Contacts of the helix formed by residues 814 - 827 (chain A) in PDB entry 3G8O
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 814 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765A TRP* 3.8 1.8 - - - -
812A GLN 3.5 3.7 + - - -
813A VAL* 1.3 77.9 - - - +
815A GLN* 1.3 65.5 + - - +
816A GLU* 3.3 17.7 + - - +
817A GLU* 3.1 35.5 + - - +
818A PHE* 3.0 18.9 + - - +
855A ALA 4.9 2.6 + - - -
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Residues in contact with GLN 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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692A MET* 3.3 35.2 - - - +
695A GLU* 4.9 5.2 - - - +
765A TRP* 3.4 36.8 + - + +
769A LYS* 6.0 1.6 - - - +
814A SER* 1.3 73.1 - - - +
816A GLU* 1.3 68.1 + - - +
818A PHE* 3.2 2.8 + - + +
819A LEU* 2.9 53.4 + - + +
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Residues in contact with GLU 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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684A ILE* 4.2 11.8 - - + +
688A ILE* 3.9 26.4 - - + +
692A MET* 3.2 20.4 - - + +
814A SER* 3.3 22.2 - - - +
815A GLN* 1.3 83.5 + - - +
817A GLU* 1.3 61.0 + - - +
819A LEU* 3.5 4.2 + - - +
820A CYS* 3.4 26.2 + - - -
855A ALA* 3.8 11.2 - - + +
858A LEU* 3.4 34.1 - - + -
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Residues in contact with GLU 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A VAL* 3.5 9.6 - - + +
814A SER* 3.1 31.1 + - - +
816A GLU* 1.3 76.4 - - - +
818A PHE* 1.3 61.2 + - - +
820A CYS* 3.4 2.9 + - - +
821A MET* 2.9 34.5 + - - +
852A LEU* 4.0 4.0 - - + +
855A ALA* 4.0 20.4 - - + -
856A ILE* 3.7 15.6 - - + +
859A ARG* 5.8 3.3 - - - +
869A ARG* 2.5 51.3 + - - -
873A LEU* 3.7 19.5 - - + +
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Residues in contact with PHE 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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695A GLU* 4.3 9.9 - - - -
761A PHE* 3.4 43.3 - + - -
762A GLY* 4.4 6.5 - - - -
765A TRP* 3.4 67.3 - + + -
808A PHE* 4.1 6.3 - + - -
813A VAL* 3.9 7.3 - - + +
814A SER 3.0 16.4 + - - +
815A GLN* 3.6 4.3 - - + +
817A GLU* 1.3 76.7 - - - +
819A LEU* 1.3 68.6 + - + +
821A MET* 3.3 6.3 + - - +
822A LYS* 2.9 62.1 + - + +
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Residues in contact with LEU 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ILE* 4.1 6.1 - - + +
691A LEU* 3.9 22.1 - - + +
692A MET* 3.4 45.1 - - + +
695A GLU* 3.5 39.9 - - + +
815A GLN* 2.9 35.8 + - + +
816A GLU 3.9 3.8 - - - +
818A PHE* 1.3 87.0 - - + +
820A CYS* 1.3 62.9 + - - +
822A LYS* 3.4 8.2 + - - +
823A VAL* 3.3 26.2 + - - +
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Residues in contact with CYS 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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688A ILE* 4.1 10.1 - - - -
691A LEU* 4.4 10.8 - - - -
816A GLU 3.4 13.4 + - - +
817A GLU 3.4 7.0 + - - +
818A PHE 3.3 0.2 - - - -
819A LEU* 1.3 76.9 - - - +
821A MET* 1.3 65.7 + - - +
823A VAL* 3.3 7.7 + - - +
824A LEU* 3.2 26.6 + - - +
848A TYR* 4.4 6.0 - - + +
851A GLU* 3.6 43.3 - - - -
852A LEU* 3.7 22.9 - - + +
855A ALA* 4.3 2.0 - - - -
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Residues in contact with MET 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A PHE* 3.7 24.9 - - + -
808A PHE* 4.9 3.4 - - + -
813A VAL* 4.6 4.7 - - - -
817A GLU* 2.9 28.3 + - - +
818A PHE* 3.7 8.7 - - - +
820A CYS* 1.3 73.6 - - - +
