Contacts of the helix formed by residues 597 - 602 (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 MET 597 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594G VAL* 5.0 6.5 - - - -
595G PRO* 3.4 10.5 - - + +
596G GLY* 1.3 80.3 - - - +
598G THR* 1.3 63.2 + - - +
600G CYS* 3.4 35.4 - - + -
601G THR* 2.6 38.4 + - - +
620G ALA* 3.0 9.6 - - - +
801G PHE 5.0 0.9 - - - +
802G GLY* 3.2 37.0 - - - +
805G VAL* 5.9 1.1 - - - -
806G MET* 3.7 6.7 - - + -
3051G FMN 2.9 52.7 - - + +
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Residues in contact with THR 598 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G MET* 1.3 74.5 - - - +
599G PRO* 1.3 82.1 - - - +
602G VAL* 3.0 22.1 + - - +
620G ALA* 3.8 4.0 - - - -
622G GLY* 3.2 35.9 - - - +
623G GLY* 5.6 0.9 - - - -
652G ILE* 5.4 0.7 - - + -
1034G LEU* 3.8 20.4 - - + +
1054G LEU* 4.8 2.3 - - - +
3051G FMN 2.7 38.4 + - + +
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Residues in contact with PRO 599 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598G THR* 1.3 102.5 - - - +
600G CYS* 1.3 62.2 + - - +
602G VAL* 3.1 22.4 - - + +
603G SER* 5.4 0.2 - - - -
806G MET* 6.1 0.7 - - + -
1034G LEU* 4.2 40.4 - - + +
1035G TRP* 6.0 0.4 - - - -
1037G SER* 5.3 6.3 - - - +
1038G GLU* 3.1 27.7 - - + +
1054G LEU* 4.9 2.0 - - + +
3051G FMN 3.6 23.8 - - + -
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Residues in contact with CYS 600 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G MET* 3.4 38.5 + - + -
598G THR 3.1 0.4 - - - -
599G PRO* 1.3 87.5 - - - +
601G THR* 1.3 60.0 + - - +
602G VAL 3.3 1.1 + - - -
603G SER* 3.9 8.8 + - - -
606G PHE* 3.6 23.0 - - + +
806G MET* 3.6 31.2 - - - -
811G VAL* 4.5 16.1 - - + +
812G LYS* 5.2 1.2 + - - +
813G THR* 4.4 13.0 - - - -
1038G GLU* 4.1 6.3 - - - +
3051G FMN 4.4 3.6 - - - -
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Residues in contact with THR 601 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594G VAL* 4.5 4.5 - - - +
595G PRO 3.5 10.0 + - - -
597G MET* 2.6 38.8 + - - +
600G CYS* 1.3 72.9 - - - +
602G VAL* 1.3 63.1 + - - +
603G SER 3.2 6.8 + - - +
606G PHE* 4.5 7.1 - - - -
607G VAL* 4.2 2.1 - - + +
617G ILE* 4.4 18.8 - - + +
618G GLU 2.4 34.8 - - - +
619G LEU* 3.0 15.5 - - + +
620G ALA* 3.2 10.8 - - - +
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Residues in contact with VAL 602 (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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597G MET 3.5 0.2 + - - -
598G THR 3.0 16.9 + - - +
599G PRO* 3.1 21.5 - - + +
601G THR* 1.3 79.5 - - - +
603G SER* 1.3 68.3 + - - +
604G PRO* 3.4 0.7 - - - +
619G LEU* 3.6 3.9 - - - +
620G ALA* 4.0 6.1 - - - +
623G GLY* 3.5 27.8 - - - +
624G TYR* 2.7 54.3 + - + +
1038G GLU* 4.5 7.6 - - - +
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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