Contacts of the helix formed by residues 283 - 300 (chain B) in PDB entry 2VZ6
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 ARG 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TYR* 2.9 19.4 + - + +
108B SER* 4.7 1.6 - - - -
109B GLU* 4.4 25.4 + - - +
207B LEU* 3.0 29.6 + - - +
208B VAL* 4.1 4.4 - - - +
236B GLU* 2.7 32.1 + - - +
239B THR* 2.9 29.5 + - - -
240B VAL* 3.6 20.6 - - - +
281B MET* 3.6 29.0 - - + +
282B HIS* 1.3 72.8 - - - +
284B GLN* 1.3 64.9 + - - +
285B GLU* 3.2 5.1 - - + +
286B THR* 3.2 24.9 + - + +
287B VAL* 3.3 14.4 + - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B HIS* 2.7 40.8 + - + +
283B ARG* 1.3 73.7 - - - +
285B GLU* 1.3 57.7 + - - +
287B VAL* 3.2 20.0 + - - +
288B ASP* 2.9 57.7 + - - +
291B LYS* 4.4 4.6 - - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL 4.9 1.3 - - - -
236B GLU* 5.5 8.5 - - + -
283B ARG* 3.2 3.7 - - + +
284B GLN* 1.3 77.0 - - - +
286B THR* 1.3 57.6 + - - +
288B ASP* 3.7 18.3 - - - +
289B CYS* 2.9 33.1 + - - +
1302B PGO 2.7 33.8 + - - +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.9 14.6 - - + -
205B ILE 4.5 0.7 - - - +
206B LEU 3.6 17.9 - - - +
207B LEU 2.6 34.2 + - - +
208B VAL* 3.6 11.5 - - - -
209B GLY* 3.8 10.8 - - - +
283B ARG* 3.2 29.0 + - - +
285B GLU* 1.3 77.0 - - - +
287B VAL* 1.3 54.1 + - - +
289B CYS* 3.4 1.2 + - - +
290B LEU* 2.8 43.0 + - + +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 4.3 10.5 - - + +
102B VAL* 3.7 30.7 - - - +
104B ARG 5.4 5.4 - - - +
107B TYR* 4.1 28.7 - - + -
282B HIS* 4.2 12.1 - - + -
283B ARG 3.7 11.7 - - - +
284B GLN* 3.2 25.9 + - - +
286B THR* 1.3 76.5 - - - +
288B ASP* 1.3 61.0 + - - +
290B LEU* 3.8 6.8 - - - +
291B LYS* 3.2 32.0 + - - +
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Residues in contact with ASP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLN* 2.9 48.7 + - - +
285B GLU* 3.7 23.6 - - - +
287B VAL* 1.3 74.7 - - - +
289B CYS* 1.3 64.7 + - - +
291B LYS* 3.4 34.0 + - - +
292B LYS* 3.7 19.5 + - - +
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Residues in contact with CYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL 3.7 13.7 - - - +
209B GLY 3.5 22.1 - - - +
210B TYR* 4.0 14.1 - - - -
285B GLU* 2.9 20.0 + - - +
286B THR 3.9 0.2 - - - +
288B ASP* 1.3 73.7 - - - +
290B LEU* 1.3 65.3 + - - +
292B LYS* 3.2 11.7 + - - +
293B PHE* 3.0 18.4 + - - +
1302B PGO 3.9 27.8 - - + +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.1 19.3 - - + +
101B ILE* 3.8 40.8 - - + -
102B VAL* 3.9 9.2 - - + -
107B TYR* 5.1 1.3 - - + -
205B ILE* 3.6 27.8 - - + +
206B LEU* 5.3 2.7 - - - +
209B GLY* 3.6 22.8 + - - +
286B THR* 2.8 27.4 + - + +
287B VAL* 3.8 4.9 - - - +
288B ASP 3.3 0.2 - - - -
289B CYS* 1.3 75.6 - - - +
291B LYS* 1.3 53.0 + - - +
293B PHE* 3.1 6.4 + - + +
294B ASN* 2.7 47.0 + - - +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.9 38.2 + - + +
284B GLN* 4.4 3.8 - - - +
287B VAL* 3.2 23.9 + - - +
288B ASP* 3.4 33.2 + - - +
290B LEU* 1.3 76.5 - - - +