822A LYS* 1.3 60.7 + - - +
824A LEU* 3.2 10.1 + - - +
825A LEU* 2.9 28.1 + - - +
852A LEU* 4.1 20.4 - - + -
873A LEU* 3.7 52.0 - - + +
876A LEU* 4.1 20.6 - - + -
877A LEU* 3.9 16.6 - - + +
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Residues in contact with LYS 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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695A GLU* 3.0 35.8 + - - -
696A PRO* 5.0 4.6 - - - +
729A VAL* 6.2 1.2 - - - +
732A TRP* 3.6 34.7 - - + -
758A LEU* 3.5 27.7 - - + +
761A PHE* 3.8 15.5 - - + -
762A GLY* 5.7 2.5 - - - -
818A PHE* 2.9 42.6 + - + +
819A LEU* 3.6 9.9 - - - +
821A MET* 1.3 79.1 - - - +
823A VAL* 1.3 61.0 + - - +
825A LEU* 3.2 5.8 + - - +
826A LEU* 3.1 18.5 + - - +
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Residues in contact with VAL 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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691A LEU* 4.2 8.1 - - + -
732A TRP* 4.2 11.0 - - + -
736A LEU* 3.7 34.3 - - + -
819A LEU 3.4 15.9 - - - +
820A CYS 3.3 6.7 + - - +
821A MET 3.3 0.2 - - - -
822A LYS* 1.3 76.3 - - - +
824A LEU* 1.3 63.7 + - - +
826A LEU* 3.1 15.9 + - - +
827A LEU* 3.2 20.8 + - + +
844A MET* 4.3 0.2 - - + -
848A TYR* 3.5 48.9 - - + -
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Residues in contact with LEU 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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820A CYS 3.2 14.7 + - - +
821A MET* 3.2 7.2 + - - +
823A VAL* 1.3 77.3 - - - +
825A LEU* 1.3 62.5 + - - +
827A LEU* 3.1 8.4 + - + +
828A ASN* 3.0 23.7 + - - +
845A ARG* 3.5 43.9 + - + +
848A TYR* 3.9 22.7 - - + +
849A ILE* 3.8 14.6 - - + -
852A LEU* 3.8 29.2 - - + -
877A LEU* 4.0 19.5 - - + -
930A PHE* 4.2 11.2 - - + -
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Residues in contact with LEU 825 (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* 3.8 9.7 - - - -
757A SER* 3.7 29.1 - - - +
758A LEU* 3.8 9.4 - - + -
761A PHE* 3.5 42.0 - - + -
821A MET 2.9 8.9 + - - +
822A LYS 3.3 10.1 - - - +
823A VAL 3.2 0.2 - - - -
824A LEU* 1.3 74.2 - - - +
826A LEU* 1.3 66.7 + - - +
828A ASN* 2.9 36.8 + - + +
829A THR 4.8 0.3 + - - -
877A LEU* 4.0 17.0 - - + +
880A LEU* 3.7 26.7 - - + -
881A HIS* 6.2 0.9 - - + -
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Residues in contact with LEU 826 (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 TRP* 3.9 11.4 - - + -
733A SER* 5.1 0.4 - - - -
736A LEU* 3.3 33.9 - - + -
739A PHE* 3.7 27.1 - - + -
750A LEU* 3.9 22.8 - - - +
751A ILE* 3.8 25.6 - - + -
753A TYR* 5.9 0.5 - - - +
754A SER* 3.3 31.5 + - - +
758A LEU* 3.8 14.3 - - + +
822A LYS 3.1 8.6 + - - +
823A VAL* 3.1 10.5 + - - +
825A LEU* 1.3 80.5 - - - +
827A LEU* 1.3 62.4 + - + +
828A ASN 3.6 1.7 + - - -
829A THR 4.9 1.0 + - - -
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Residues in contact with LEU 827 (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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739A PHE* 4.6 1.3 - - + -
742A LEU* 4.8 0.2 - - + -
750A LEU* 3.9 17.9 - - + -
823A VAL* 3.4 21.5 - - + +
824A LEU* 3.1 12.4 + - + +
825A LEU 3.0 0.6 - - - -
826A LEU* 1.3 87.3 - - + +
828A ASN* 1.3 56.9 + - - +
829A THR 3.5 3.1 - - - -
841A PHE* 3.3 43.4 - - + -
844A MET* 3.9 46.0 - - + +
845A ARG* 3.0 38.0 + - + +
848A TYR* 4.8 0.9 - - + -
928A LEU* 3.5 3.8 - - - +
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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