Contacts of the strand formed by residues 1014 - 1023 (chain C) in PDB entry 6VVS
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 VAL1014 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714C ILE 4.2 0.9 - - - +
715C MET* 3.4 49.6 - - + +
998C LYS* 3.8 1.8 - - - -
999C SER* 2.6 42.5 + - - +
1001C LEU* 4.1 20.4 - - + +
1010C PHE* 4.6 13.0 - - + -
1012C TYR* 3.5 16.6 - - + +
1013C PRO* 1.3 73.9 - - - +
1015C THR* 1.3 71.2 + - - +
1016C VAL* 3.4 2.9 + - - +
727D GLY* 5.9 4.3 - - - -
729D THR* 3.5 13.2 - - + -
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Residues in contact with THR1015 (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 3.9 0.2 - - - +
713C ALA* 3.6 3.8 - - - -
714C ILE* 3.2 45.0 + - + +
922C ILE* 5.2 0.7 - - + -
925C THR* 4.7 3.8 - - + -
926C HIS* 3.4 24.0 - - + +
997C GLY 3.0 19.7 - - - +
998C LYS* 3.5 5.2 - - - +
1014C VAL* 1.3 75.8 - - - +
1016C VAL* 1.3 64.1 + - - +
729D THR* 3.7 8.7 + - - +
730D VAL 2.8 16.2 + - - +
731D SER* 2.2 29.2 + - - -
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Residues in contact with VAL1016 (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* 5.1 2.9 - - + -
712C VAL 3.1 13.0 - - - +
713C ALA* 4.8 0.4 - - + -
898C LEU* 3.9 19.3 - - + -
904C VAL* 4.7 5.8 - - + -
925C THR* 4.3 8.5 - - - +
926C HIS* 4.6 3.3 + - - -
929C TRP* 4.6 8.0 - - + +
993C VAL* 3.4 31.5 - - + +
997C GLY* 3.3 13.4 + - - +
999C SER* 4.1 4.0 - - - +
1001C LEU* 3.7 38.4 - - + -
1014C VAL 3.4 9.8 + - - +
1015C THR* 1.3 81.5 - - - +
1017C GLY* 1.3 60.9 + - - +
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Residues in contact with GLY1017 (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* 3.1 8.5 - - - +
712C VAL* 2.5 41.8 + - - +
925C THR* 3.4 13.0 - - - -
929C TRP* 3.9 16.4 - - - -
1016C VAL* 1.3 81.0 - - - +
1018C TYR* 1.3 63.5 + - - -
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Residues in contact with TYR1018 (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* 4.5 8.1 - - + -
617C VAL* 5.0 1.2 - - - +
709C ASN* 4.3 13.5 - - + +
710C LEU* 3.0 24.9 - - - +
711C LEU* 3.7 35.4 - - + +
902C THR* 5.4 5.4 - - - +
905C ASP* 5.2 1.8 - - - -
924C GLU* 3.1 22.5 - - - +
925C THR* 3.5 6.8 + - - -
928C GLY* 3.2 22.3 - - - +
929C TRP* 3.8 18.8 - + - +
932C LYS* 3.2 55.6 - - + -
1017C GLY* 1.3 75.6 - - - -
1019C MET* 1.3 59.2 + - - +
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Residues in contact with MET1019 (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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708C LYS 3.6 0.2 - - - +
709C ASN* 3.6 4.3 - - - -
710C LEU* 2.9 32.8 + - - +
712C VAL* 4.5 12.3 - - + +
878C GLY* 4.3 9.4 - - - -
880C HIS* 3.9 11.9 - - + -
882C ASN* 3.0 33.0 - - - +
906C ILE* 5.0 1.6 - - + -
908C LEU* 4.2 20.2 - - - -
921C GLN* 3.2 28.5 - - + -
924C GLU* 3.5 15.9 - - - +
925C THR* 4.0 20.0 - - - +
1017C GLY 4.2 0.6 - - - -
1018C TYR* 1.3 75.6 - - - +
1020C TYR* 1.3 67.8 + - - +
1021C ILE* 3.6 14.2 + - + +
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Residues in contact with TYR1020 (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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613C GLU 3.4 1.0 + - - -
614C ALA 3.9 2.9 - - - -
615C PRO* 3.4 31.1 - - + +
616C LEU 5.3 0.2 - - - +
617C VAL* 5.5 1.5 - - + +
704C MET 5.4 0.7 - - - -
705C ALA* 3.1 11.1 - - - -
706C LEU* 2.7 30.6 + - + -
707C GLY 2.7 37.2 + - - -
708C LYS 3.3 14.4 - - - -
709C ASN* 3.4 19.7 + - - +
878C GLY* 3.7 16.1 - - - -
879C ARG* 3.0 52.3 + - - +
924C GLU* 3.1 9.3 + - - +
1019C MET* 1.3 73.5 - - - +
1021C ILE* 1.3 60.6 + - - +
1022C LEU* 3.9 14.1 - - + +
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Residues in contact with ILE1021 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707C GLY* 3.3 1.0 - - - -
708C LYS 3.1 24.8 + - - -
710C LEU* 3.2 46.4 - - + -
738C LEU* 5.2 7.3 - - + +
876C LEU* 4.6 18.4 - - + -
877C ALA* 3.2 20.2 - - - +
878C GLY 4.5 1.6 - - - +
882C ASN* 5.6 0.9 - - - +
906C ILE* 3.9 28.5 - - + -
908C LEU* 5.8 2.9 - - + -
1019C MET* 4.4 19.1 - - + +
1020C TYR* 1.3 78.1 - - - +
1022C LEU* 1.3 65.6 + - - +
1023C LYS 4.3 0.3 + - - -
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Residues in contact with LEU1022 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602C MET* 4.0 7.2 - - + +
603C GLN* 3.9 39.3 - - + +
606C ALA* 4.1 4.5 - - + -
706C LEU* 3.5 31.0 - - + +
707C GLY* 4.1 0.2 - - - -
738C LEU* 5.9 1.6 - - - -
876C LEU* 3.3 9.5 - - - +
877C ALA* 2.6 40.3 + - + +
878C GLY* 4.8 7.2 - - - +
879C ARG* 4.7 9.9 - - + -
1020C TYR* 3.9 31.6 - - + +
1021C ILE* 1.3 82.4 - - - +
1023C LYS* 1.3 61.3 + - - +
1024C LEU* 3.5 11.7 - - + +
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Residues in contact with LYS1023 (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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606C ALA* 3.0 7.4 - - - -
607C VAL* 3.0 36.9 + - + +
609C LEU* 4.0 18.6 - - + +
706C LEU 4.3 3.8 + - - -
707C GLY* 5.0 1.8 - - - -
738C LEU* 3.2 39.0 + - + +
740C SER* 3.5 15.8 + - - +
868C ARG* 3.4 25.9 + - - +
869C LYS 4.2 9.3 + - - -
870C ILE* 4.0 24.5 - - + +
874C ASP* 4.3 3.0 + - + -
875C LYS 4.2 4.9 - - - +
876C LEU* 4.9 4.0 - - + +
1021C ILE 4.3 0.6 + - - -
1022C LEU* 1.3 72.9 - - - +
1024C LEU* 1.3 67.3 + - - +
1027C LEU* 3.9 22.9 - - + +
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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
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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