Contacts of the helix formed by residues 908 - 922 (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 SER 908 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906u GLU 3.9 1.5 + - - -
907u ASP* 1.3 75.3 - - - +
909u VAL* 1.3 64.4 + - - +
910u MET 3.3 2.0 - - - -
911u LEU* 3.4 15.9 + - - +
912u ASN* 3.2 21.8 + - - +
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Residues in contact with VAL 909 (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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866u LYS* 6.5 0.7 - - + -
869u MET* 5.8 2.6 - - - +
870u GLU* 6.2 4.3 - - + -
907u ASP* 3.6 8.2 - - + +
908u SER* 1.3 78.0 - - - +
910u MET* 1.3 59.1 + - - +
912u ASN* 3.5 6.0 + - - +
913u GLY* 2.9 24.4 + - - -
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Residues in contact with MET 910 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869u MET* 5.3 13.7 - - + -
899u ALA* 6.0 5.8 - - + +
900u PHE* 6.1 5.2 - - + -
907u ASP* 5.1 4.3 + - - +
908u SER* 3.3 0.6 - - - +
909u VAL* 1.3 76.5 - - - +
911u LEU* 1.3 60.1 + - - +
913u GLY* 3.7 1.9 - - - +
914u PHE* 2.9 30.0 + - - +
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Residues in contact with LEU 911 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907u ASP 5.4 0.8 + - - +
908u SER* 3.4 22.4 + - - +
909u VAL 3.3 0.8 - - - -
910u MET* 1.3 78.2 - - - +
912u ASN* 1.3 56.9 + - - +
914u PHE* 3.3 6.1 + - - +
915u GLY* 2.9 24.4 + - - -
953u ASP* 5.5 14.1 - - + +
954u LEU* 6.4 1.3 - - - -
957u ARG* 4.8 7.0 - - - +
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Residues in contact with ASN 912 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873u GLU* 5.2 1.3 - - - -
908u SER 3.2 12.6 + - - +
909u VAL* 4.1 5.4 - - - +
911u LEU* 1.3 77.0 - - - +
913u GLY* 1.3 61.2 + - - +
915u GLY* 3.8 2.1 - - - +
916u THR* 2.9 30.1 + - - -
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Residues in contact with GLY 913 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869u MET* 5.2 4.0 - - - -
873u GLU* 3.7 26.6 - - - +
909u VAL 2.9 17.8 + - - -
910u MET* 3.7 3.1 - - - -
912u ASN* 1.3 74.5 - - - +
914u PHE* 1.3 58.7 + - - +
916u THR* 3.3 2.8 + - - -
917u VAL* 2.9 29.0 + - - +
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Residues in contact with PHE 914 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896u ILE* 5.9 9.0 - - + -
910u MET 2.9 16.7 + - - +
911u LEU* 3.7 5.8 - - - +
913u GLY* 1.3 74.0 - - - +
915u GLY* 1.3 59.1 + - - +
917u VAL* 3.3 7.4 + - - +
918u VAL* 2.9 30.5 + - - +
954u LEU* 6.5 0.9 - - + -
957u ARG* 6.2 1.3 - - + -
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Residues in contact with GLY 915 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911u LEU 2.9 14.5 + - - -
912u ASN* 3.8 4.5 - - - -
913u GLY 3.3 0.2 - - - -
914u PHE* 1.3 77.8 - - - +
916u THR* 1.3 55.8 + - - +
918u VAL* 3.9 3.8 - - - +
919u ASN* 2.9 30.8 + - - +
957u ARG* 4.4 21.9 - - - +
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Residues in contact with THR 916 (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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873u GLU* 4.6 19.1 - - - -
876u MET* 5.3 4.9 - - - +
877u GLY* 5.3 9.2 - - - -
912u ASN 2.9 18.0 + - - -
913u GLY* 3.3 6.5 + - - -
915u GLY* 1.3 73.0 - - - +
917u VAL* 1.3 59.9 - - - +
919u ASN* 3.4 5.8 + - - +
920u ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 917 (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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876u MET* 5.4 8.0 - - + +
913u GLY 2.9 17.6 + - - +
914u PHE* 3.7 7.9 - - - +
915u GLY 3.3 0.2 - - - -
916u THR* 1.3 75.4 - - - +
918u VAL* 1.3 58.0 + - - +
920u ALA* 3.3 6.0 + - - +
921u LEU* 2.9 28.3 + - - +
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Residues in contact with VAL 918 (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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914u PHE 2.9 17.5 + - - +
915u GLY* 4.3 3.4 - - - +
917u VAL* 1.3 75.5 - - - +
919u ASN* 1.3 58.0 + - - +
921u LEU* 4.3 5.8 - - - -
922u GLY* 2.9 27.7 + - - -
925u VAL* 5.6 6.8 - - + +
957u ARG 6.0 1.6 - - - +
958u THR* 5.7 9.6 - - - -
961u VAL* 3.9 21.4 - - + +
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Residues in contact with ASN 919 (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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915u GLY 2.9 19.8 + - - +
916u THR* 3.8 6.3 - - - +
918u VAL* 1.3 78.8 - - - +
920u ALA* 1.3 58.8 + - - +
921u LEU 4.6 0.3 - - - -
922u GLY* 4.2 5.6 + - - -
961u VAL* 5.0 4.2 - - - +
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Residues in contact with ALA 920 (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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876u MET* 4.3 21.3 - - + +
880u GLY* 4.8 1.6 - - - -
881u ALA* 3.9 31.6 - - + +
916u THR 2.9 17.0 + - - +
917u VAL* 3.3 6.3 + - - +
919u ASN* 1.3 75.3 - - - +
921u LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 921 (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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881u ALA* 4.9 4.2 - - - +
917u VAL 2.9 16.8 + - - +
918u VAL* 3.8 5.2 - - - +
919u ASN 3.3 0.2 - - - -
920u ALA* 1.3 80.6 - - - +
922u GLY* 1.3 60.8 + - - +
923u LYS 3.1 8.0 + - - -
924u ARG* 3.5 18.7 + - + +
925u VAL* 4.0 26.2 - - + +
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Residues in contact with GLY 922 (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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918u VAL 2.9 20.3 + - - -
919u ASN* 4.2 5.1 + - - -
920u ALA 3.7 1.0 - - - -
921u LEU* 1.3 70.6 - - - +
923u LYS* 1.3 60.7 + - - -
924u ARG 3.6 0.3 + - - -
925u VAL* 3.9 11.6 + - - +
961u VAL* 4.2 13.8 - - - +
964u THR* 5.2 7.6 - - - -
965u CYS* 4.0 15.7 - - - +
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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