Contacts of the helix formed by residues 948 - 964 (chain u) in PDB entry 6FF7
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 ARG 948 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939u ARG 5.1 2.0 - - - -
940u LEU* 4.5 19.3 - - - +
941u ASN 5.1 4.5 - - - +
944u SER* 6.0 4.5 - - - -
946u LYS* 3.4 4.8 - - - -
947u VAL* 1.3 76.7 - - - +
949u GLN* 1.3 65.5 + - - +
950u GLN 3.2 2.2 + - - -
951u ALA* 3.5 11.8 + - - +
952u ALA* 3.5 18.7 + - - +
989u VAL* 4.6 17.2 - - + +
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Residues in contact with GLN 949 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946u LYS 4.5 5.8 + - - +
948u ARG* 1.3 75.3 - - - +
950u GLN* 1.3 60.6 + - - +
952u ALA* 3.9 0.9 - - - -
953u ASP* 2.9 30.5 + - - +
988u GLU* 3.4 27.1 - - + +
989u VAL* 4.2 8.2 - - - +
992u SER* 3.5 18.0 - - - -
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Residues in contact with GLN 950 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900u PHE 6.1 1.3 - - - +
946u LYS 5.6 0.4 + - - -
947u VAL* 5.6 6.3 - - + +
948u ARG* 3.2 3.2 - - - +
949u GLN* 1.3 77.0 - - - +
951u ALA* 1.3 60.8 + - - +
953u ASP* 3.5 5.9 + - - +
954u LEU* 2.9 29.5 + - - +
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Residues in contact with ALA 951 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936u VAL* 4.3 30.8 - - + +
939u ARG* 4.6 13.9 - - + -
940u LEU* 4.8 12.6 - - + -
947u VAL 5.9 0.6 - - - +
948u ARG* 3.5 11.6 + - - +
949u GLN 3.3 0.4 - - - -
950u GLN* 1.3 79.5 - - - +
952u ALA* 1.3 56.3 + - - +
954u LEU* 3.2 8.1 + - - +
955u ILE* 2.9 27.2 + - - +
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Residues in contact with ALA 952 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948u ARG 3.5 10.1 + - - +
949u GLN 4.0 0.7 - - - +
950u GLN 3.4 0.2 - - - -
951u ALA* 1.3 75.6 - - - +
953u ASP* 1.3 61.1 + - - +
955u ILE* 3.2 5.9 + - - -
956u SER* 2.9 23.2 + - - -
989u VAL 5.0 1.1 - - - +
992u SER* 3.4 36.6 - - - +
993u ILE* 3.8 9.6 - - + +
996u ALA* 3.3 15.2 - - + +
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Residues in contact with ASP 953 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911u LEU* 5.5 12.2 - - + +
949u GLN 2.9 19.9 + - - +
950u GLN* 3.9 6.5 - - - +
952u ALA* 1.3 76.5 - - - +
954u LEU* 1.3 57.3 + - - +
956u SER* 3.2 9.6 + - - -
957u ARG* 2.9 27.0 + - - +
992u SER* 4.3 7.3 - - - -
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Residues in contact with LEU 954 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911u LEU* 6.2 1.8 - - - +
914u PHE* 6.5 1.1 - - + -
936u VAL* 6.0 4.0 - - + -
950u GLN 2.9 18.2 + - - +
951u ALA* 3.4 10.3 - - - +
952u ALA 3.2 0.2 - - - -
953u ASP* 1.3 75.2 - - - +
955u ILE* 1.3 58.8 + - - +
957u ARG* 3.3 6.7 + - - +
958u THR* 2.9 31.2 + - - -
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Residues in contact with ILE 955 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951u ALA 2.9 13.3 + - - +
952u ALA* 3.2 11.0 + - - +
954u LEU* 1.3 76.4 - - - +
956u SER* 1.3 56.8 + - - +
958u THR* 3.3 5.1 + - - +
959u ALA* 2.9 30.8 + - - +
996u ALA* 4.2 12.3 - - + -
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Residues in contact with SER 956 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952u ALA 2.9 14.4 + - - -
953u ASP* 3.2 12.7 + - - -
955u ILE* 1.3 76.6 - - - +
957u ARG* 1.3 61.3 + - - +
959u ALA* 3.9 4.5 - - - +
