Contacts of the helix formed by residues 918 - 934 (chain C) in PDB entry 6VVT
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 ASN 918 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C ASP* 3.7 10.4 - - - +
592C ASP 6.0 1.1 - - - +
595C ARG* 4.0 29.1 - - + +
880C HIS* 3.6 32.9 + - - +
882C ASN* 4.0 16.2 - - - +
911C HIS* 4.3 9.4 - - + -
912C GLY* 4.9 7.4 - - - +
916C ARG 2.9 9.5 + - - +
917C MET* 1.3 82.6 - - - +
919C ILE* 1.3 63.2 + - - +
920C GLY 3.4 0.4 - - - -
921C GLN* 3.6 31.9 + - - +
922C ILE* 4.2 6.9 + - - +
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Residues in contact with ILE 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C HIS* 2.9 54.3 - - + +
591C ASP* 3.7 0.6 + - - -
917C MET* 4.4 15.0 - - + -
918C ASN* 1.3 72.7 - - - +
920C GLY* 1.3 66.8 + - - +
922C ILE* 2.9 26.3 + - + +
923C LEU* 3.4 25.5 + - + -
732D MET* 6.3 2.2 - - + -
735D VAL* 5.0 24.0 - - + -
736D LEU 6.1 0.4 - - - +
839D PHE* 4.2 13.7 - - + +
840D ARG* 5.0 7.6 - - + -
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Residues in contact with GLY 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C PHE* 3.8 17.8 - - - -
590C HIS* 4.0 3.3 - - - +
591C ASP* 2.6 30.9 + - - -
880C HIS* 3.5 18.2 - - - -
919C ILE* 1.3 76.4 - - - +
921C GLN* 1.3 60.8 + - - +
923C LEU* 3.2 13.0 + - - +
924C GLU 3.3 10.6 + - - -
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Residues in contact with GLN 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C ASP* 4.0 0.4 + - - -
714C ILE* 5.2 9.7 - - - +
880C HIS* 3.5 18.7 - - + -
882C ASN* 3.3 26.7 + - - +
908C LEU* 4.5 16.2 - - - +
909C ASN 5.4 4.4 + - - -
911C HIS* 5.9 4.6 - - - +
918C ASN* 3.6 26.0 + - - +
919C ILE 3.0 0.8 + - - -
920C GLY* 1.3 77.9 - - - +
922C ILE* 1.3 72.7 + - + +
923C LEU 3.3 0.2 + - - -
924C GLU* 3.4 3.8 - - - +
925C THR* 2.8 29.4 + - - +
1019C MET* 3.4 30.6 - - + -
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Residues in contact with ILE 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C ILE* 3.5 32.1 - - + -
917C MET 6.0 0.7 - - - +
918C ASN 4.5 8.1 - - - +
919C ILE* 2.9 21.5 + - + +
921C GLN* 1.3 87.5 - - + +
923C LEU* 1.3 65.5 + - - +
925C THR* 3.3 5.4 + - - +
926C HIS* 3.3 41.2 + - + +
730D VAL* 4.1 29.2 - - + +
731D SER* 4.0 19.5 - - - +
732D MET* 4.2 4.5 - - + +
735D VAL* 5.7 2.2 - - + -
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Residues in contact with LEU 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C PHE* 3.3 34.3 - - + -
590C HIS* 3.4 48.0 - - + +
919C ILE* 3.7 25.8 - - + +
920C GLY 3.2 2.0 + - - +
921C GLN 3.2 0.8 - - - -
922C ILE* 1.3 77.0 - - + +
924C GLU* 1.3 62.8 + - - +
926C HIS* 3.1 7.5 + - - +
927C LEU* 3.0 22.0 + - - +
973C GLU* 6.2 1.1 - - - -
976C LEU* 4.6 9.5 - - + +
732D MET* 4.3 34.1 - - + -
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Residues in contact with GLU 924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586C PRO* 4.6 3.1 - - + -
587C PHE* 3.2 20.9 - - + -
617C VAL* 3.7 20.3 - - + +
879C ARG* 2.9 32.8 + - - -
880C HIS* 2.7 33.3 + - - +
920C GLY 3.3 2.0 + - - +
921C GLN 3.4 11.4 - - - +
923C LEU* 1.3 78.9 - - - +
925C THR* 1.3 56.0 + - - +
927C LEU* 4.3 3.8 - - - -
928C GLY* 2.7 27.9 + - - -
1018C TYR 3.3 6.8 - - - +
1019C MET* 3.6 20.7 - - + +
1020C TYR 3.2 19.2 + - - +
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Residues in contact with THR 925 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C VAL* 3.4 30.8 - - + +
714C ILE* 4.6 16.6 - - + +
921C GLN* 2.8 20.3 + - - +
922C ILE* 3.5 12.5 - - - -
923C LEU 3.1 0.6 - - - -
924C GLU* 1.3 80.0 - - - +
926C HIS* 1.3 62.4 + - - +
928C GLY 3.3 1.0 + - - -
929C TRP 3.2 15.6 + - - -
1015C THR* 5.0 4.0 - - + -
1016C VAL 4.4 4.5 - - - +
1017C GLY* 3.5 13.7 - - - +
1018C TYR 3.4 14.7 + - - -
1019C MET* 4.0 17.2 - - - +
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Residues in contact with HIS 926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C ILE* 3.3 22.2 + - + +
923C LEU* 3.1 6.8 + - - +
925C THR* 1.3 75.7 - - + +
