Contacts of the helix formed by residues 754 - 767 (chain A) in PDB entry 4NC6
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 SER 754 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A GLU 5.7 2.0 - - - -
752A GLY* 3.1 2.8 + - - -
753A ILE* 1.3 82.7 - - - +
755A VAL* 1.3 63.2 + - - +
756A ILE 3.1 0.4 - - - -
757A PHE* 3.0 28.5 + - - +
758A ASN* 3.2 10.3 - - - +
809A ILE 5.6 2.0 - - - -
811A GLN* 3.0 33.7 + - - -
814A LEU* 3.7 19.8 - - - +
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Residues in contact with VAL 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A ILE* 4.6 3.4 - - + +
747A LEU* 4.0 17.0 - - + +
748A LEU* 3.5 33.0 - - + +
751A GLU* 3.6 28.9 - - + +
752A GLY 3.4 18.8 - - - +
753A ILE 2.9 1.2 + - - -
754A SER* 1.3 78.0 - - - +
756A ILE* 1.3 66.8 + - + +
757A PHE 3.1 0.2 - - - -
758A ASN* 3.1 18.3 + - + +
759A VAL* 3.0 30.6 + - + +
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Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A TRP* 3.9 11.0 - - + +
728A PHE* 3.5 37.5 - - + +
731A LEU* 3.8 28.5 - - + -
732A PHE* 3.5 37.8 - - + -
744A ILE* 4.4 8.3 - - + -
748A LEU* 3.8 19.3 - - + -
753A ILE* 3.1 17.5 + - + +
754A SER 3.0 0.8 + - - -
755A VAL* 1.3 76.2 - - - +
757A PHE* 1.3 57.2 + - + +
759A VAL* 3.5 1.4 + - - +
760A ALA* 2.9 28.3 + - + +
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Residues in contact with PHE 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LYS* 3.5 36.1 - - + -
697A GLN* 3.5 36.8 - - + -
698A LEU* 3.8 11.9 - - + -
701A LEU* 3.9 24.9 - - + -
728A PHE* 3.6 27.8 - + - -
753A ILE 5.3 0.7 - - - -
754A SER* 3.0 23.6 + - - +
756A ILE* 1.3 76.5 - - - +
758A ASN* 1.3 66.2 + - - +
760A ALA* 3.7 3.0 - - - +
761A LEU* 3.0 31.3 + - + +
809A ILE* 4.9 5.8 - - + -
814A LEU* 3.8 27.1 - - + -
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Residues in contact with ASN 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A SER* 3.2 17.2 - - - +
755A VAL* 3.1 20.4 + - + +
757A PHE* 1.3 77.5 - - - +
759A VAL* 1.3 60.4 + - + +
761A LEU* 3.4 6.3 + - - +
762A GLY 2.9 23.6 + - - -
804A ALA* 3.2 31.2 + - + +
805A CYS* 4.9 0.6 - - - +
807A MET* 4.5 5.3 - - - +
808A LYS* 2.6 49.2 - - - +
809A ILE* 3.5 12.0 + - - +
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Residues in contact with VAL 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A PHE* 3.6 30.3 - - + -
740A MET* 5.3 1.1 - - + -
744A ILE* 4.0 26.9 - - + -
747A LEU* 5.4 2.0 - - + -
755A VAL* 3.0 21.5 + - + +
756A ILE 4.0 0.2 - - - +
758A ASN* 1.3 76.4 - - + +
760A ALA* 1.3 58.7 + - - +
762A GLY* 3.2 1.2 + - - -
763A LEU* 2.8 38.9 + - + +
800A LEU* 4.2 15.8 - - + +
801A MET* 4.0 22.9 - - + -
804A ALA* 3.9 9.4 - - + -
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Residues in contact with ALA 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A LEU* 3.9 21.5 - - + -
727A TRP* 3.8 29.8 - - + -
728A PHE* 5.2 2.5 - - + -
732A PHE* 4.0 4.2 - - + -
756A ILE* 2.9 21.4 + - + +
757A PHE* 3.7 5.2 - - - +
759A VAL* 1.3 77.1 - - - +
761A LEU* 1.3 62.8 + - - +
763A LEU* 3.3 3.4 + - - +
764A LEU* 3.0 31.6 + - - +
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Residues in contact with LEU 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A LEU* 4.2 10.1 - - + -
