Contacts of the strand formed by residues 883 - 890 (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 883 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595C ARG* 5.2 1.2 - - - +
602C MET* 3.2 36.8 - - + -
724C ASP* 3.7 18.9 - - - +
726C ILE* 5.2 3.1 - - - -
875C LYS* 4.0 11.2 - - - +
876C LEU 3.4 6.5 - - - +
877C ALA* 3.8 3.1 - - + +
881C GLY 3.3 4.0 + - - +
882C ASN* 1.3 72.9 - - - +
884C GLY* 1.3 59.0 + - - +
537D ASP* 4.0 12.6 - - + +
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Residues in contact with GLY 884 (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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724C ASP 3.0 16.8 - - - -
726C ILE* 3.7 11.6 - - - +
875C LYS* 4.5 4.1 - - - +
876C LEU 3.0 31.0 + - - +
883C LYS* 1.3 77.6 - - - +
885C VAL* 1.3 67.5 + - - -
536D PHE 3.7 6.1 - - - -
537D ASP* 4.0 6.2 - - - +
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Residues in contact with VAL 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C ASP 3.7 0.4 + - - -
725C ALA* 4.7 2.9 - - + -
726C ILE* 2.9 27.4 + - - +
873C GLY 3.9 11.0 - - - +
874C ASP 3.2 9.9 - - - +
875C LYS* 4.8 4.9 - - + -
884C GLY* 1.3 76.9 - - - -
886C ILE* 1.3 62.1 + - - +
887C GLY 4.5 1.1 - - - +
429D VAL* 3.7 14.1 - - + -
430D ILE 3.6 19.5 - - - +
431D VAL* 3.7 14.8 - - + -
536D PHE* 3.1 19.5 + - + +
538D GLY* 3.0 37.9 - - - +
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Residues in contact with ILE 886 (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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726C ILE* 3.4 7.0 - - + +
728C LEU* 3.3 27.4 - - + -
870C ILE* 3.2 37.2 - - + -
871C SER 3.6 9.2 - - - +
872C ASP* 3.5 9.5 - - - +
873C GLY 2.9 29.8 + - - +
874C ASP 3.0 6.8 + - - +
876C LEU* 3.2 24.5 - - + -
885C VAL* 1.3 72.7 - - - +
887C GLY* 1.3 60.7 + - - +
888C LYS 3.6 20.9 - - - +
889C ILE* 3.6 18.2 - - + -
431D VAL* 3.5 7.8 - - - +
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Residues in contact with GLY 887 (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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720C HIS* 4.4 8.2 + - - -
725C ALA* 4.3 14.6 - - - -
726C ILE 2.6 14.1 + - - +
872C ASP* 4.7 4.2 - - - +
885C VAL 3.4 5.1 + - - -
886C ILE* 1.3 73.3 - - - +
888C LYS* 1.3 61.5 + - - +
431D VAL* 3.8 28.4 - - - +
432D VAL* 4.4 9.0 - - - +
523D GLN* 5.0 5.9 + - - -
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Residues in contact with LYS 888 (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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720C HIS* 3.5 40.8 - - + +
726C ILE 3.4 3.0 + - - -
727C ILE* 3.1 22.5 - - + +
728C LEU 3.1 20.6 + - - -
872C ASP* 4.7 5.4 - - - -
886C ILE* 3.4 3.8 - - - +
887C GLY* 1.3 80.1 - - - +
889C ILE* 1.3 76.7 + - - +
890C LEU* 3.3 24.9 - - + -
1005C ARG* 4.7 6.7 - - - +
435D GLN* 4.9 6.7 + - - +
523D GLN* 4.9 12.7 - - - +
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Residues in contact with ILE 889 (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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728C LEU* 3.2 25.4 - - + +
729C SER 3.9 2.9 - - - +
730C ASN* 3.7 34.1 - - + +
733C VAL* 4.5 9.2 - - + -
870C ILE* 3.7 24.0 - - + +
871C SER* 4.3 0.7 - - - -
872C ASP* 3.8 25.6 - - + +
886C ILE* 3.6 14.8 - - + -
888C LYS* 1.3 86.7 - - - +
890C LEU* 1.3 62.6 + - - +
891C PRO* 3.8 4.2 - - - +
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Residues in contact with LEU 890 (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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717C TRP* 4.2 16.4 - - + -
727C ILE* 3.8 36.6 - - + -
728C LEU 3.0 6.9 + - - +
730C ASN* 2.9 25.7 + - - -
888C LYS* 3.3 37.5 - - + -
889C ILE* 1.3 72.9 - - - +
891C PRO* 1.3 70.4 - - + +
894C ASP* 3.6 19.3 - - - +
895C MET* 3.3 31.0 - - + +
907C ILE* 4.9 0.9 - - + -
1005C ARG* 3.9 14.6 - - - +
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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
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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