Contacts of the helix formed by residues 837 - 845 (chain A) in PDB entry 6Q6Q
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 GLU 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.3 23.1 + - + +
276A LYS* 3.3 36.0 + - - +
277A PHE* 4.9 14.6 - - + -
683A GLU* 4.5 5.8 - - - +
687A LYS* 3.6 33.9 + - - +
755A THR* 4.4 0.9 - - - -
835A VAL 5.2 0.7 - - - +
836A LEU* 1.3 77.4 - - - +
838A ARG* 1.3 55.4 + - - +
839A GLY* 3.4 4.3 - - - +
840A GLU* 3.2 24.3 + - + +
841A ASP* 2.7 33.8 + - - +
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Residues in contact with ARG 838 (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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42A TYR* 3.1 7.5 + - - -
43A GLY* 3.0 23.4 + - - +
44A CYS* 3.6 36.1 - - + +
751A PHE* 3.8 48.2 - - + +
752A TYR* 2.7 38.8 + - - -
753A MET* 3.3 18.6 + - - +
755A THR* 3.5 17.8 - - - +
837A GLU* 1.3 74.2 - - - +
839A GLY* 1.3 63.3 + - - +
841A ASP* 3.0 17.9 + - - +
842A MET* 3.1 35.1 + - + +
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Residues in contact with GLY 839 (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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277A PHE* 5.4 12.5 - - - -
837A GLU* 3.4 2.2 - - - +
838A ARG* 1.3 78.4 - - - +
840A GLU* 1.3 61.6 + - - +
842A MET* 3.8 13.7 + - - +
843A LEU* 3.4 23.1 + - - +
1230A THR* 5.5 6.3 - - - -
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Residues in contact with GLU 840 (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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613A THR* 3.3 21.6 + - - -
614A PHE* 3.8 16.7 + - - +
616A THR* 5.9 4.1 - - + +
687A LYS* 3.7 12.1 - - - -
835A VAL 4.8 0.3 - - - +
836A LEU* 4.0 21.3 - - + +
837A GLU* 3.2 44.5 + - + +
839A GLY* 1.3 75.7 - - - +
841A ASP* 1.3 62.7 + - - +
843A LEU* 3.3 5.4 + - - +
844A ILE* 3.0 38.4 + - + +
3006A MLI 5.3 6.5 - - - +
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Residues in contact with ASP 841 (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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749A GLU* 5.0 3.5 - - - +
752A TYR* 2.7 35.0 + - - -
755A THR* 3.4 9.4 - - + -
756A GLN* 2.9 38.5 + - - +
836A LEU* 4.5 9.6 - - + -
837A GLU 2.7 20.4 + - - +
838A ARG* 3.0 14.2 + - - +
840A GLU* 1.3 73.6 - - - +
842A MET* 1.3 59.7 + - - +
845A THR* 2.8 45.0 + - - +
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Residues in contact with MET 842 (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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749A GLU* 3.2 44.6 - - + +
751A PHE* 4.1 28.7 - - + -
838A ARG* 3.1 37.5 + - + +
839A GLY* 4.3 8.7 - - - +
841A ASP* 1.3 76.8 - - + +
843A LEU* 1.3 57.0 + - - +
845A THR 3.2 9.8 - - - +
915A PRO* 5.6 1.4 - - - +
1220A LEU* 6.1 0.9 - - - -
1228A LEU* 4.3 21.8 - - + +
1230A THR* 3.9 23.8 - - - +
1236A TYR* 4.6 15.5 - - + -
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Residues in contact with LEU 843 (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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616A THR* 4.1 19.1 - - + +
617A SER 5.1 2.2 - - - +
671A VAL* 3.8 27.3 - - + +
672A GLY* 3.6 22.8 - - - +
839A GLY 3.4 16.8 + - - +
840A GLU* 3.3 6.0 + - - +
841A ASP 3.1 0.8 - - - -
842A MET* 1.3 79.9 - - - +
844A ILE* 1.3 64.4 + - + +
915A PRO* 3.8 17.5 - - + +
1228A LEU* 4.4 25.1 - - + +
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Residues in contact with ILE 844 (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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614A PHE* 4.9 7.4 - - + -
616A THR* 4.0 16.4 - - + -
672A GLY 3.7 17.8 - - - +
674A LEU* 3.9 30.1 - - + -
813A LYS* 2.9 49.4 + - + +
817A ILE* 4.8 9.6 - - + -
836A LEU* 3.9 28.7 - - + -
840A GLU* 3.0 25.3 + - + +
841A ASP 4.3 0.7 - - - +
843A LEU* 1.3 79.8 - - + +
845A THR* 1.3 64.8 + - - +
915A PRO* 4.6 4.0 - - - +
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Residues in contact with THR 845 (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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749A GLU* 4.8 3.6 - - - -
750A HIS* 3.9 19.5 - - + +
752A TYR* 3.2 19.8 + - - +
756A GLN* 3.8 10.2 + - - +
809A GLY* 3.7 17.3 - - - +
813A LYS* 4.6 14.1 - - + +
836A LEU* 5.5 0.3 - - - +
841A ASP* 2.8 32.5 + - - -
842A MET 3.2 17.3 - - - +
843A LEU 4.1 2.1 - - - +
844A ILE* 1.3 80.3 - - - +
846A GLY* 1.3 69.8 + - - +
915A PRO* 4.4 5.0 - - - +
918A THR* 5.1 2.9 - - - +
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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