701A LEU* 4.2 26.0 - - + +
702A MET* 4.1 21.8 - - + +
705A TYR* 4.7 7.2 - - + -
706A ILE* 3.8 24.1 - - + +
757A PHE 3.0 21.1 + - - +
758A ASN* 3.8 4.0 - - - +
760A ALA* 1.3 75.6 - - - +
762A GLY* 1.3 59.8 + - - +
764A LEU* 4.5 0.7 - - + -
765A LYS* 2.9 32.9 + - - +
807A MET* 4.1 19.9 - - + +
809A ILE* 3.7 35.4 - - + -
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Residues in contact with GLY 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A ASN 2.9 16.2 + - - -
759A VAL* 3.2 3.5 + - - -
761A LEU* 1.3 77.1 - - - +
763A LEU* 1.3 59.7 + - - +
765A LYS* 3.9 0.5 - - - +
766A THR* 2.8 30.0 + - - -
800A LEU* 3.4 13.7 - - - -
803A LEU* 4.1 17.3 - - - -
804A ALA* 4.8 4.9 - - - -
807A MET* 4.2 5.5 - - - -
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Residues in contact with LEU 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A TRP* 4.6 12.8 - - + -
732A PHE* 3.5 34.8 - - + -
736A PHE* 4.2 18.8 - - + -
740A MET* 4.5 4.0 - - + -
759A VAL* 2.8 28.9 + - + +
760A ALA* 3.6 6.3 - - - +
762A GLY* 1.3 74.3 - - - +
764A LEU* 1.3 58.0 + - - +
766A THR* 3.4 2.7 + - - -
767A SER* 3.1 33.4 + - - -
787A LEU* 4.3 14.4 - - + +
791A TYR* 3.5 37.8 + - + -
800A LEU* 3.6 14.5 - - + +
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Residues in contact with LEU 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A LEU* 4.4 8.1 - - + -
702A MET* 3.7 34.3 - - + -
706A ILE* 3.6 16.2 - - + -
709A LEU* 3.8 19.5 - - + +
713A PHE* 4.7 0.9 - - + -
723A TYR* 4.3 8.7 - - + -
727A TRP* 4.1 18.2 - - + -
760A ALA 3.0 25.4 + - - +
761A LEU* 4.8 0.2 - - - -
763A LEU* 1.3 77.6 - - - +
765A LYS* 1.3 57.4 + - - +
767A SER 3.8 0.5 - - - -
768A LYS* 3.0 32.4 + - - +
771A LEU* 4.5 5.4 - - + -
783A PHE* 3.8 34.3 - - + -
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Residues in contact with LYS 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A TYR 3.1 20.6 + - - +
706A ILE* 3.8 28.8 - - + +
707A PRO* 5.3 2.0 - - - +
708A ASP* 5.2 0.8 + - - -
761A LEU 2.9 18.9 + - - +
762A GLY 3.9 2.2 - - - +
764A LEU* 1.3 77.2 - - - +
766A THR* 1.3 66.0 + - - +
767A SER 3.4 0.3 + - - -
768A LYS* 3.5 35.3 + - + +
803A LEU* 4.4 8.5 - - + -
807A MET* 4.1 23.1 - - + -
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Residues in contact with THR 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A GLY 2.8 21.8 + - - -
763A LEU 3.9 1.6 - - - -
765A LYS* 1.3 77.4 - - - +
767A SER* 1.3 57.5 + - - +
768A LYS 3.8 0.3 + - - -
769A ASP* 5.1 1.4 + - - +
790A ARG* 3.6 28.9 + - - +
791A TYR* 3.5 24.2 - - - +
800A LEU* 3.7 8.7 - - + +
803A LEU* 3.3 19.2 - - - +
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Residues in contact with SER 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A LEU 3.1 15.9 + - - -
764A LEU 3.8 1.3 - - - -
766A THR* 1.3 76.5 - - - +
768A LYS* 1.3 65.5 + - - +
769A ASP 3.2 2.7 - - - -
770A ASP* 2.9 23.3 + - - +
771A LEU* 3.5 13.8 + - - +
782A PHE* 3.5 34.7 - - - -
787A LEU* 3.7 12.7 - - - +
790A ARG* 4.0 15.9 - - - -
791A TYR* 4.7 1.4 + - - -
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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