Contacts of the helix formed by residues 931 - 943 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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877A LYS* 3.5 47.3 - - + +
907A ILE* 5.6 9.0 - - + -
925A GLN* 4.4 4.1 + - - +
927A PRO* 3.6 6.8 - - - +
928A LEU* 2.7 42.0 + - + +
930A SER* 1.3 79.5 + - - +
932A PHE* 1.3 62.8 + - - -
933A GLU 3.3 2.9 - - - -
934A ASP* 3.4 16.6 + - + +
935A PHE* 2.9 23.0 + - - +
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Residues in contact with PHE 932 (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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927A PRO* 3.9 15.9 - - + -
928A LEU 3.1 25.1 + - - -
929A LYS* 3.4 37.1 + - + +
930A SER 3.5 0.6 - - - -
931A THR* 1.3 76.8 - - - +
933A GLU* 1.3 63.9 + - + +
935A PHE* 3.2 6.4 + - - +
936A TRP* 3.1 29.4 + - + -
962A ASP* 3.6 18.4 - - + -
963A GLN 3.3 29.6 - - - -
964A TYR* 3.5 24.7 - - + -
973A TYR* 3.8 30.1 - + + -
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Residues in contact with GLU 933 (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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930A SER 5.1 2.4 + - - +
931A THR 3.3 0.4 - - - -
932A PHE* 1.3 76.1 - - + +
934A ASP* 1.3 72.1 + - - +
935A PHE 3.2 0.2 + - - -
936A TRP* 3.3 2.9 + - - +
937A ARG* 2.9 27.8 + - - +
973A TYR* 3.7 14.7 - - + +
974A GLY* 3.3 37.6 + - - +
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Residues in contact with ASP 934 (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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877A LYS* 4.2 23.0 - - - +
893A LEU* 3.7 33.5 - - + +
904A SER* 4.8 2.3 - - - +
906A TYR 4.2 5.3 - - - +
907A ILE* 4.1 11.4 - - + +
930A SER 4.6 3.7 - - - +
931A THR* 3.4 22.8 + - - +
933A GLU* 1.3 81.9 - - - +
935A PHE* 1.3 57.9 + - - +
937A ARG* 3.5 13.5 + - - -
938A MET* 3.0 29.8 + - - +
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Residues in contact with PHE 935 (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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907A ILE* 4.1 12.7 - - + +
924A THR* 4.3 9.9 - - + -
927A PRO* 3.2 35.7 - - + -
931A THR* 2.9 18.4 + - - +
932A PHE* 3.3 8.1 - - - +
933A GLU 3.1 0.2 - - - -
934A ASP* 1.3 76.7 - - - +
936A TRP* 1.3 73.2 + + - +
938A MET* 3.3 13.3 + - + +
939A ILE* 3.1 41.8 + - + +
947A ILE* 4.7 2.0 - - + -
964A TYR* 3.6 40.4 - + + -
1057A LEU* 3.8 37.5 - - + -
1059A HIS* 4.8 1.6 - + - -
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Residues in contact with TRP 936 (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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932A PHE* 3.1 24.5 + - - +
933A GLU 4.1 1.8 - - - +
935A PHE* 1.3 85.0 - + - +
937A ARG* 1.3 54.9 + - - +
939A ILE* 3.1 36.0 + - + +
940A TRP* 2.7 36.5 + - - +
947A ILE* 4.2 18.8 - - + -
964A TYR* 2.9 44.4 + + - +
965A TRP* 4.5 3.6 - - + -
973A TYR* 3.5 26.4 - + + +
976A ILE* 4.1 20.8 - - + +
978A VAL* 3.6 35.2 - - + -
994A PHE* 4.9 10.8 - + - -
996A ILE* 3.9 24.3 - - + +
1018A VAL* 4.6 4.5 - - + -
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Residues in contact with ARG 937 (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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893A LEU* 3.5 21.8 - - + +
894A ARG 2.8 24.2 + - - -
