Contacts of the helix formed by residues 242 - 253 (chain A) in PDB entry 2VN9
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 THR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLU* 2.9 34.8 + - - +
240A THR 3.8 1.8 + - - +
241A VAL* 1.3 80.5 - - - +
243A PRO* 1.4 71.2 - - + +
244A GLU* 3.3 14.6 + - - +
245A ALA* 3.3 21.1 + - - +
246A LYS* 3.4 10.4 + - - +
271A TRP* 3.7 6.1 - - - -
278A VAL 3.7 15.5 - - - +
280A SER* 3.9 15.3 - - - +
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Residues in contact with PRO 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A VAL 3.7 2.7 - - - +
242A THR* 1.4 85.0 - - - +
244A GLU* 1.3 72.2 + - - +
246A LYS* 3.3 14.2 + - + +
247A ASP* 2.8 30.1 + - - +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 3.2 20.5 - - - +
243A PRO* 1.3 88.3 - - - +
245A ALA* 1.3 64.5 + - - +
247A ASP* 3.3 5.9 + - - +
248A LEU* 3.1 19.6 + - - +
269A HIS* 3.2 19.9 - - + -
270A PRO* 5.3 6.5 - - + -
271A TRP* 4.2 7.2 - - + +
278A VAL* 3.6 34.1 - - + +
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 4.1 2.0 - - - +
204A LEU* 4.6 0.9 - - - +
208A LEU* 3.8 24.5 - - + -
241A VAL* 3.8 7.9 - - + -
242A THR* 3.3 21.5 + - - +
244A GLU* 1.3 78.5 - - - +
246A LYS* 1.3 62.2 + - - +
248A LEU* 3.4 5.2 + - - +
249A ILE* 3.1 27.6 + - - +
271A TRP* 3.6 27.0 - - + +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A PHE* 3.7 39.1 + - + +
238A TRP* 3.0 47.4 + - + +
239A ASP* 4.7 4.9 + - - +
241A VAL* 3.6 21.5 + - + -
242A THR 3.4 10.5 + - - +
243A PRO* 3.3 14.3 + - + +
245A ALA* 1.3 74.5 - - - +
247A ASP* 1.3 61.3 + - - +
249A ILE* 3.3 4.8 + - - +
250A ASN* 2.8 37.8 + - - +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PRO 2.8 18.3 + - - +
244A GLU* 3.5 9.4 - - - +
246A LYS* 1.3 77.4 - - - +
248A LEU* 1.3 55.7 + - - +
250A ASN* 3.3 13.6 + - - +
251A LYS* 2.4 66.5 + - - +
269A HIS* 3.2 12.1 + - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 5.0 0.4 - - + -
204A LEU* 3.9 12.3 - - + -
244A GLU 3.1 14.0 + - - +
245A ALA* 3.7 9.0 - - - +
246A LYS 3.3 0.2 - - - -
247A ASP* 1.3 73.2 - - - +
249A ILE* 1.3 64.7 + - - +
251A LYS* 3.1 4.5 + - - +
252A MET* 3.1 51.3 + - + +
261A ILE* 4.0 18.4 - - + -
266A ALA* 4.3 3.6 - - + -
269A HIS* 3.5 37.8 + - + +
271A TRP* 3.8 26.9 - - + -
272A ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY* 4.5 2.9 - - - +
204A LEU* 3.6 24.2 - - + -
205A TYR* 4.0 16.2 - - + +
208A LEU* 3.6 30.1 - - + -
231A TYR* 4.2 2.0 - - + -
233A PHE* 4.0 19.5 - - + -
238A TRP* 3.6 24.5 - - + -
245A ALA 3.1 14.9 + - - +
246A LYS 3.6 7.0 - - - +
248A LEU* 1.3 75.2 - - - +
250A ASN* 1.3 53.4 + - - +
252A MET* 3.3 4.8 + - - +
253A LEU* 2.8 60.0 + - + +
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Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 2.7 28.6 + - - +
233A PHE* 3.4 22.7 - - - -
246A LYS* 2.8 22.7 + - - +
247A ASP* 3.4 16.3 + - - +
249A ILE* 1.3 75.8 - - - +
251A LYS* 1.3 59.2 + - + +
253A LEU 3.5 12.5 - - - +
254A THR* 3.0 16.5 + - - -
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASP* 2.4 57.4 + - - +
248A LEU 3.1 5.6 + - - +
250A ASN* 1.3 76.8 - - + +
252A MET* 1.3 58.8 + - - +
254A THR* 3.1 15.7 + - - -
259A LYS 4.7 0.5 - - - +
260A ARG* 3.5 2.1 - - - +
261A ILE* 3.0 55.4 + - + +
269A HIS* 4.2 12.1 + - + -
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 4.7 3.8 - - + -
121A LEU* 4.1 13.7 - - + -
197A MET* 3.4 24.0 - - + +
198A TRP* 3.7 7.4 - - - -
200A CYS* 3.8 10.3 - - + +
201A GLY* 3.6 31.2 - - - -
204A LEU* 4.1 12.1 - - + -
248A LEU* 3.1 41.1 + - + +
249A ILE 3.7 3.1 - - - +
251A LYS* 1.3 74.7 - - - +
253A LEU* 1.3 58.8 + - - +
254A THR 3.1 6.7 + - - -
260A ARG* 3.1 29.9 + - - -
261A ILE* 3.6 16.2 - - + -
266A ALA* 4.0 16.4 - - + -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TRP* 3.4 57.8 - - + +
201A GLY* 3.9 12.8 - - - +
202A VAL* 3.8 13.5 - - + +
205A TYR* 4.7 0.7 - - + -
213A PRO* 4.6 9.6 - - + -
214A PHE* 4.4 7.6 - - + -
229A GLY* 5.6 0.7 - - - -
231A TYR* 3.7 45.8 + - + -
249A ILE* 2.8 42.7 + - + +
250A ASN 3.5 7.4 - - - +
252A MET* 1.3 71.1 - - - +
254A THR* 1.3 56.7 + - - +
255A ILE* 4.0 2.8 + - - +
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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