Contacts of the strand formed by residues 708 - 713 (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 LYS 708 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609C LEU* 3.3 25.3 - - + +
611C ARG* 3.3 23.0 - - - +
612C SER* 3.4 11.6 - - - +
613C GLU* 3.2 48.5 - - + +
707C GLY* 1.3 73.6 - - - +
709C ASN* 1.3 60.5 + - - +
710C LEU* 3.1 25.6 - - + +
737C VAL* 2.5 50.8 + - + +
738C LEU* 4.1 4.0 - - + +
1020C TYR* 3.4 9.5 - - - -
1021C ILE 3.1 25.5 + - - -
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Residues in contact with ASN 709 (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* 3.1 30.3 + - - +
614C ALA 2.9 24.7 + - - -
616C LEU* 3.0 40.3 + - + +
617C VAL* 5.8 0.5 - - - +
708C LYS* 1.3 72.2 - - - +
710C LEU* 1.3 63.8 + - - +
731C ARG* 5.1 4.2 + - - -
737C VAL* 6.0 0.2 - - - +
905C ASP* 4.5 1.7 - - - +
1018C TYR* 4.2 19.0 - - + -
1019C MET 3.9 4.6 - - - +
1020C TYR* 2.9 31.9 + - - +
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Residues in contact with LEU 710 (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* 3.1 37.2 - - + +
709C ASN* 1.3 77.4 - - - +
711C LEU* 1.3 63.6 + - - +
712C VAL* 3.5 1.8 + - - +
731C ARG* 5.2 0.7 - - - +
732C LEU* 3.3 41.5 - - + -
737C VAL* 4.9 2.9 - - + -
738C LEU* 4.6 4.7 - - + -
905C ASP* 3.5 14.4 - - + +
906C ILE* 3.5 13.9 - - + +
1018C TYR* 3.1 28.1 - - - -
1019C MET 3.1 13.8 + - - +
1021C ILE* 3.2 35.9 - - + -
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Residues in contact with LEU 711 (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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710C LEU* 1.3 70.5 - - - +
712C VAL* 1.3 59.7 + - - +
898C LEU* 4.6 9.6 - - + -
902C THR* 4.2 19.3 - - + +
903C PRO 3.4 24.9 - - - +
904C VAL* 3.5 21.6 - - + -
905C ASP* 2.8 43.1 + - - +
906C ILE* 3.0 11.6 + - - +
929C TRP* 4.4 12.6 - - + -
1016C VAL* 5.0 4.5 - - + -
1017C GLY 3.3 21.1 - - - +
1018C TYR* 3.6 35.2 - - + +
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Residues in contact with VAL 712 (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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710C LEU 3.5 2.9 + - - +
711C LEU* 1.3 74.5 - - - +
713C ALA* 1.3 71.8 + - - +
714C ILE* 4.6 6.5 - - + -
904C VAL* 4.8 2.5 - - - -
906C ILE* 3.3 15.3 - - + +
908C LEU* 3.5 38.8 - - + -
925C THR* 3.4 30.5 - - + +
1016C VAL* 3.0 9.8 - - - +
1017C GLY 2.6 45.5 + - - +
1018C TYR 4.2 0.7 - - - +
1019C MET* 4.4 13.2 - - + +
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Residues in contact with ALA 713 (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* 1.3 77.1 - - - +
714C ILE* 1.3 59.5 + - - +
715C MET* 3.2 16.9 + - + -
896C PRO* 5.1 0.4 - - + -
904C VAL* 4.3 16.6 - - + -
906C ILE 3.2 5.4 + - - +
907C ILE* 3.5 7.3 - - + +
908C LEU 2.9 24.1 + - - -
1001C LEU* 3.8 28.7 - - + -
1015C THR 3.3 9.0 - - - +
1016C VAL* 4.3 2.7 - - + -
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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