Contacts of the strand formed by residues 267 - 272 (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 LEU 267 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G LEU* 3.5 24.2 - - + +
158G ALA* 3.7 37.5 - - + +
249G TYR* 4.9 11.9 - - + +
263G LEU* 3.4 22.4 - - + +
264G ARG* 3.2 19.9 - - + +
265G SER 3.0 4.9 - - - +
266G TYR* 1.3 82.2 - - - +
268G LYS* 1.3 62.0 + - - +
269G GLY 3.0 5.6 + - - +
270G ALA* 4.7 1.1 - - + -
283G ILE* 5.1 2.9 - - + -
457G ILE* 3.4 41.5 - - + +
502G LEU* 6.1 2.7 - - + -
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Residues in contact with LYS 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G GLN* 4.5 23.0 + - + +
156G LEU 2.7 15.5 + - - +
157G VAL* 4.4 9.9 - - + -
266G TYR 3.9 2.4 + - - -
267G LEU* 1.3 71.2 - - - +
269G GLY* 1.3 55.7 + - - +
457G ILE* 5.0 0.2 - - - -
458G PRO* 3.3 22.0 - - - +
460G TYR* 3.9 17.7 + - - +
496G PHE* 4.6 2.9 - - - -
497G LYS* 3.2 38.7 + - - +
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Residues in contact with GLY 269 (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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156G LEU 3.9 0.2 + - - -
157G VAL* 3.3 13.6 - - - +
158G ALA 3.2 18.7 + - - -
267G LEU* 3.0 7.0 - - - +
268G LYS* 1.3 81.0 - - - +
270G ALA* 1.3 60.4 - - - +
457G ILE* 3.9 10.8 - - - -
458G PRO* 3.4 19.3 - - - -
460G TYR* 4.2 8.1 - - - -
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Residues in contact with ALA 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G VAL* 4.3 1.6 - - - -
158G ALA* 3.1 28.0 - - + +
269G GLY* 1.3 75.5 - - - +
271G THR* 1.3 71.1 + - - +
280G ALA* 4.1 18.8 - - + +
283G ILE* 4.5 9.4 - - + -
457G ILE* 4.1 12.5 - - + +
458G PRO 2.9 18.1 + - - +
459G VAL* 3.1 11.3 - - + -
460G TYR* 3.2 4.2 + - - -
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Residues in contact with THR 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G VAL* 5.6 0.9 - - - -
158G ALA 2.9 5.7 + - - +
159G ILE* 3.2 11.0 - - + +
160G PHE* 2.9 21.0 + - - -
270G ALA* 1.3 80.2 + - - +
272G GLY* 1.3 74.4 + - - +
277G LEU* 6.0 0.2 - - - -
280G ALA* 3.7 10.6 - - - +
459G VAL* 4.9 2.2 - - - -
460G TYR* 2.8 45.3 + - - +
490G TRP* 4.0 15.0 - - + -
493G THR* 4.0 17.9 - - - +
496G PHE* 5.1 8.5 - - + -
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Residues in contact with GLY 272 (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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160G PHE 3.3 9.4 - - - -
271G THR* 1.3 85.1 - - - +
273G HIS* 1.3 60.7 + - - -
276G GLY 3.3 5.6 - - - -
277G LEU* 3.3 33.8 + - - +
280G ALA* 3.9 1.4 - - - +
462G THR* 3.6 15.9 + - - -
490G TRP* 3.6 8.5 - - - -
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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