960u VAL* 5.0 0.7 + - - +
992u SER 5.4 0.2 - - - -
995u GLY 3.9 9.9 - - - -
996u ALA* 3.8 19.9 - - - +
999u ALA* 3.7 23.9 - - - +
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Residues in contact with ARG 957 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911u LEU* 4.8 8.3 - - + +
914u PHE* 5.7 1.1 - - + -
915u GLY* 4.4 24.6 - - - +
918u VAL* 6.0 1.7 - - - +
953u ASP 2.9 15.4 + - - +
954u LEU* 3.7 7.6 - - - +
955u ILE 3.2 0.2 - - - -
956u SER* 1.3 79.0 - - - +
958u THR* 1.3 56.9 + - - +
959u ALA 3.2 4.6 + - - -
960u VAL* 3.8 12.8 + - - +
961u VAL* 4.8 1.9 + - - +
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Residues in contact with THR 958 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918u VAL* 5.7 8.1 - - - -
954u LEU 2.9 17.2 + - - -
955u ILE* 3.6 5.8 - - - -
957u ARG* 1.3 72.1 - - - +
959u ALA* 1.3 64.3 + - - +
960u VAL 3.2 1.7 + - - -
961u VAL* 4.1 8.8 - - - +
962u MET* 3.6 22.5 + - - +
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Residues in contact with ALA 959 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955u ILE 2.9 15.8 + - - +
956u SER 3.9 3.1 - - - +
957u ARG 3.2 1.6 - - - -
958u THR* 1.3 78.6 - - - +
960u VAL* 1.3 61.6 + - - +
962u MET* 4.0 7.5 + - - +
963u LYS* 4.1 6.4 + - - +
996u ALA 5.5 0.7 - - - +
999u ALA* 3.8 39.0 - - + +
1000u ILE* 4.5 3.8 - - + +
1003u VAL* 3.7 15.6 - - + +
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Residues in contact with VAL 960 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956u SER 5.0 0.6 + - - -
957u ARG 3.8 9.4 + - - +
958u THR 3.2 0.4 - - - -
959u ALA* 1.3 78.4 - - - +
961u VAL* 1.3 65.6 + - + +
962u MET 3.3 0.7 + - - -
963u LYS* 3.4 13.2 + - - +
964u THR* 3.6 11.3 + - - -
1003u VAL* 4.7 9.0 - - + -
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Residues in contact with VAL 961 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918u VAL* 3.9 35.0 - - + +
919u ASN* 5.0 3.1 - - - +
922u GLY* 4.2 12.9 - - - +
925u VAL* 6.6 0.2 - - + -
957u ARG 4.8 1.7 + - - +
958u THR* 3.8 10.3 + - - +
959u ALA 3.5 0.2 - - - -
960u VAL* 1.3 79.6 - - + +
962u MET* 1.3 59.9 + - - +
963u LYS 3.4 0.2 - - - -
964u THR* 3.7 8.7 + - - +
965u CYS* 3.4 22.5 + - - +
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Residues in contact with MET 962 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929u LEU* 6.4 2.5 - - + -
958u THR 3.6 15.8 + - - +
959u ALA* 4.5 4.0 - - - +
960u VAL 3.3 1.0 - - - -
961u VAL* 1.3 78.4 - - - +
963u LYS* 1.3 61.9 + - - +
965u CYS* 3.5 8.1 + - - -
967u GLU* 3.1 46.1 + - + +
971u MET* 6.2 2.5 - - + -
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Residues in contact with LYS 963 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959u ALA 4.1 8.9 + - - +
960u VAL 3.4 9.1 + - - +
961u VAL 3.4 0.6 - - - -
962u MET* 1.3 78.6 - - - +
964u THR* 1.3 57.1 + - - +
965u CYS 3.2 3.2 + - - -
966u GLN* 3.5 11.3 + - - -
967u GLU 4.7 4.0 - - - +
1003u VAL* 4.6 20.2 - - + +
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Residues in contact with THR 964 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922u GLY* 5.5 7.0 - - - -
923u LYS* 4.9 10.9 + - - +
960u VAL 3.6 11.1 + - - -
961u VAL* 3.7 8.2 + - - -
963u LYS* 1.3 77.4 - - - +
965u CYS* 1.3 56.6 + - - +
966u GLN 3.5 0.9 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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