Contacts of the helix formed by residues 241 - 252 (chain B) in PDB entry 1VDV
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 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B PRO 5.8 0.9 - - - +
239B ALA* 3.6 0.9 - - - +
240B SER* 1.3 95.1 + - - +
242B LEU* 1.3 64.8 + - - +
243B LYS* 2.9 27.8 + - - +
244B GLU* 3.1 14.7 + - - +
245B LEU 3.1 17.8 + - - -
284B ILE* 3.7 13.5 - - - +
285B PRO* 5.4 1.6 - - - -
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Residues in contact with LEU 242 (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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241B THR* 1.3 75.1 - - - +
243B LYS* 1.3 57.7 + - - +
244B GLU 2.9 7.4 + - - -
245B LEU* 3.1 8.3 + - + +
246B LEU* 3.0 57.0 + - + +
284B ILE* 3.7 16.3 - - + +
286B GLU* 4.0 29.0 + - + +
287B LEU* 4.0 13.0 - - + -
375B VAL* 4.7 3.1 - - + -
380B ARG* 6.1 0.7 - - - +
403B ILE* 4.7 2.7 - - + -
405B LEU* 4.0 38.1 - - + -
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Residues in contact with LYS 243 (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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241B THR* 2.9 14.6 + - - +
242B LEU* 1.3 75.7 - - - +
244B GLU* 1.3 61.9 + - - +
246B LEU* 5.0 7.2 - - - +
247B ASP* 2.9 30.6 + - - +
377B ARG* 4.9 12.5 - - - +
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Residues in contact with GLU 244 (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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226B GLN* 3.2 36.4 + - - +
239B ALA* 3.8 3.3 - - + -
240B SER* 2.7 45.6 + - - -
241B THR* 3.1 22.7 + - - +
242B LEU 2.9 1.2 + - - -
243B LYS* 1.3 73.8 - - - +
245B LEU* 1.3 64.1 + - - +
246B LEU 3.3 2.1 - - - +
247B ASP* 3.8 11.9 - - - +
248B LEU* 2.9 38.7 + - - +
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Residues in contact with LEU 245 (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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239B ALA* 4.3 6.2 - - + +
241B THR 3.1 2.2 + - - -
242B LEU* 3.6 8.5 - - + +
244B GLU* 1.3 82.0 - - - +
246B LEU* 1.3 58.7 + - - +
248B LEU* 3.3 3.4 + - - +
249B LYS* 2.9 33.5 + - + +
257B LEU* 3.8 22.7 - - + -
279B ILE* 3.8 24.9 - - + -
281B PRO* 3.8 15.7 - - + -
284B ILE* 3.6 32.5 - - + -
287B LEU* 4.2 15.3 - - + -
403B ILE* 4.2 26.9 - - + -
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.0 39.5 + - + +
243B LYS* 5.1 4.0 - - - -
244B GLU 5.1 0.4 - - - +
245B LEU* 1.3 78.4 - - + +
247B ASP* 1.3 61.9 + - - +
249B LYS* 3.5 4.8 + - - +
250B ALA* 3.2 21.0 + - - +
375B VAL* 4.0 22.4 - - + +
376B SER* 3.7 24.0 - - - +
377B ARG* 4.1 23.4 + - + +
378B GLY 5.3 0.4 - - - +
401B GLU 5.1 3.0 - - - +
403B ILE* 3.7 31.9 - - + -
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Residues in contact with ASP 247 (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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243B LYS* 2.9 42.8 + - - +
244B GLU* 3.5 12.1 + - - +
245B LEU 3.3 0.4 - - - -
246B LEU* 1.3 74.7 - - - +
248B LEU* 1.3 62.0 + - + +
250B ALA* 3.1 4.8 + - - +
251B GLN* 3.0 42.4 + - + +
377B ARG* 2.7 41.0 + - - +
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Residues in contact with LEU 248 (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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226B GLN* 3.8 21.3 - - - +
237B ILE* 3.7 46.4 - - + -
239B ALA* 4.0 15.3 - - + -
244B GLU* 2.9 28.7 + - - +
245B LEU 3.6 3.6 - - - +
247B ASP* 1.3 78.6 - - + +
249B LYS* 1.3 56.2 + - - +
251B GLN* 3.2 18.8 + - - +
252B HIS* 2.8 38.3 + - + +
279B ILE* 3.7 23.1 - - + +
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Residues in contact with LYS 249 (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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245B LEU* 2.9 26.6 + - + +
246B LEU* 3.7 7.6 - - - +
248B LEU* 1.3 76.7 - - - +
250B ALA* 1.3 61.5 + - - +
252B HIS 4.3 3.8 - - - +
253B PRO* 3.1 43.4 + - - +
255B ALA 3.9 11.4 + - - +
257B LEU* 3.9 19.5 - - + +
279B ILE* 4.5 5.4 - - + -
399B GLY 5.2 0.2 + - - -
400B PRO 2.9 28.7 + - - -
401B GLU* 3.6 19.0 - - - +
402B GLU 3.8 19.7 + - - -
403B ILE* 3.4 24.7 - - + -
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Residues in contact with ALA 250 (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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246B LEU 3.2 10.1 + - - +
247B ASP* 3.1 11.7 + - - +
249B LYS* 1.3 82.5 - - - +
251B GLN* 1.3 63.2 + - + +
252B HIS 3.5 0.2 + - - -
253B PRO* 3.6 12.6 - - - +
377B ARG* 4.8 15.9 - - + -
401B GLU* 3.7 27.2 - - + +
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Residues in contact with GLN 251 (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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247B ASP* 3.0 29.0 + - - +
248B LEU* 3.6 26.5 - - - +
250B ALA* 1.3 80.7 - - + +
252B HIS* 1.3 84.6 + - + +
253B PRO* 3.7 3.6 - - - +
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Residues in contact with HIS 252 (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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237B ILE* 5.0 10.3 - - + +
248B LEU* 2.8 18.3 + - + +
249B LYS* 3.4 8.3 - - - +
251B GLN* 1.3 106.3 + - + +
253B PRO* 1.3 65.8 - - - +
254B GLU* 3.2 23.1 + - - +
255B ALA* 3.0 17.9 + - + +
277B MET* 4.0 33.3 - - + -
279B ILE* 5.2 1.3 - - + -
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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