Contacts of the strand formed by residues 500 - 503 (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 HIS 500 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G LEU* 3.5 28.1 - - + +
154G ALA* 4.1 6.8 - - + +
155G GLN 3.1 6.4 + - - +
156G LEU* 3.5 22.5 - - + -
157G VAL 3.0 23.7 + - - -
498G ALA* 3.4 4.0 - - - +
499G THR* 1.3 124.3 + - + +
501G ILE* 1.3 65.8 + - - +
502G LEU* 4.2 2.7 - - + -
526G ARG* 3.6 19.3 + - + +
528G ILE* 4.8 8.4 - - + +
546G GLU* 5.3 2.5 - - - -
554G GLY 5.6 0.9 - - - -
555G LEU* 4.1 15.9 - - + +
556G LYS 3.1 29.6 + - - -
557G LYS* 4.3 3.0 - - - +
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Residues in contact with ILE 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G VAL* 3.5 12.3 - - + +
159G ILE* 3.2 38.1 - - + -
494G THR* 4.7 1.3 - - - +
496G PHE* 3.9 30.1 - - + -
498G ALA* 5.2 1.1 - - + -
500G HIS* 1.3 77.0 - - - +
502G LEU* 1.3 61.3 + - - +
516G THR* 4.5 13.0 - - - +
520G LYS* 4.4 15.5 - - + -
525G VAL* 3.3 32.5 - - + -
526G ARG 3.4 5.7 + - - +
527G VAL* 3.5 13.8 - - + +
528G ILE 2.9 27.9 + - - +
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Residues in contact with LEU 502 (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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145G LEU* 4.6 1.8 - - + -
146G PHE* 4.4 17.5 - - + -
156G LEU* 4.0 25.4 - - + -
157G VAL 3.0 10.8 + - - +
158G ALA* 4.8 1.6 - - - -
159G ILE* 3.0 32.0 + - - +
252G THR* 5.3 0.2 - - + -
263G LEU* 6.0 0.7 - - + -
267G LEU* 6.1 2.0 - - + -
500G HIS* 4.2 1.3 - - + -
501G ILE* 1.3 73.7 - - - +
503G ASP* 1.3 59.9 + - - +
504G PHE* 3.3 32.2 - - + -
528G ILE* 3.5 39.9 - - + -
547G ILE* 3.9 31.9 - - + -
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Residues in contact with ASP 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G ILE* 3.7 10.6 - - + +
161G GLY 5.6 0.2 - - - -
501G ILE 4.0 0.4 + - - -
502G LEU* 1.3 69.4 - - - +
504G PHE* 1.3 60.4 + - - +
505G GLY* 2.9 26.3 + - - +
508G GLY 5.1 2.0 - - - +
511G GLY 4.1 0.8 - - - -
512G LEU* 3.3 16.6 + - - +
513G GLY* 2.5 42.5 + - - -
527G VAL* 4.9 0.9 - - + -
528G ILE 3.0 17.2 + - - +
529G VAL* 4.2 16.1 - - - +
530G ALA* 2.9 24.6 + - - +
531G GLY 3.9 2.6 + - - -
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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