Contacts of the helix formed by residues 928 - 940 (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 TYR 928 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893u ILE* 5.4 11.4 - - + -
925u VAL* 3.5 19.1 - - + +
926u LYS 3.1 1.8 + - - -
927u PRO* 1.3 78.8 - - - +
929u LEU* 1.3 62.0 + - - +
930u PRO 3.5 2.7 - - - -
931u GLN* 3.3 11.3 + - - +
932u ILE* 3.1 28.5 + - + +
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Residues in contact with LEU 929 (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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925u VAL 3.5 10.1 + - - +
926u LYS* 3.9 8.5 + - - +
928u TYR* 1.3 74.3 - - - +
930u PRO* 1.4 60.3 - - - +
932u ILE* 4.5 5.4 - - - -
933u CYS* 2.9 32.2 + - - +
962u MET* 6.4 2.0 - - + -
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Residues in contact with PRO 930 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926u LYS 5.3 1.2 - - - -
928u TYR 3.5 0.6 - - - -
929u LEU* 1.4 76.8 - - - +
931u GLN* 1.3 58.0 + - - +
933u CYS* 4.2 2.9 - - + +
934u GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 931 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928u TYR* 3.3 14.0 + - - +
930u PRO* 1.3 78.4 - - - +
932u ILE* 1.3 58.0 + - - +
934u GLY* 3.4 1.5 + - - -
935u THR* 2.9 28.9 + - - -
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Residues in contact with ILE 932 (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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928u TYR* 3.1 17.7 + - + +
929u LEU* 4.1 5.6 - - - +
931u GLN* 1.3 75.2 - - - +
933u CYS* 1.3 59.8 + - - +
935u THR* 3.2 8.9 + - - -
936u VAL* 2.9 27.4 + - - +
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Residues in contact with CYS 933 (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 2.9 19.5 + - - +
930u PRO* 4.2 3.1 - - + +
932u ILE* 1.3 76.7 - - - +
934u GLY* 1.3 58.0 + - - +
936u VAL* 3.3 7.8 + - - +
937u LEU* 2.9 29.9 + - - +
970u LEU* 6.0 5.8 - - + -
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Residues in contact with GLY 934 (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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930u PRO 2.9 18.8 + - - -
931u GLN* 3.8 1.3 - - - -
933u CYS* 1.3 73.2 - - - +
935u THR* 1.3 60.5 + - - +
937u LEU* 3.8 5.6 - - - +
938u TRP* 2.9 31.7 + - - +
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Residues in contact with THR 935 (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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897u LEU* 6.2 4.5 - - - -
931u GLN 2.9 15.8 + - - -
932u ILE* 3.4 11.7 - - - -
934u GLY* 1.3 75.2 - - - +
936u VAL* 1.3 56.6 + - - +
938u TRP* 3.9 4.0 - - - +
939u ARG* 2.8 32.3 + - - +
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Residues in contact with VAL 936 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932u ILE 2.9 15.4 + - - +
933u CYS* 3.6 9.2 - - - +
934u GLY 3.2 0.2 - - - -
935u THR* 1.3 78.0 - - - +
937u LEU* 1.3 57.4 + - - +
939u ARG* 3.1 7.1 + - - +
940u LEU* 3.0 31.4 + - - +
951u ALA* 4.3 20.4 - - + +
954u LEU* 6.0 3.8 - - + -
955u ILE* 6.3 2.5 - - + +
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Residues in contact with LEU 937 (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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933u CYS 2.9 18.4 + - - +
934u GLY* 4.0 5.6 - - - +
936u VAL* 1.3 76.1 - - - +
938u TRP* 1.3 60.1 + - - +
940u LEU* 4.0 13.7 + - - +
941u ASN* 5.1 0.5 + - - +
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Residues in contact with TRP 938 (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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1755A SER* 5.7 4.0 - - - -
1760A GLU* 5.6 11.9 - - + -
934u GLY 2.9 17.1 + - - +
935u THR* 4.1 4.3 - - - +
937u LEU* 1.3 75.2 - - - +
939u ARG* 1.3 63.5 + - - +
940u LEU 3.2 1.5 + - - -
941u ASN* 3.8 12.6 + - - +
942u ASN* 4.6 2.8 + - - +
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Residues in contact with ARG 939 (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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935u THR 2.8 21.7 + - - +
936u VAL* 3.1 8.7 + - - +
938u TRP* 1.3 75.8 - - - +
940u LEU* 1.3 56.0 + - - +
941u ASN 3.0 7.6 + - - -
942u ASN* 3.3 21.4 - - + +
947u VAL 3.8 9.0 - - - +
948u ARG* 5.1 0.5 - - - -
951u ALA* 4.6 10.5 - - + +
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Residues in contact with LEU 940 (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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936u VAL 3.0 14.5 + - - +
937u LEU* 4.1 12.3 - - - +
938u TRP 3.2 2.2 - - - -
939u ARG* 1.3 74.3 - - - +
941u ASN* 1.3 57.7 + - - +
948u ARG* 4.5 15.6 - - - +
951u ALA* 4.8 11.9 - - + -
981u TYR* 6.5 0.7 - - + -
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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