927C LEU* 1.3 67.4 + - - +
929C TRP* 3.0 9.3 + - - +
930C VAL* 2.9 25.6 + - - +
976C LEU* 4.7 4.5 - - + -
980C LEU* 4.3 24.1 - - + +
996C ASP 4.0 6.1 + - - -
997C GLY* 3.8 25.2 + - - -
1015C THR* 3.5 31.3 - - + +
1016C VAL 4.5 4.2 + - - -
731D SER* 3.9 2.4 - - - -
732D MET* 3.4 46.1 + - + +
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Residues in contact with LEU 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 4.8 1.8 - - + -
587C PHE* 3.7 13.0 - - + -
617C VAL* 3.7 26.7 - - + -
923C LEU 3.0 16.1 + - - +
924C GLU* 4.0 3.8 - - - +
926C HIS* 1.3 75.1 - - - +
928C GLY* 1.3 53.3 + - - +
930C VAL* 3.1 21.5 + - + -
931C ALA* 2.7 36.4 + - + +
935C TRP* 5.7 0.4 - - + -
963C VAL* 4.2 27.6 - - + -
965C THR* 3.7 23.3 - - + -
971C ALA* 4.7 7.4 - - + -
976C LEU* 4.1 17.1 - - + +
979C LEU* 4.8 10.1 - - + -
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Residues in contact with GLY 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU* 3.5 10.8 - - - +
617C VAL* 4.5 9.8 - - - +
924C GLU 2.7 16.2 + - - -
925C THR 3.6 0.2 - - - -
926C HIS 3.1 0.4 - - - -
927C LEU* 1.3 74.4 - - - +
929C TRP* 1.3 56.5 + - - +
931C ALA* 4.8 2.7 - - - -
932C LYS* 3.0 28.4 + - - +
1018C TYR* 3.3 30.1 - - - +
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Residues in contact with TRP 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C LEU* 4.4 9.2 - - + -
898C LEU* 4.3 16.4 - - + -
925C THR 3.2 5.0 + - - +
926C HIS* 3.0 10.9 + - - +
928C GLY* 1.3 73.1 - - - +
930C VAL* 1.3 70.6 + - + +
932C LYS* 3.3 4.3 + - + +
933C ALA* 3.0 30.6 + - + +
980C LEU* 5.3 5.6 - - + -
983C THR* 3.7 31.6 - - + +
984C LEU 6.0 0.2 - - - -
992C MET* 3.7 27.4 - - + -
993C VAL* 3.3 47.6 - - + +
1016C VAL* 4.6 4.0 - - + +
1017C GLY* 4.0 17.9 - - - -
1018C TYR* 3.9 32.1 - + - +
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Residues in contact with VAL 930 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C HIS 2.9 18.6 + - - +
927C LEU* 3.4 14.8 - - + +
929C TRP* 1.3 80.6 - - + +
931C ALA* 1.3 58.3 + - - +
933C ALA* 3.2 1.1 + - - -
934C GLY* 2.8 39.4 + - - +
935C TRP* 3.3 29.3 - - + -
976C LEU* 5.3 1.1 - - + -
979C LEU* 3.7 48.2 - - + +
980C LEU* 4.4 16.8 - - + -
982C SER 5.2 0.2 - - - +
983C THR* 5.5 2.9 - - - +
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Residues in contact with ALA 931 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU* 3.8 21.3 - - + +
617C VAL* 5.5 0.9 - - + -
927C LEU* 2.7 20.9 + - + +
928C GLY* 4.1 0.9 - - - +
930C VAL* 1.3 73.8 - - - +
932C LYS* 1.3 56.7 + - - +
934C GLY 3.9 2.6 + - - -
935C TRP* 4.3 10.5 - - - -
958C PRO 4.3 0.2 - - - +
960C ASP* 3.0 4.5 + - - -
961C SER* 2.9 50.2 + - - +
963C VAL* 3.9 16.6 - - + -
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Residues in contact with LYS 932 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LEU* 3.8 15.9 - - + +
928C GLY 3.0 19.7 + - - +
929C TRP* 3.7 8.7 - - + +
930C VAL 3.2 0.6 - - - -
931C ALA* 1.3 78.6 - - - +
933C ALA* 1.3 57.4 + - + +
959C ALA* 3.5 6.8 - - - +
960C ASP* 2.8 47.6 + - - +
1018C TYR* 3.3 46.4 + - + -
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Residues in contact with ALA 933 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929C TRP* 3.0 30.1 + - + +
930C VAL* 5.3 0.4 - - - -
932C LYS* 1.3 76.9 - - + +
934C GLY* 1.3 65.2 + - - +
959C ALA* 3.9 10.4 - - - +
983C THR* 4.0 24.7 - - + -
984C LEU* 3.3 32.9 - - - +
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Residues in contact with GLY 934 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930C VAL* 2.8 17.9 + - - +
931C ALA 3.9 0.8 + - - -
932C LYS 3.6 1.6 - - - -
933C ALA* 1.3 84.9 - - - +
935C TRP* 1.3 74.9 + - - +
957C ALA 3.3 14.8 - - - -
958C PRO 3.3 17.3 + - - -
982C SER 3.7 7.3 - - - +
983C THR* 4.1 4.0 + - - -
984C LEU* 3.3 2.6 - - - +
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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
------------------------------------------------------------
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