Contacts of the helix formed by residues 1034 - 1039 (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 LEU1034 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598G THR* 3.8 33.2 - - + +
599G PRO* 4.2 23.3 - - + +
622G GLY 6.1 0.4 - - - +
856G LYS* 4.9 5.2 - - - +
1032G ASP 3.7 1.0 - - - -
1033G SER* 1.3 86.9 - - - +
1035G TRP* 1.3 63.6 + - + +
1036G GLN* 3.3 4.0 + - - -
1037G SER* 3.5 20.4 + - - -
1038G GLU* 5.3 0.3 - - - +
1052G CYS* 4.4 7.4 - - + +
1054G LEU* 4.2 31.4 - - + -
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Residues in contact with TRP1035 (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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599G PRO* 6.0 0.7 - - - -
901G LYS* 6.2 0.2 - - - +
939G PHE* 3.2 42.0 - + - -
943G TRP* 4.1 18.2 - + - -
1013G LYS* 3.2 19.1 - - - +
1014G PRO 5.8 0.7 - - - -
1016G PRO* 5.1 9.2 - - + -
1032G ASP* 2.9 40.8 + - - +
1034G LEU* 1.3 75.7 - - + +
1036G GLN* 1.3 97.0 + - + +
1037G SER 3.3 2.7 - - - -
1038G GLU* 3.4 6.8 + - - +
1039G HIS* 3.3 30.5 - + + -
1042G ALA* 4.0 25.1 - - + -
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Residues in contact with GLN1036 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900G GLN* 3.1 42.8 + - + +
901G LYS* 5.3 6.1 - - - +
1032G ASP 3.8 8.1 + - - -
1033G SER* 3.4 15.0 - - - +
1034G LEU 3.3 0.7 - - - -
1035G TRP* 1.3 121.2 - - + +
1037G SER* 1.3 63.6 + - - +
1038G GLU 2.9 6.7 + - - -
1039G HIS 3.0 6.7 + - - +
1040G LEU* 2.9 22.0 + - - +
1043G VAL* 3.6 26.7 - - + -
1051G THR* 3.7 14.7 - - + +
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Residues in contact with SER1037 (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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599G PRO* 5.3 6.6 - - - +
813G THR* 4.0 4.8 - - - -
814G SER* 3.0 27.9 + - - -
817G ALA* 3.7 9.8 - - - +
1034G LEU 3.5 11.8 + - - -
1035G TRP 3.3 0.4 - - - -
1036G GLN* 1.3 77.1 - - - +
1038G GLU* 1.3 65.1 + - - +
1040G LEU* 3.5 4.9 - - - +
1051G THR* 3.7 9.6 - - - +
1052G CYS 2.6 29.8 + - - -
1053G ILE* 3.9 15.3 - - - +
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Residues in contact with GLU1038 (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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599G PRO* 3.1 38.7 - - + +
600G CYS* 4.1 5.2 - - - +
602G VAL* 4.5 8.1 - - - +
812G LYS* 3.4 46.6 + - + +
813G THR* 3.6 11.5 + - - +
814G SER* 3.2 14.0 + - - -
1034G LEU 5.3 0.4 - - - +
1035G TRP* 3.4 6.5 + - - +
1036G GLN 2.9 0.4 - - - -
1037G SER* 1.3 89.9 - - - +
1039G HIS* 1.3 82.8 + - + +
1041G GLU* 4.5 1.4 - - - +
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Residues in contact with HIS1039 (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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939G PHE* 3.7 28.4 - + + -
1035G TRP* 3.3 33.2 + + + +
1036G GLN 3.0 6.8 + - - -
1038G GLU* 1.3 108.3 + - + +
1040G LEU* 1.3 58.3 + - - +
1041G GLU* 2.8 40.8 + - - +
1042G ALA* 2.9 15.4 + - - +
1043G VAL* 3.9 3.5 + - - +
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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
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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