Contacts of the helix formed by residues 931 - 942 (chain B) in PDB entry 3QCF
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 THR 931 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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877B LYS* 3.8 38.1 - - + +
907B ILE* 5.7 6.1 - - - -
925B GLN* 4.5 3.9 + - - +
927B PRO* 3.5 8.3 - - - +
928B LEU* 2.8 35.4 + - + -
930B SER* 1.3 92.8 - - - +
932B PHE* 1.3 66.6 + - - +
933B GLU 3.2 3.4 - - - +
934B ASP* 3.1 17.7 + - - +
935B PHE* 2.8 23.7 + - - +
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Residues in contact with PHE 932 (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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927B PRO* 3.9 14.6 - - + -
928B LEU 2.9 30.6 + - - -
929B LYS* 3.6 38.9 + - + +
930B SER 3.6 0.2 - - - -
931B THR* 1.3 76.2 - - - +
933B GLU* 1.3 64.3 + - + +
935B PHE* 3.3 4.4 + - - +
936B TRP* 3.2 31.7 + - + -
962B ASP* 3.7 15.3 - - + -
963B GLN 3.2 31.0 - - - -
964B TYR* 3.6 21.5 - - + -
973B TYR* 3.7 32.8 - + + -
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Residues in contact with GLU 933 (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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930B SER 5.2 2.4 + - - +
931B THR 3.2 0.8 - - - -
932B PHE* 1.3 76.9 - - + +
934B ASP* 1.3 70.3 + - - +
936B TRP* 4.1 0.9 - - - +
937B ARG* 2.9 30.5 + - - +
973B TYR* 3.7 13.8 - - + +
974B GLY* 3.2 39.8 - - - +
976B ILE* 5.9 0.3 - - - +
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Residues in contact with ASP 934 (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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877B LYS* 4.4 15.8 + - - +
893B LEU* 3.6 29.8 - - + +
896B LEU* 5.8 1.2 - - - +
904B SER* 5.2 2.1 - - - +
906B TYR 4.2 8.6 - - - +
907B ILE* 3.9 13.7 - - + -
930B SER 4.2 5.9 - - - +
931B THR* 3.1 24.5 + - - +
933B GLU* 1.3 79.5 - - - +
935B PHE* 1.3 52.6 + - - +
937B ARG* 3.5 12.9 + - - +
938B MET* 2.8 35.5 + - - +
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Residues in contact with PHE 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B ILE* 3.9 13.4 - - + +
924B THR* 4.4 8.3 - - + -
925B GLN 5.2 0.2 - - - -
927B PRO* 3.2 35.9 - - + -
931B THR* 2.8 15.7 + - - +
932B PHE 3.5 3.8 - - - +
933B GLU 3.1 0.2 - - - -
934B ASP* 1.3 75.3 - - - +
936B TRP* 1.3 78.9 + + - +
938B MET* 3.5 10.3 + - + +
939B ILE* 3.1 50.0 + - + +
947B ILE* 4.3 5.4 - - + -
964B TYR* 3.5 42.4 - + + -
1057B LEU* 3.7 35.0 - - + -
1059B HIS* 4.9 1.3 - + - -
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Residues in contact with TRP 936 (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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932B PHE* 3.2 23.6 + - - +
933B GLU 4.3 1.6 - - - +
935B PHE* 1.3 88.5 - + - +
937B ARG* 1.3 60.6 + - - +
939B ILE* 3.2 29.1 + - + +
940B TRP* 2.9 28.9 + - - +
947B ILE* 4.0 18.4 - - + -
964B TYR* 2.7 43.9 + + + +
965B TRP* 4.5 4.9 - - + -
973B TYR* 3.6 28.0 - + + +
976B ILE* 4.2 21.8 - - + +
978B VAL* 3.6 36.1 - - + -
994B PHE* 4.8 11.9 - + - -
996B ILE* 3.8 24.3 - - + +
1018B VAL* 4.6 5.6 - - + -
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Residues in contact with ARG 937 (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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893B LEU* 3.5 23.4 - - + +
894B ARG 2.6 26.8 + - - -
896B LEU* 3.4 39.5 - - - +
904B SER* 2.8 28.9 + - - -
933B GLU* 2.9 22.0 + - - +
934B ASP* 3.5 12.6 + - - +
936B TRP* 1.3 75.3 - - - +
938B MET* 1.3 61.0 + - - +
940B TRP* 3.2 3.5 + - + +
941B GLU* 2.9 58.8 + - + +
976B ILE* 4.5 18.3 - - + +
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Residues in contact with MET 938 (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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891B VAL* 3.7 35.0 - - + -
893B LEU* 3.5 18.0 - - + +
907B ILE* 3.9 29.6 - - + -
909B ALA* 4.0 5.4 - - + -
922B ILE* 3.8 22.4 - - + -
924B THR* 4.4 7.4 - - + +
934B ASP 2.8 20.5 + - - +
935B PHE* 3.6 8.3 - - + +
937B ARG* 1.3 72.8 - - - +
939B ILE* 1.3 57.4 + - - +
941B GLU* 4.7 2.7 - - - -
942B GLN* 2.8 41.2 + - + +
1057B LEU* 3.5 31.4 - - + -
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Residues in contact with ILE 939 (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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935B PHE* 3.1 46.2 + - + +
936B TRP* 3.4 18.2 - - + +
937B ARG 3.2 0.2 - - - -
938B MET* 1.3 75.1 - - - +
940B TRP* 1.3 66.0 + - - +
943B ASN* 3.1 3.1 + - - -
944B THR* 3.1 51.1 + - + +
947B ILE* 3.8 18.8 - - + -
996B ILE* 4.2 11.0 - - + -
1016B ARG* 4.4 0.2 + - - -
1018B VAL* 4.2 14.6 - - + -
1057B LEU* 3.6 21.3 - - + -
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Residues in contact with TRP 940 (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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936B TRP 2.9 13.9 + - - +
937B ARG* 3.7 6.7 - - - +
939B ILE* 1.3 77.6 - - - +
941B GLU* 1.3 75.4 + - + +
943B ASN* 3.0 3.8 + - - +
976B ILE* 4.2 15.3 - - + -
996B ILE* 3.8 41.3 - - + -
998B ASN* 2.9 52.0 - - + +
1000B LYS* 4.5 11.7 - - - +
1015B GLU* 3.9 18.4 - - + -
1016B ARG* 2.6 71.6 + - + +
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Residues in contact with GLU 941 (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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892B LYS 4.3 2.9 - - - +
893B LEU* 3.6 10.0 - - - +
894B ARG* 2.8 41.4 + - + +
937B ARG* 2.9 50.2 + - + +
938B MET* 4.1 2.2 - - - +
940B TRP* 1.3 88.1 - - + +
942B GLN* 1.3 68.0 + - - +
943B ASN* 3.2 6.4 + - - +
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Residues in contact with GLN 942 (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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891B VAL* 4.0 9.1 - - + +
892B LYS 4.5 9.1 + - - -
911B TYR* 2.9 40.5 + - - -
922B ILE* 4.0 17.0 - - + -
938B MET* 2.8 31.7 + - + +
941B GLU* 1.3 78.4 + - + +
943B ASN* 1.3 70.6 + - - +
944B THR* 3.2 13.8 + - - +
1054B GLY* 3.4 16.3 - - - -
1055B PRO* 3.8 9.4 - - + +
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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