Contacts of the strand formed by residues 853 - 857 (chain G) in PDB entry 2VKZ
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 PRO 853 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406G ARG* 4.1 11.9 - - - +
740G HIS* 3.8 4.5 - - + +
741G HIS* 3.3 49.2 + - + +
742G SER 4.9 2.0 - - - +
743G PHE* 3.6 32.8 - - + -
836G TYR* 4.7 8.3 - - + +
845G THR* 5.0 2.9 - - - -
846G VAL 3.9 4.3 - - - +
847G ARG* 4.3 9.0 - - + -
851G GLY 4.0 2.4 - - - +
852G GLU* 1.4 88.5 - - + +
854G ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 854 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739G GLY* 3.4 5.6 - - - +
740G HIS* 3.8 30.5 - - - +
741G HIS* 4.4 1.8 - - - -
845G THR* 3.1 6.0 - - - -
846G VAL* 2.7 43.5 + - + +
847G ARG 5.0 0.2 - - - -
848G SER* 4.2 15.5 - - - +
852G GLU* 3.8 14.8 - - - +
853G PRO* 1.3 82.1 - - - +
855G HIS* 1.3 66.1 + - - +
856G LYS* 3.5 36.1 + - + +
865G TRP* 6.5 0.4 - - + -
1054G LEU* 4.2 11.2 - - + -
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Residues in contact with HIS 855 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G GLY 3.6 7.9 - - - -
737G GLY 2.7 20.7 + - - +
739G GLY 2.5 27.7 + - - +
741G HIS* 2.4 50.1 + + - -
832G TRP* 4.4 3.1 - + - -
835G THR* 3.2 33.8 + - + +
843G ILE* 3.8 7.9 - - + -
844G VAL 4.0 0.2 - - - -
845G THR* 3.2 9.6 - - + -
854G ILE* 1.3 69.4 - - - +
856G LYS* 1.3 61.4 + - - +
1054G LEU* 3.4 10.2 - - - +
1055G HIS 3.3 32.1 + - - +
1057G PRO* 3.6 14.9 - - + +
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Residues in contact with LYS 856 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843G ILE* 3.4 8.0 - - - +
844G VAL* 2.9 36.9 + - - +
846G VAL* 4.4 12.5 - - + +
854G ILE* 3.5 20.0 + - + +
855G HIS* 1.3 74.7 - - - +
857G ILE* 1.3 63.7 + - - +
862G VAL* 3.9 24.2 - - + -
865G TRP* 3.5 28.0 - - + -
1033G SER* 4.6 2.0 + - - -
1034G LEU* 4.9 6.2 - - - +
1052G CYS* 2.7 40.5 - - + -
1053G ILE 3.5 4.5 - - - +
1054G LEU* 3.3 32.8 - - + -
1055G HIS 4.9 0.9 - - - -
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Residues in contact with ILE 857 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820G CYS* 4.4 7.4 - - - -
821G ILE* 3.8 33.0 - - + +
824G CYS* 3.8 22.9 - - - -
842G GLY 4.0 4.3 - - - +
843G ILE* 4.3 6.9 - - + +
856G LYS* 1.3 72.8 - - - +
858G ALA* 1.3 59.1 + - - +
859G THR* 2.9 36.7 + - + +
862G VAL* 3.3 16.5 - - - +
1053G ILE* 2.7 55.4 + - + +
1054G LEU* 4.7 0.6 - - - +
1055G HIS* 4.7 11.5 - - + +
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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