Contacts of the helix formed by residues 241 - 252 (chain B) in PDB entry 3V4P
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 GLY 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B PHE* 4.1 8.7 - - - -
178B VAL 3.3 10.2 + - - +
179B ASP* 3.7 9.5 + - - -
209B SER* 4.3 7.8 + - - +
240B GLU* 1.3 75.1 - - - +
242B GLY* 1.3 61.6 + - - -
243B PHE 3.4 2.9 + - - -
244B ASP* 3.7 18.9 + - - +
245B ALA 4.1 1.9 + - - -
274B HIS* 4.4 0.9 - - - -
308B TYR* 3.6 27.6 - - - -
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Residues in contact with GLY 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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177B PHE* 3.6 26.7 - - - -
240B GLU* 3.6 4.8 + - - +
241B GLY* 1.3 72.5 - - - +
243B PHE* 1.3 62.1 + - - +
244B ASP 3.2 2.7 - - - -
245B ALA* 3.1 5.2 + - - +
246B ILE* 2.9 30.2 + - - +
267B PHE* 3.8 18.7 - - - -
273B PHE* 4.8 5.1 - - - +
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Residues in contact with PHE 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 GLY 3.4 1.0 - - - -
242B GLY* 1.3 79.3 - - - +
244B ASP* 1.3 57.0 + - - +
246B ILE* 3.8 18.7 - - + +
247B LEU* 2.9 32.7 + - - +
267B PHE* 6.1 1.3 - + - -
273B PHE* 3.4 45.7 - + + +
274B HIS 3.5 17.2 + - - +
275B THR* 4.6 3.8 - - - -
308B TYR* 5.5 0.7 - - + -
309B PRO* 3.4 39.9 - - + +
311B VAL* 4.1 24.2 - - + -
314B VAL* 3.9 22.7 - - + +
327B PHE* 6.0 0.2 - + - -
337B TYR* 6.0 0.9 - + - -
340B LEU* 4.3 27.1 - - + -
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Residues in contact with ASP 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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180B LYS* 2.7 40.9 + - - +
209B SER* 3.3 21.7 + - - +
241B GLY 3.7 7.7 + - - +
242B GLY 3.2 0.2 - - - -
243B PHE* 1.3 78.2 - - - +
245B ALA* 1.3 63.0 + - - +
247B LEU* 3.8 1.9 - - - +
248B GLN* 2.9 30.7 + - - +
288B SER* 4.4 2.3 + - - -
300B TYR* 3.8 19.2 + - + -
307B ASP 4.2 2.8 - - - +
308B TYR* 3.7 11.7 - - - -
309B PRO* 3.2 25.7 - - - +
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Residues in contact with ALA 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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138B LEU* 3.6 17.7 - - + +
177B PHE* 3.7 22.4 - - + -
209B SER 4.5 0.2 - - - +
210B PHE* 3.4 39.8 - - + +
241B GLY 4.1 0.6 + - - -
242B GLY* 3.1 10.1 + - - +
244B ASP* 1.3 78.2 - - - +
246B ILE* 1.3 58.3 + - - +
248B GLN* 3.5 2.3 + - - +
249B ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 246 (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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138B LEU* 3.9 9.6 - - + -
242B GLY 2.9 17.2 + - - +
243B PHE* 3.8 22.0 - - + +
245B ALA* 1.3 73.0 - - - +
247B LEU* 1.3 67.8 + - - +
249B ALA* 2.8 17.4 + - - +
250B ALA* 2.9 12.1 + - - +
265B LEU* 4.6 10.3 - - + -
267B PHE* 3.6 38.1 - - + -
314B VAL* 3.7 23.3 - - + -
318B LEU* 4.1 23.7 - - + +
325B PRO* 6.5 0.4 - - + -
327B PHE* 4.5 15.9 - - + -
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Residues in contact with LEU 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 PHE 2.9 21.1 + - - +
244B ASP* 3.8 3.4 - - - +
246B ILE* 1.3 74.9 - - - +
248B GLN* 1.3 63.4 + - - +
250B ALA* 3.2 5.7 + - - +
251B LEU* 2.9 57.5 + - + +
288B SER* 4.0 9.9 - - - -
289B ASP 4.6 2.7 - - - +
290B GLY* 5.5 1.6 - - - -
300B TYR* 6.1 0.4 - - + +
309B PRO* 3.8 22.7 - - + -
313B GLN* 3.4 34.1 - - + +
314B VAL* 4.7 7.0 - - + -
317B ALA* 3.6 29.2 - - + -
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Residues in contact with GLN 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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210B PHE* 3.9 20.0 - - + -
244B ASP 2.9 21.0 + - - +
245B ALA 3.6 4.9 - - - +
247B LEU* 1.3 82.2 - - - +
249B ALA* 1.3 55.3 + - - +
251B LEU* 3.9 8.9 - - - +
252B CYS* 2.7 50.7 + - - +
289B ASP 5.0 2.6 + - - -
291B HIS 3.4 18.9 + - - -
292B CYS* 3.7 1.4 - - - -
293B HIS* 3.0 30.1 + - - -
294B LEU* 4.4 1.8 + - + +
300B TYR* 3.7 43.0 + - + -
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Residues in contact with ALA 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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136B TYR* 4.8 7.9 - - + -
138B LEU* 5.2 1.8 - - + -
210B PHE* 4.9 4.0 - - + -
245B ALA 2.9 13.8 + - - +
246B ILE* 2.8 13.3 + - - +
248B GLN* 1.3 77.5 - - - +
250B ALA* 1.3 60.7 + - - +
252B CYS 4.1 4.0 + - - +
253B GLN* 5.4 0.2 - - - -
256B ILE* 3.4 23.3 - - + +
258B TRP* 3.4 24.7 + - + -
265B LEU* 4.4 22.7 - - + -
323B ILE* 4.0 3.9 - - + +
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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 ILE 2.9 10.4 + - - +
247B LEU* 3.6 9.6 - - - +
249B ALA* 1.3 77.6 - - - +
251B LEU* 1.3 61.6 + - + +
253B GLN* 3.1 25.3 + - - -
317B ALA* 4.1 21.8 - - + +
318B LEU* 4.3 15.3 - - + +
321B ALA* 3.7 20.4 - - + +
323B ILE* 4.0 9.6 - - - +
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Residues in contact with LEU 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 LEU* 2.9 49.9 + - + +
248B GLN* 3.1 10.5 + - - +
250B ALA* 1.3 79.2 - - - +
252B CYS* 1.3 55.5 + - - +
253B GLN* 2.7 25.1 + - - +
289B ASP 4.0 1.1 - - - +
290B GLY* 3.2 34.8 - - - +
291B HIS 3.3 31.4 - - - +
292B CYS* 4.6 6.4 - - - +
317B ALA* 5.2 5.6 - - + -
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Residues in contact with CYS 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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248B GLN* 2.7 37.3 + - - +
249B ALA 4.1 3.7 - - - +
251B LEU* 1.3 66.9 - - - +
253B GLN* 1.3 64.5 + - - +
254B GLU 3.5 1.3 - - - -
255B GLN* 3.5 13.9 - - + +
256B ILE* 3.2 27.8 + - + +
292B CYS* 2.0 50.3 - - - -
294B LEU* 3.7 25.8 - - + -
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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