896A LEU* 3.4 37.1 - - - +
904A SER* 2.9 27.5 + - - -
933A GLU* 2.9 17.8 + - - +
934A ASP* 3.8 14.7 + - - +
936A TRP* 1.3 77.4 - - - +
938A MET* 1.3 54.2 + - - +
940A TRP* 3.6 7.5 - - + +
941A GLU* 2.7 75.3 + - + +
975A ASN* 6.2 0.2 - - - -
976A ILE* 4.5 14.2 - - + +
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Residues in contact with MET 938 (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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891A VAL* 3.9 25.1 - - + -
893A LEU* 3.9 15.4 - - + +
907A ILE* 3.7 27.1 - - + -
909A ALA* 3.7 26.2 - - + -
922A ILE* 3.9 14.4 - - + -
924A THR* 4.5 3.4 - - + -
934A ASP 3.0 17.1 + - - +
935A PHE* 3.5 11.7 - - + +
936A TRP 3.1 0.2 - - - -
937A ARG* 1.3 73.0 - - - +
939A ILE* 1.3 57.3 + - - +
941A GLU* 3.2 3.8 + - - +
942A GLN* 2.7 46.5 + - + +
1057A LEU* 3.5 32.1 - - + -
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Residues in contact with ILE 939 (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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935A PHE* 3.1 38.3 + - + +
936A TRP* 3.1 29.6 + - + +
938A MET* 1.3 77.5 - - - +
940A TRP* 1.3 63.7 + - - +
943A ASN* 3.3 1.7 + - - -
944A THR* 3.1 54.3 + - + +
947A ILE* 3.7 17.7 - - + -
996A ILE* 4.2 9.9 - - + +
1016A ARG* 4.5 0.9 + - - -
1018A VAL* 4.1 16.6 - - + -
1057A LEU* 3.9 17.3 - - + -
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Residues in contact with TRP 940 (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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936A TRP 2.7 19.3 + - - +
937A ARG* 3.6 4.7 - - + +
939A ILE* 1.3 75.6 - - - +
941A GLU* 1.3 74.3 + - + +
943A ASN* 3.1 5.5 + - - +
976A ILE* 4.1 17.5 - - + -
996A ILE* 3.4 40.8 - - + +
998A ASN* 3.2 54.9 - - + +
1000A LYS* 4.5 10.8 - - - +
1015A GLU* 4.3 11.7 - - + -
1016A ARG* 2.9 76.5 + - + +
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Residues in contact with GLU 941 (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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892A LYS 4.2 3.3 - - - +
893A LEU* 3.7 9.0 - - - +
894A ARG* 2.9 38.9 + - - +
896A LEU* 5.5 0.5 - - - +
937A ARG* 2.7 58.7 + - + +
938A MET* 4.0 2.9 - - - +
940A TRP* 1.3 83.5 - - + +
942A GLN* 1.3 71.2 + - - +
943A ASN* 3.4 1.1 + - - +
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Residues in contact with GLN 942 (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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891A VAL* 3.8 11.1 - - - +
892A LYS 4.2 10.3 + - - -
911A TYR* 2.7 35.1 + - - -
922A ILE* 3.6 21.3 - - + +
938A MET* 2.7 32.1 + - + +
941A GLU* 1.3 85.3 + - - +
943A ASN* 1.3 72.3 + - - +
944A THR* 3.6 15.5 - - - +
1054A GLY* 3.3 13.9 - - - -
1055A PRO* 3.6 9.1 - - + +
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Residues in contact with ASN 943 (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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939A ILE 3.3 1.1 + - - -
940A TRP 3.1 15.1 + - - +
941A GLU 3.4 1.9 - - - +
942A GLN* 1.3 80.7 - - - +
944A THR* 1.3 60.9 + - - +
945A GLY 3.8 0.7 + - - -
1016A ARG* 3.9 27.6 + - - +
1052A GLU 4.6 3.4 + - - -
1053A THR* 3.8 15.1 - - - +
1054A GLY* 2.7 42.1 + - - +
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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