Contacts of the helix formed by residues 234 - 247 (chain M) in PDB entry 4V1N
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 GLN 234 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233M ALA* 1.3 81.0 - - - +
235M ASN* 1.3 67.6 + - - +
236M LEU* 2.9 33.4 - - + +
237M THR* 2.7 28.7 - - - +
238M TYR* 3.3 5.9 - - - -
264M LYS* 3.1 30.6 - - - +
274M PRO* 4.2 9.9 - - - -
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Residues in contact with ASN 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M GLN* 1.3 83.9 - - - +
236M LEU* 1.3 81.8 + - - +
237M THR 3.0 1.9 + - - -
238M TYR* 3.5 7.4 + - - -
239M ILE* 3.3 15.8 + - - +
257M GLU* 3.6 11.7 + - - +
260M ALA* 2.9 43.4 - - + +
261M LYS* 3.4 18.0 - - - +
264M LYS* 5.3 10.3 + - - +
274M PRO* 4.3 13.5 - - + +
277M ILE* 5.0 5.2 - - + -
278M ALA* 4.0 20.4 - - + +
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Residues in contact with LEU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M GLN* 2.9 45.3 - - + +
235M ASN* 1.3 90.7 - - - +
237M THR* 1.3 74.4 + - - +
239M ILE* 4.0 9.7 - - - +
240M PRO* 3.5 17.3 - - - +
257M GLU* 4.2 23.7 - - + +
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Residues in contact with THR 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 5.9 0.9 - - - +
186M ALA* 2.3 44.1 - - - +
188M THR* 5.1 0.2 - - + -
233M ALA* 3.4 15.7 - - + -
234M GLN 2.7 26.7 - - - +
235M ASN 3.0 1.2 + - - -
236M LEU* 1.3 89.8 - - - +
238M TYR* 1.3 95.8 + - + +
240M PRO* 3.7 12.6 - - - +
241M ARG* 4.9 7.1 + - - +
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Residues in contact with TYR 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M ALA 6.6 0.2 - - - -
188M THR* 1.5 51.4 - - + +
233M ALA* 3.5 9.5 - - + +
234M GLN 3.3 13.0 - - - -
235M ASN* 3.5 7.4 + - - +
237M THR* 1.3 106.2 - - + +
239M ILE* 1.3 66.2 + - - +
240M PRO 3.3 1.6 - - - -
241M ARG* 3.0 32.9 + - - +
242M PHE* 2.9 57.1 + + + -
274M PRO* 4.8 7.1 - - + +
275M ILE* 4.6 31.5 - - + +
278M ALA* 4.7 5.4 - - + -
188O GLU* 5.3 4.3 - - - +
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Residues in contact with ILE 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M ASN* 3.3 15.9 - - - +
236M LEU* 4.0 10.5 - - - +
237M THR 3.4 0.2 - - - -
238M TYR* 1.3 75.4 - - - +
240M PRO* 1.3 72.6 - - + +
242M PHE* 4.7 2.2 - - - +
243M CYS* 2.9 38.0 + - - -
253M THR* 3.7 25.1 - - - +
256M ALA* 4.4 9.9 - - + +
257M GLU* 4.3 21.3 - - + +
260M ALA* 5.3 1.8 - - + -
278M ALA* 3.9 22.4 - - + +
281M SER* 5.7 0.2 - - - -
282M ILE* 3.8 26.5 - - + -
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Residues in contact with PRO 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 3.8 28.5 - - + +
108B VAL* 3.0 25.4 - - + +
47L ARG* 6.0 0.4 - - - +
236M LEU 3.5 12.8 - - - +
237M THR 3.7 11.7 - - - +
238M TYR 3.6 0.4 - - - -
239M ILE* 1.3 101.3 - - + +
241M ARG* 1.3 58.9 + - + +
243M CYS* 3.8 3.2 - - + +
244M SER* 2.9 27.9 + - - -
253M THR* 5.5 3.5 - - + +
257M GLU* 5.0 4.9 - - - +
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Residues in contact with ARG 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP 4.2 2.9 - - - +
107B GLY* 3.6 36.1 - - - +
108B VAL* 4.4 2.0 - - - +
186M ALA* 4.9 12.7 + - - +
187M ARG* 5.4 13.4 - - - +
188M THR* 5.0 4.8 + - - +
237M THR 4.9 8.5 + - - +
238M TYR* 3.0 42.7 + - - +
240M PRO* 1.3 73.1 - - - +
242M PHE* 1.3 78.7 + - - +
244M SER* 3.0 15.7 + - - -
245M HIS* 2.7 42.1 + - + -
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Residues in contact with PHE 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M TYR* 2.9 62.6 + + + +
239M ILE 4.5 0.2 - - - +
241M ARG* 1.3 91.3 - - - +
243M CYS* 1.3 58.7 + - - +
245M HIS* 3.3 2.3 + + - -
246M LEU* 2.8 33.5 + - - +
275M ILE* 3.9 6.3 - - + -
282M ILE* 3.9 11.2 - - + -
301M THR* 2.7 43.4 - - + +
302M LEU* 3.0 56.3 - - + -
303M GLN* 5.4 2.9 - - + -
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Residues in contact with CYS 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M ILE* 2.9 40.4 + - - +
240M PRO 3.8 2.0 - - - +
242M PHE* 1.3 77.3 - - - +
244M SER* 1.3 50.7 + - - +
246M LEU* 3.0 9.9 + - - +
247M GLY 2.6 30.8 + - - -
248M LEU* 3.2 23.2 + - + +
252M VAL 5.2 0.2 - - - -
253M THR* 3.1 43.1 - - + -
256M ALA* 5.2 1.3 - - - -
282M ILE* 4.6 15.7 - - - -
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Residues in contact with SER 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.2 21.7 - - - +
109B THR* 4.4 16.3 + - - -
240M PRO 2.9 17.6 + - - -
241M ARG* 3.0 10.8 + - - -
243M CYS* 1.3 76.6 - - - +
245M HIS* 1.3 60.1 - - - +
247M GLY* 2.9 21.3 + - - +
248M LEU 5.4 2.0 - - - -
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Residues in contact with HIS 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ARG* 2.7 53.2 + - + -
242M PHE* 5.1 0.9 - + - -
244M SER* 1.3 79.5 - - - +
246M LEU* 1.3 62.9 + - - +
247M GLY* 3.3 0.9 + - - -
301M THR* 3.4 29.9 + - + +
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Residues in contact with LEU 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M PHE 2.8 25.0 + - - +
243M CYS* 3.2 14.4 - - - +
245M HIS* 1.3 77.8 - - - +
247M GLY* 1.4 58.8 + - - +
248M LEU* 3.4 22.6 - - + +
282M ILE* 3.3 39.9 - - + -
291M ILE* 5.6 0.3 - - - +
293M ILE* 3.7 36.0 - - + +
297M LYS* 3.8 3.4 - - + +
298M VAL* 4.0 8.3 - - + -
301M THR* 3.3 27.8 - - - +
302M LEU* 4.7 0.9 - - + -
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Residues in contact with GLY 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243M CYS 2.6 11.5 + - - -
244M SER* 2.9 14.0 + - - -
245M HIS 4.2 0.9 - - - -
246M LEU* 1.4 76.1 - - - +
248M LEU* 1.3 61.2 + - - -
249M PRO* 4.2 0.2 - - - +
291M ILE* 3.4 13.7 - - - +
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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