Contacts of the helix formed by residues 812 - 824 (chain A) in PDB entry 4G2W
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 LYS 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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811A ASN* 1.3 88.0 - - - +
813A ILE* 1.3 65.0 + - - +
814A PRO 3.4 1.1 - - - -
815A SER* 3.4 14.7 + - - +
816A MET* 3.1 39.0 + - + +
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Residues in contact with ILE 813 (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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779A ALA* 5.5 1.8 - - + +
783A ALA* 3.7 26.2 - - + -
787A PHE* 4.4 10.8 - - + -
811A ASN 4.8 9.6 - - - +
812A LYS* 1.3 76.5 - - - +
814A PRO* 1.3 74.9 - - + +
816A MET* 3.2 23.5 + - + +
817A GLN* 2.9 26.8 + - + +
853A TRP* 4.4 13.9 - - + -
901A NI0 4.2 22.2 - - + -
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Residues in contact with PRO 814 (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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811A ASN* 3.7 17.9 - - - +
812A LYS 3.7 2.7 - - - -
813A ILE* 1.3 94.8 - - + +
815A SER* 1.3 59.9 + - - +
817A GLN* 3.4 3.3 + - - +
818A VAL* 3.1 27.5 + - - +
853A TRP* 3.6 47.9 - - + +
856A LEU* 3.9 20.6 - - + +
857A ALA* 3.8 12.6 - - - +
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Residues in contact with SER 815 (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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811A ASN 5.3 1.1 + - - -
812A LYS* 3.4 19.7 + - - +
813A ILE 3.3 0.2 - - - -
814A PRO* 1.3 76.6 - - - +
816A MET* 1.3 66.2 + - - +
818A VAL* 3.3 8.0 + - - +
819A GLY* 2.9 25.6 + - - -
857A ALA* 4.5 15.1 - - - +
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Residues in contact with MET 816 (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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787A PHE* 3.7 26.9 - - + -
812A LYS* 3.1 21.3 + - + +
813A ILE* 3.5 39.3 - - + +
815A SER* 1.3 83.6 + - - +
817A GLN* 1.3 65.3 + - - +
819A GLY* 3.2 2.2 + - - +
820A PHE* 2.9 24.9 + - - +
901A NI0 3.9 33.8 + - + +
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Residues in contact with GLN 817 (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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768A ILE* 3.5 10.4 - - - +
775A GLN* 3.2 19.6 + - - -
779A ALA* 4.2 1.6 - - - +
813A ILE* 2.9 23.4 + - + +
814A PRO 3.7 0.7 - - - +
815A SER 3.3 0.2 - - - -
816A MET* 1.3 71.9 - - - +
818A VAL* 1.3 52.9 + - - +
820A PHE* 3.2 3.8 + - - +
821A ILE* 2.8 41.5 + - + +
853A TRP* 3.6 40.4 - - + -
901A NI0 2.8 75.7 + - + +
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Residues in contact with VAL 818 (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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814A PRO 3.1 15.7 + - - +
815A SER* 3.6 10.5 - - - +
816A MET 3.2 0.2 - - - -
817A GLN* 1.3 77.0 - - - +
819A GLY* 1.3 57.6 + - - +
821A ILE* 3.4 8.2 + - - +
822A ASP* 2.9 31.6 + - - +
850A ARG* 3.6 35.4 - - + +
853A TRP* 3.8 6.1 - - + +
854A GLN* 3.5 46.0 - - + +
857A ALA* 5.0 0.9 - - + -
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Residues in contact with GLY 819 (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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815A SER 2.9 14.7 + - - -
816A MET* 3.2 4.2 + - - -
818A VAL* 1.3 76.7 - - - +
820A PHE* 1.3 53.0 + - - +
822A ASP* 3.8 4.3 - - - +
823A ALA* 2.8 39.7 + - - +
901A NI0 5.6 1.8 - - - -
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Residues in contact with PHE 820 (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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725A LEU* 5.1 5.4 - - + -
765A LEU* 4.1 12.8 - - + -
768A ILE* 3.7 21.3 - - + -
816A MET 2.9 15.0 + - - +
817A GLN* 3.5 6.1 - - - +
819A GLY* 1.3 73.5 - - - +
821A ILE* 1.3 61.4 + - - +
824A ILE* 2.9 46.4 + - + -
825A CYS* 3.4 30.5 + - - -
901A NI0 3.4 99.0 + + + +
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Residues in contact with ILE 821 (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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768A ILE* 3.6 34.5 - - + -
817A GLN 2.8 24.3 + - - +
818A VAL* 3.7 4.3 - - - +
820A PHE* 1.3 72.7 - - - +
822A ASP* 1.3 62.0 + - - +
825A CYS* 3.1 10.0 + - - -
826A LEU* 3.0 50.6 + - + +
846A CYS* 3.8 16.2 - - - +
849A ASN* 4.2 5.2 - - + -
850A ARG* 3.6 48.2 - - + +
853A TRP* 4.3 9.6 - - + -
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Residues in contact with ASP 822 (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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818A VAL* 2.9 19.9 + - - +
819A GLY* 3.9 4.8 - - - +
821A ILE* 1.3 79.7 - - - +
823A ALA* 1.3 62.0 + - - +
824A ILE 5.0 0.2 - - - -
825A CYS 4.9 0.3 + - - -
826A LEU* 3.7 19.7 + - - +
827A GLN* 4.3 13.0 - - - +
850A ARG* 2.7 48.7 + - - -
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Residues in contact with ALA 823 (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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732A ARG* 2.9 31.8 + - - +
819A GLY 2.8 23.3 + - - +
822A ASP* 1.3 75.9 - - - +
824A ILE* 1.3 73.9 + - + +
827A GLN* 4.3 2.2 - - - +
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Residues in contact with ILE 824 (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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725A LEU* 4.3 12.8 - - + -
728A TYR* 2.7 45.3 + - + -
729A ILE* 5.1 14.8 - - + -
732A ARG* 3.6 4.8 + - - +
765A LEU* 3.4 30.3 - - + -
820A PHE* 2.9 34.2 + - + +
822A ASP 5.0 0.2 - - - -
823A ALA* 1.3 90.1 - - + +
825A CYS* 1.3 61.7 + - - +
826A LEU 3.9 0.7 - - - -
827A GLN 4.8 1.5 + - - -
828A LEU* 3.9 3.5 + - - +
901A NI0 3.1 31.4 - - - +
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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