9 15.4 + - - +
678C GLU* 1.3 80.5 - - - +
680C LYS* 1.3 60.7 - - - +
682C ASN* 3.5 8.0 + - - +
683C LEU* 3.5 23.2 + - - +
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Residues in contact with LYS 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671C GLU* 3.4 41.2 + - + +
672C ASP* 4.4 10.1 + - - +
674C VAL* 3.3 23.5 + - - +
675C GLU* 3.7 16.1 + - - +
676C GLU 2.9 17.0 + - - +
677C GLU* 3.7 14.8 - - - +
678C GLU 3.3 0.2 - - - -
679C GLY* 1.3 72.5 - - - +
681C PHE* 1.3 66.5 + - - +
683C LEU* 3.1 10.4 + - - -
684C MET* 3.2 16.0 + - + +
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Residues in contact with PHE 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677C GLU* 3.4 10.8 + - - +
678C GLU* 3.8 9.6 - - + +
679C GLY 3.4 0.4 - - - -
680C LYS* 1.3 78.7 - - - +
682C ASN* 1.3 72.4 + - - +
684C MET* 3.2 33.7 + - - +
686C MET* 4.2 13.2 - - - -
697C PRO* 3.4 40.8 - - + +
709C VAL* 3.7 31.9 - - + -
717C TRP* 4.0 15.0 - + - -
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Residues in contact with ASN 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678C GLU* 3.3 36.7 + - - +
679C GLY* 4.0 6.8 - - - +
680C LYS 3.3 0.8 - - - -
681C PHE* 1.3 85.5 - - - +
683C LEU* 1.3 62.1 + - + +
684C MET 3.5 0.2 - - - -
696C HIS* 3.4 12.3 - - - +
697C PRO* 3.6 18.1 - - - +
698C GLY* 3.0 40.5 + - - +
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Residues in contact with LEU 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669C GLY* 3.4 0.5 - - - -
670C LYS* 2.8 69.5 + - + +
671C GLU* 4.1 2.0 - - - -
673C THR* 4.6 3.8 - - - +
674C VAL* 4.3 17.5 - - + -
679C GLY 3.5 14.7 + - - +
680C LYS 3.1 6.9 + - - +
682C ASN* 1.3 83.4 - - + +
684C MET* 1.3 58.7 + - - +
696C HIS* 3.3 25.2 - - + +
699C CYS* 6.2 1.8 - - - -
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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