292B LYS* 1.3 59.1 + - + +
294B ASN* 3.5 5.6 + - - +
295B ALA* 3.0 26.7 + - - +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ASP* 3.7 18.8 + - - +
289B CYS* 3.2 12.8 + - - +
291B LYS* 1.3 76.4 - - + +
293B PHE* 1.3 60.3 + - - +
295B ALA* 3.2 6.4 + - - +
296B ARG* 2.8 31.2 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.9 24.0 - + - -
138B PRO* 4.0 0.9 - - + -
179B TYR* 3.6 22.4 - - - -
205B ILE* 3.7 19.5 - - + -
209B GLY 3.6 13.7 - - - +
210B TYR* 4.7 0.2 - - - -
211B PRO* 4.1 31.4 - - + -
289B CYS 3.0 13.2 + - - +
290B LEU* 3.3 9.9 - - + +
292B LYS* 1.3 73.2 - - - +
294B ASN* 1.3 72.4 + - - +
296B ARG* 3.3 6.5 + - - +
297B ARG* 3.1 59.5 + - + +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.1 37.0 + - - +
99B GLU* 3.8 21.4 - - - +
102B VAL* 3.4 22.6 - - - +
290B LEU* 2.7 19.5 + - - +
291B LYS* 3.7 5.6 - - - +
293B PHE* 1.3 80.1 - - - +
295B ALA* 1.3 61.4 + - - +
297B ARG* 2.8 36.0 + - - +
298B LYS* 3.2 24.3 + - - +
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Residues in contact with ALA 295 (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 LYS 3.0 18.1 + - - +
292B LYS* 3.7 7.0 - - - +
293B PHE 3.2 0.4 - - - -
294B ASN* 1.3 73.9 - - - +
296B ARG* 1.3 64.6 + - - +
298B LYS* 3.2 16.7 + - - +
299B LEU* 3.4 21.0 + - + +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LYS 2.8 20.0 + - - +
293B PHE* 4.0 5.6 - - + +
295B ALA* 1.3 71.4 - - - +
297B ARG* 1.3 62.6 + - - +
298B LYS 3.3 0.3 + - - -
299B LEU* 3.5 11.7 + - - +
300B LYS* 3.5 21.7 + - - +
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Residues in contact with ARG 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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96B GLU* 2.9 34.8 + - - -
98B PHE* 3.6 9.9 - - - +
138B PRO* 3.9 12.1 - - - +
139B GLU* 3.0 43.9 + - - +
179B TYR* 5.1 0.9 - - - -
293B PHE* 3.1 48.8 + - + +
294B ASN* 2.8 37.0 + - - +
295B ALA 3.2 0.2 - - - -
296B ARG* 1.3 76.4 - - - +
298B LYS* 1.3 71.1 + - - +
299B LEU 3.5 0.2 - - - -
300B LYS* 3.7 18.2 - - - +
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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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96B GLU* 3.0 29.9 + - - +
99B GLU* 3.2 25.9 + - - +
139B GLU* 5.3 1.7 - - - +
294B ASN 3.2 17.3 - - - +
295B ALA* 3.2 10.1 + - - +
297B ARG* 1.3 98.2 - - - +
299B LEU* 1.3 66.2 + - + +
300B LYS 4.5 2.3 - - - +
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Residues in contact with LEU 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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295B ALA* 3.4 17.0 + - + +
296B ARG* 4.1 10.5 - - - +
297B ARG 3.5 0.2 - - - -
298B LYS* 1.3 81.3 - - + +
300B LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG 3.5 14.4 + - - +
297B ARG* 3.7 15.6 - - - +
298B LYS 3.7 2.5 - - - +
299B LEU* 1.3 83.7 - - - +
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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