Contacts of the helix formed by residues 845 - 857 (chain B) in PDB entry 3QCC
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 GLN 845 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840B LEU 3.3 13.0 - - - +
841B TYR* 3.0 34.1 + - + +
843B ASN 2.9 1.6 - - - -
844B ASN* 1.3 84.5 + - - +
846B HIS* 1.3 65.4 + - - +
847B GLY 3.1 2.5 - - - -
848B PHE* 3.1 27.1 + - + -
849B SER* 3.0 22.2 + - - -
1106B GLU* 4.3 7.3 + - - +
1110B ILE* 3.7 19.5 - - + +
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Residues in contact with HIS 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B SER 3.4 3.4 + - - +
843B ASN* 3.6 24.8 + - - +
844B ASN 3.4 4.1 - - - -
845B GLN* 1.3 75.9 - - - +
847B GLY* 1.3 62.9 + - - +
849B SER* 3.1 12.5 + - - -
850B GLU* 2.9 64.8 + - + +
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Residues in contact with GLY 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839B GLU* 4.6 2.2 - - - -
840B LEU* 3.7 24.0 - - - -
842B SER 3.4 8.6 + - - -
845B GLN 3.1 0.8 - - - -
846B HIS* 1.3 80.6 + - - +
848B PHE* 1.3 60.6 + - - +
850B GLU* 3.3 11.6 + - - +
851B ASP* 3.0 28.2 + - - +
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Residues in contact with PHE 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B ILE* 4.4 1.3 - - + -
840B LEU* 3.4 37.5 + - + -
841B TYR* 3.6 45.8 - + - -
845B GLN* 3.1 18.4 + - + +
847B GLY* 1.3 74.4 - - - +
849B SER* 1.3 57.7 + - - +
851B ASP* 3.9 2.5 - - - +
852B PHE* 3.0 31.9 + - - +
1106B GLU* 4.1 4.2 - - + +
1109B TYR* 3.9 21.6 - + + -
1110B ILE* 3.5 35.4 - - + -
1113B HIS* 3.3 47.8 - + + -
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Residues in contact with SER 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844B ASN 5.1 1.6 + - - -
845B GLN* 3.0 11.6 + - - +
846B HIS* 3.1 15.2 + - - -
848B PHE* 1.3 78.0 - - - +
850B GLU* 1.3 62.0 + - - +
852B PHE* 4.1 1.6 - - - +
853B GLU* 3.1 25.0 + - - +
1106B GLU* 2.9 35.3 + - - +
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Residues in contact with GLU 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846B HIS* 2.9 55.6 + - + +
847B GLY* 3.8 9.3 - - - +
849B SER* 1.3 74.4 - - - +
851B ASP* 1.3 63.3 + - - +
853B GLU* 3.4 23.0 + - - +
854B GLU* 3.0 28.7 + - - +
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Residues in contact with ASP 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836B HIS* 4.1 11.1 + - - -
840B LEU* 3.6 20.8 - - - +
847B GLY 3.0 19.1 + - - +
848B PHE* 3.9 1.8 - - - +
850B GLU* 1.3 78.8 - - - +
852B PHE* 1.3 59.0 + - - +
854B GLU* 3.1 15.3 - - - +
855B VAL* 3.0 29.1 + - - +
1089B LEU* 3.8 21.4 - - + +
1109B TYR* 3.8 28.7 + - + +
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Residues in contact with PHE 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848B PHE 3.0 16.8 + - - +
849B SER 4.1 2.7 - - - +
851B ASP* 1.3 71.8 - - - +
853B GLU* 1.3 60.1 + - - +
854B GLU 3.0 1.3 - - - -
855B VAL* 2.8 33.0 + - + +
856B GLN* 2.8 42.2 + - + +
1096B ARG* 4.0 13.2 - - - -
1103B VAL* 3.4 26.5 - - + -
1104B GLN 3.2 25.4 - - - -
1105B THR* 3.5 9.9 - - - -
1106B GLU* 3.6 31.4 - - + -
1109B TYR* 3.8 26.4 - + + -
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Residues in contact with GLU 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849B SER 3.1 18.4 + - - +
850B GLU* 3.5 21.9 - - - +
852B PHE* 1.3 78.2 - - - +
854B GLU* 1.3 61.7 + - - +
856B GLN* 3.6 16.2 + - - +
857B ARG* 3.5 42.2 + - - +
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Residues in contact with GLU 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850B GLU 3.0 13.9 + - - +
851B ASP* 3.1 19.6 - - - +
852B PHE 3.0 0.4 - - - -
853B GLU* 1.3 78.9 - - - +
855B VAL* 1.3 61.0 + - - +
857B ARG* 3.4 4.1 + - - +
858B CYS* 3.2 25.5 + - - +
1089B LEU* 3.7 16.6 - - - +
1093B LYS* 2.6 36.8 + - - +
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Residues in contact with VAL 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851B ASP 3.0 15.2 + - - +
852B PHE* 2.8 21.4 + - + +
854B GLU* 1.3 78.1 - - - +
856B GLN* 1.3 59.0 + - - +
858B CYS* 3.0 29.3 - - - -
1089B LEU* 3.3 24.5 - - + -
1092B LEU* 3.6 40.2 - - + +
1093B LYS* 4.8 3.4 - - + -
1096B ARG* 3.6 30.6 + - + +
1109B TYR* 4.3 4.0 - - + -
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Residues in contact with GLN 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A ARG* 5.6 5.5 + - - -
852B PHE* 2.8 49.7 + - + +
853B GLU* 3.9 16.2 - - - +
854B GLU 3.3 0.4 - - - -
855B VAL* 1.3 77.1 - - - +
857B ARG* 1.3 63.3 + - + +
858B CYS 3.5 0.2 - - - -
859B THR* 5.2 5.4 + - - +
1096B ARG* 3.7 20.8 + - - +
1104B GLN 4.4 5.5 + - - -
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Residues in contact with ARG 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959A ARG* 6.5 0.7 - - - -
853B GLU* 3.5 32.1 + - + +
854B GLU* 3.4 5.2 + - - +
855B VAL 3.2 0.4 - - - -
856B GLN* 1.3 82.1 - - + +
858B CYS* 1.3 63.6 + - - +
859B THR* 3.1 3.8 - - - -
860B ALA* 3.1 28.1 - - + +
861B ASP* 4.8 0.5 + - - -
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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