Contacts of the helix formed by residues 292 - 303 (chain B) in PDB entry 2VZE
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 ASP 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LEU* 4.3 4.1 - - - +
290B LYS* 4.2 13.8 - - + +
291B PHE* 1.3 73.9 - - - +
293B PRO* 1.3 73.7 - - - +
294B LEU* 3.0 23.8 + - - +
295B VAL* 3.1 35.2 + - + +
296B ILE* 3.1 15.2 + - - +
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Residues in contact with PRO 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B PHE 3.6 1.1 - - - +
292B ASP* 1.3 92.2 - - - +
294B LEU* 1.3 55.0 + - - +
296B ILE* 3.2 14.6 + - + +
297B LEU* 3.0 27.9 + - - +
317B MET* 3.6 49.4 - - + +
318B LEU* 3.7 6.1 - - + +
321B GLN* 3.4 29.8 - - + +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.0 13.8 + - - +
293B PRO* 1.3 79.9 - - - +
295B VAL* 1.3 56.9 + - + +
297B LEU* 3.3 11.6 + - + +
298B LYS* 2.9 59.3 + - + +
321B GLN* 3.8 25.4 - - - +
322B ASP* 6.1 1.6 - - + +
326B TYR* 4.3 17.9 - - + -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY* 5.8 1.3 - - - -
286B HIS* 3.7 27.1 - - + +
288B LEU* 3.7 19.7 - - + -
289B PRO* 6.3 0.7 - - + -
292B ASP* 3.1 31.2 + - + +
294B LEU* 1.3 76.2 - - + +
296B ILE* 1.3 64.1 + - - +
298B LYS* 3.4 10.8 + - + +
299B THR* 2.9 29.9 + - - +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B TRP* 3.7 22.5 - - + -
260B ILE* 4.1 13.2 - - + -
288B LEU* 3.6 31.2 - - + -
291B PHE* 4.7 23.1 - - + -
292B ASP 3.1 18.3 + - - +
293B PRO* 3.2 15.2 + - + +
295B VAL* 1.3 77.0 - - - +
297B LEU* 1.3 61.8 + - - +
299B THR* 3.4 2.6 + - - -
300B LEU* 3.0 24.6 + - + +
314B VAL* 4.7 11.7 - - + +
317B MET* 5.5 3.8 - - + -
318B LEU* 3.7 26.9 - - + -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PRO 3.0 14.2 + - - +
294B LEU* 3.6 13.9 - - + +
296B ILE* 1.3 77.2 - - - +
298B LYS* 1.3 62.2 + - - +
300B LEU* 3.2 4.1 + - + +
301B SER* 3.0 20.8 + - - -
318B LEU* 3.8 13.9 - - + +
321B GLN* 3.9 22.9 - - + -
322B ASP 3.6 26.7 - - - +
323B LEU* 3.8 13.5 - - + -
326B TYR* 3.6 29.8 - - + +
328B PHE* 3.5 30.3 - - + -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU* 2.9 47.4 + - + +
295B VAL* 3.8 9.6 - - + +
297B LEU* 1.3 75.4 - - - +
299B THR* 1.3 57.3 + - - +
301B SER* 3.3 5.6 + - - -
302B SER* 2.5 40.3 + - - +
326B TYR* 3.6 40.4 - - + -
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B TRP* 3.4 28.0 - - + -
284B PHE* 3.7 26.2 - - + -
286B HIS* 3.3 24.3 + - + -
295B VAL* 2.9 21.0 + - - +
296B ILE 3.6 4.5 - - - -
297B LEU 3.2 0.2 - - - -
298B LYS* 1.3 74.4 - - - +
300B LEU* 1.3 64.6 + - - +
303B TYR* 3.1 42.7 + - + +
305B ILE* 4.4 2.0 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TRP* 3.6 26.7 - - + -
296B ILE* 3.0 17.3 + - + +
297B LEU* 3.2 7.2 + - - +
299B THR* 1.3 75.6 - - - +
301B SER* 1.3 53.3 + - - +
303B TYR 3.3 2.9 - - - +
305B ILE* 4.4 21.2 - - + +
308B MET* 3.8 34.3 - - + -
318B LEU* 4.0 24.2 - - + -
328B PHE* 3.5 29.4 - - + +
330B HIS* 2.6 33.6 + - - -
331B LEU* 4.6 10.5 - - + -
349B TRP* 5.0 0.7 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B LEU 3.0 15.8 + - - -
298B LYS 3.6 5.4 - - - -
300B LEU* 1.3 79.6 - - - +
302B SER* 1.3 60.3 + - - +
303B TYR 3.5 0.2 - - - -
326B TYR* 3.7 30.9 - - - -
327B LYS 2.6 28.8 + - - +
328B PHE* 4.3 1.6 - - - -
330B HIS* 3.6 13.7 - - - -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS* 2.5 26.4 + - - +
299B THR 3.3 0.2 + - - -
301B SER* 1.3 80.8 - - - +
303B TYR* 1.3 78.3 + - - +
304B PRO* 4.5 1.9 - - - +
326B TYR* 5.9 0.9 - - - -
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TRP* 3.6 31.6 - + - -
72B VAL* 3.6 20.9 - - + +
78B GLU* 2.6 34.0 + - - -
284B PHE* 3.7 12.6 - + + -
286B HIS* 5.5 0.7 - + - -
299B THR* 3.1 38.3 + - + +
300B LEU 3.3 4.0 - - - +
302B SER* 1.3 95.1 - - - +
304B PRO* 1.3 59.2 - - + +
305B ILE* 2.7 33.7 + - + +
330B HIS* 2.9 18.4 + - - -
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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