Contacts of the helix formed by residues 754 - 764 (chain C) in PDB entry 3CMM
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 ASN 754 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747C ASP* 4.8 12.9 + - + +
748C ASP* 4.0 7.2 + - - +
749C SER* 5.9 2.9 - - - +
752C LYS 3.5 4.7 + - - +
753C PRO* 1.3 67.2 - - - +
755C VAL* 1.3 65.8 + - - +
756C ASP* 3.6 16.6 + - - +
757C GLU* 3.1 41.3 + - + +
758C TYR* 3.3 12.0 - - - -
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Residues in contact with VAL 755 (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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115A ASP* 4.8 10.9 - - + +
116A ASP* 4.3 18.6 - - - +
117A VAL* 4.2 14.6 - - + -
722C ILE* 4.9 6.5 - - + -
723C TYR* 5.7 9.4 - - + -
728C PHE* 4.1 28.3 - - + -
753C PRO 3.2 11.6 + - - +
754C ASN* 1.3 69.9 + - - +
756C ASP* 1.3 61.3 + - - +
758C TYR* 3.3 7.9 + - - +
759C LYS* 2.8 40.4 + - + +
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Residues in contact with ASP 756 (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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115A ASP* 4.4 21.8 - - - +
754C ASN* 3.3 11.7 + - - +
755C VAL* 1.3 78.3 - - - +
757C GLU* 1.3 59.1 + - - +
759C LYS* 3.3 9.0 + - - +
760C SER* 2.8 33.7 + - - -
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Residues in contact with GLU 757 (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 PHE* 3.7 8.1 - - - -
670C GLU* 3.8 23.4 - - - +
673C ILE* 4.0 16.2 - - + -
747C ASP* 2.7 41.8 - - + +
754C ASN* 3.1 33.2 + - + +
756C ASP* 1.3 79.6 - - - +
758C TYR* 1.3 69.8 + - + +
760C SER* 3.7 5.0 + - - -
761C VAL* 3.1 28.8 + - - +
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Residues in contact with TYR 758 (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 PHE* 3.2 24.5 - + - -
673C ILE* 3.6 28.9 - - + -
722C ILE* 4.1 17.7 - - + -
728C PHE* 4.6 4.9 - + + -
731C VAL* 3.7 23.8 - - + -
732C VAL* 3.7 38.3 + - + +
735C ALA* 4.3 0.9 - - + -
748C ASP* 2.9 34.8 + - - -
753C PRO* 3.9 13.9 - - + -
754C ASN 3.3 25.1 - - - -
755C VAL* 3.3 8.3 + - - +
757C GLU* 1.3 81.3 - - + +
759C LYS* 1.3 63.9 + - - +
761C VAL* 4.0 0.3 - - - +
762C ILE* 3.1 30.8 + - + +
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Residues in contact with LYS 759 (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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139A LYS* 4.5 8.9 - - - +
722C ILE* 4.2 32.4 - - + +
723C TYR* 3.7 26.4 + - - +
755C VAL* 2.8 23.2 + - + +
756C ASP* 3.4 11.2 - - - +
758C TYR* 1.3 78.9 - - - +
760C SER* 1.3 63.6 + - - +
762C ILE* 3.8 1.9 - - - +
763C ASP* 2.9 53.6 + - - +
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Residues in contact with SER 760 (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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756C ASP 2.8 19.1 + - - -
757C GLU* 3.7 6.4 + - - -
759C LYS* 1.3 73.9 - - - +
761C VAL* 1.3 66.6 + - - +
763C ASP* 3.2 4.6 + - - -
764C HIS* 2.8 44.6 + - - +
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Residues in contact with VAL 761 (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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670C GLU* 3.4 47.8 - - + +
673C ILE* 3.7 30.1 - - + -
674C LYS* 4.4 18.8 + - + +
757C GLU* 3.1 22.7 + - - +
758C TYR 4.0 2.5 - - - +
760C SER* 1.3 78.8 + - - +
762C ILE* 1.3 63.8 + - - +
764C HIS* 3.4 9.3 + - - +
765C MET* 3.2 19.2 + - - +
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Residues in contact with ILE 762 (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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673C ILE* 4.0 12.8 - - + -
677C ARG* 3.8 36.6 - - + +
720C PHE* 3.8 37.9 - - + -
722C ILE* 4.1 10.3 - - + -
731C VAL* 4.0 21.5 - - + -
758C TYR 3.1 19.4 + - - +
759C LYS* 3.9 3.4 - - - +
761C VAL* 1.3 75.7 - - - +
763C ASP* 1.3 67.0 + - - +
764C HIS 3.4 0.5 + - - -
765C MET* 3.5 24.0 + - - +
767C ILE* 4.6 4.0 - - - +
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Residues in contact with ASP 763 (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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759C LYS* 2.9 48.7 + - - +
760C SER* 3.2 7.1 + - - +
762C ILE* 1.3 83.8 - - - +
764C HIS* 1.3 66.9 + - + +
765C MET 3.3 5.5 + - - +
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Residues in contact with HIS 764 (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 LYS* 5.4 3.5 + - - -
760C SER* 2.8 39.5 + - - +
761C VAL* 3.4 7.1 + - - +
762C ILE 3.3 0.4 - - - -
763C ASP* 1.3 82.7 - - + +
765C MET* 1.3 60.2 + - - +
766C ILE* 4.1 3.5 + - - +
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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