Contacts of the helix formed by residues 825 - 838 (chain W) in PDB entry 6G0L
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 VAL 825 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626W TYR* 4.2 0.6 + - - -
651W ILE 4.8 4.5 - - - +
652W MET* 5.3 7.2 - - + +
655W LEU* 2.9 35.2 - - + +
656W LYS* 3.0 57.1 - - + +
659W SER* 4.2 1.6 - - - +
824W THR* 1.3 74.3 - - - +
826W GLU* 1.3 61.6 + - - +
828W GLU* 2.7 30.1 + - + +
829W VAL* 4.0 5.1 + - + +
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Residues in contact with GLU 826 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656W LYS* 3.0 33.2 + - + +
659W SER* 4.2 5.4 - - - +
660W ASN* 4.1 14.4 - - - +
790W ASP* 5.1 4.5 - - + -
791W SER* 3.8 27.1 + - - +
819W LEU 5.3 1.6 - - - +
820W VAL* 3.3 31.0 - - - +
821W SER* 3.9 26.1 + - - +
824W THR* 3.4 0.8 - - - +
825W VAL* 1.3 82.3 - - - +
827W GLU* 1.3 64.1 + - - +
830W LEU* 3.2 28.1 + - - +
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Residues in contact with GLU 827 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820W VAL* 5.3 3.4 - - + -
821W SER 4.5 9.5 + - - +
822W LYS* 5.2 1.0 - - - -
823W ASP* 3.6 19.6 + - - +
824W THR* 2.7 44.6 + - - +
826W GLU* 1.3 86.2 + - - +
828W GLU* 1.3 81.7 + - - +
830W LEU* 3.1 9.1 - - - +
831W GLU* 3.0 25.8 + - + +
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Residues in contact with GLU 828 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824W THR 3.2 7.4 - - - +
825W VAL* 2.7 36.0 - - + +
827W GLU* 1.3 92.6 - - - +
829W VAL* 1.3 62.1 + - + +
831W GLU* 2.9 11.5 + - - +
832W ARG* 2.9 33.8 + - - +
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Residues in contact with VAL 829 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656W LYS* 2.9 41.5 - - + +
791W SER* 6.1 2.2 - - - +
793W TRP* 3.2 43.3 - - + -
794W ASN 4.5 15.5 - - - +
825W VAL* 4.1 4.3 - - + +
826W GLU 3.6 1.0 + - - -
828W GLU* 1.3 74.3 - - + +
830W LEU* 1.3 57.0 + - - +
832W ARG* 3.0 15.2 + - + +
833W ALA* 2.5 42.3 + - + +
836W LYS* 5.0 7.0 - - - +
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Residues in contact with LEU 830 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656W LYS* 4.6 0.2 - - - +
791W SER* 5.2 9.6 - - - +
818W ARG* 5.1 11.7 - - + +
820W VAL* 3.6 31.4 - - + -
826W GLU* 3.2 35.8 + - - +
827W GLU* 3.1 15.2 + - - +
828W GLU 3.0 0.4 - - - -
829W VAL* 1.3 81.5 - - - +
831W GLU* 1.3 75.6 + - - +
833W ALA* 3.3 9.0 - - + +
834W ARG* 3.1 19.1 + - + +
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Residues in contact with GLU 831 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827W GLU* 3.0 16.0 + - + +
828W GLU* 2.9 15.7 + - - +
830W LEU* 1.3 89.2 - - + +
832W ARG* 1.3 61.4 + - + +
834W ARG* 3.1 44.2 + - - +
835W LYS* 3.0 34.7 + - - +
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Residues in contact with ARG 832 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I A 4.7 13.4 + - - -
25I G 3.4 34.1 + - - -
652W MET* 6.3 0.4 - - - +
793W TRP* 4.7 18.0 - - - -
828W GLU* 2.9 22.8 + - - +
829W VAL* 3.7 15.5 - - + +
831W GLU* 1.3 69.6 - - + +
833W ALA* 1.3 56.5 + - - +
835W LYS* 2.7 17.2 + - + +
836W LYS* 2.6 51.0 + - + +
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Residues in contact with ALA 833 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791W SER* 5.4 4.9 - - - +
794W ASN 4.4 4.3 - - - +
795W PRO* 3.2 40.9 - - + +
829W VAL* 2.5 26.7 + - + +
830W LEU* 3.3 12.1 - - + +
832W ARG* 1.3 70.5 - - - +
834W ARG* 1.3 57.7 - - - +
836W LYS* 3.0 25.5 + - - +
837W MET* 3.1 7.7 + - - +
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Residues in contact with ARG 834 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830W LEU* 3.1 10.3 + - + +
831W GLU* 3.1 38.7 + - - +
832W ARG 3.0 0.4 - - - -
833W ALA* 1.3 76.8 - - - +
835W LYS* 1.3 85.6 + - - +
836W LYS 3.0 0.2 - - - -
837W MET* 3.2 11.1 + - + +
838W ILE* 2.9 46.5 + - + +
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Residues in contact with LYS 835 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831W GLU* 3.0 31.5 + - - +
832W ARG* 2.7 22.3 + - + +
834W ARG* 1.3 93.6 - - - +
836W LYS* 1.3 61.7 + - + +
837W MET 3.4 0.2 + - - -
838W ILE* 3.5 33.7 + - + +
839W LEU 5.0 0.2 + - - -
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Residues in contact with LYS 836 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I A 4.9 12.8 + - - -
546W GLN 5.0 1.4 - - - +
547W ASN* 3.8 36.9 + - - +
793W TRP* 4.4 15.4 + - - +
794W ASN* 4.1 15.8 - - - +
795W PRO* 3.1 36.6 - - + +
796W GLN* 5.5 0.6 + - - +
829W VAL* 5.0 8.1 - - - +
832W ARG* 2.6 32.3 + - - +
833W ALA* 3.1 11.7 - - - +
834W ARG 3.0 0.4 - - - -
835W LYS* 1.3 75.9 - - + +
837W MET* 1.3 55.9 + - - +
838W ILE 3.6 0.3 + - - -
839W LEU* 4.0 8.7 + - - +
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Residues in contact with MET 837 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795W PRO* 3.9 16.4 - - + -
796W GLN* 3.6 42.0 - - - +
799W LEU* 4.9 11.7 - - + -
818W ARG* 6.1 3.4 - - - +
833W ALA 3.1 10.8 + - - +
834W ARG* 3.2 10.3 + - + +
836W LYS* 1.3 75.5 - - - +
838W ILE* 1.4 66.1 - - - +
839W LEU 3.2 14.1 + - - +
840W GLU* 4.2 8.1 + - + +
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Residues in contact with ILE 838 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834W ARG* 2.9 42.4 + - + +
835W LYS* 3.5 36.8 - - + +
836W LYS 3.3 1.4 - - - -
837W MET* 1.4 78.7 - - - +
839W LEU* 1.3 73.1 + - + +
840W GLU 4.0 1.0 + - - -
841W TYR* 5.4 1.2 + - - -
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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