Contacts of the helix formed by residues 270 - 282 (chain A) in PDB entry 7CAL
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 ASN 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ILE 4.9 2.4 + - - -
223A TYR* 3.3 61.9 - - + +
228A LYS* 4.0 8.3 - - + +
229A THR* 4.0 3.2 - - - +
269A GLU* 1.3 76.6 + - - +
271A PRO* 1.3 65.2 - - + +
272A ARG* 3.1 12.1 + - + +
273A GLU* 3.1 46.6 + - - +
274A MET* 3.3 13.0 + - - +
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Residues in contact with PRO 271 (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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223A TYR* 4.8 4.3 - - - +
269A GLU 4.5 1.8 - - - +
270A ASN* 1.3 86.2 - - + +
272A ARG* 1.3 60.0 + - + +
273A GLU 3.5 0.2 - - - -
274A MET* 3.9 19.1 - - + +
275A LEU* 3.7 25.5 + - - +
235B TYR* 5.8 1.8 - - - +
246B ARG* 6.2 4.0 - - + -
248B VAL* 5.0 10.1 - - + +
249B THR* 6.1 0.2 - - - +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 3.8 27.1 + - + +
222A ARG* 3.3 27.9 + - - +
223A TYR* 3.8 31.2 - - + +
224A PRO* 3.5 21.4 - - - +
270A ASN* 3.1 6.9 - - + +
271A PRO* 1.3 79.4 - - + +
273A GLU* 1.3 62.9 + - - +
274A MET 3.3 0.2 - - - -
275A LEU* 3.5 8.7 + - - +
276A PHE* 3.3 19.6 + - - +
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Residues in contact with GLU 273 (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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216A ASN* 4.2 12.6 - - - +
219A ILE* 3.7 17.1 - - + +
220A ALA* 4.3 6.6 - - - -
229A THR* 3.5 18.9 - - - +
230A TRP* 3.2 46.9 + - + +
268A ALA* 3.7 13.3 - - + +
269A GLU 3.6 9.9 + - - -
270A ASN* 3.1 25.4 + - - +
272A ARG* 1.3 75.3 - - - +
274A MET* 1.3 60.0 + - - +
275A LEU 3.3 0.9 - - - -
276A PHE* 3.7 6.1 - - - +
277A ASP* 3.0 36.2 + - - +
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Residues in contact with MET 274 (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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268A ALA* 3.9 25.1 - - + +
269A GLU 4.5 3.8 - - - +
270A ASN 3.3 14.0 + - - +
271A PRO* 4.2 15.0 - - + -
272A ARG 3.3 0.4 - - - -
273A GLU* 1.3 78.4 - - - +
275A LEU* 1.3 61.5 + - - +
277A ASP* 4.2 1.0 - - - +
278A ILE* 3.2 29.6 + - - +
235B TYR* 4.0 21.1 - - - +
248B VAL* 4.0 15.9 - - + -
249B THR* 3.8 33.2 - - + +
252B TYR* 4.0 24.0 - - + -
266B PHE* 4.1 24.7 - - + -
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Residues in contact with LEU 275 (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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271A PRO 3.7 15.3 + - - +
272A ARG* 3.5 11.1 + - - +
273A GLU 3.3 0.4 - - - -
274A MET* 1.3 77.9 - - - +
276A PHE* 1.3 63.8 + - - +
278A ILE* 3.4 8.7 + - + +
279A PHE* 3.2 49.4 + - + -
246B ARG* 3.5 31.6 - - - +
248B VAL* 4.0 14.8 - - + -
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Residues in contact with PHE 276 (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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212A ALA* 4.2 16.4 - - + -
215A PHE* 3.9 38.8 - + + -
216A ASN* 3.2 38.4 - - + +
219A ILE* 4.9 11.4 - - + -
253A TRP* 4.1 9.9 - + - -
272A ARG 3.3 13.5 + - - +
273A GLU* 3.5 6.5 + - - +
274A MET 3.4 0.2 - - - -
275A LEU* 1.3 78.7 - - - +
277A ASP* 1.3 63.6 + - - +
279A PHE* 3.5 9.1 + + + -
280A PHE* 2.9 38.1 + + + +
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Residues in contact with ASP 277 (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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216A ASN* 4.4 2.8 + - - +
253A TRP* 3.3 36.8 + - - -
268A ALA* 4.2 8.9 + - - +
273A GLU* 3.0 20.8 + - - +
275A LEU 3.3 0.2 - - - -
276A PHE* 1.3 79.2 - - - +
278A ILE* 1.3 60.6 + - - +
280A PHE* 4.3 4.5 - - - -
281A MET* 2.9 41.7 + - + +
252B TYR* 3.8 30.7 + - + -
263B TYR* 3.7 16.2 + - - -
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Residues in contact with ILE 278 (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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274A MET 3.2 21.2 + - - +
275A LEU* 3.8 8.3 - - + +
276A PHE 3.2 0.4 - - - -
277A ASP* 1.3 78.1 - - - +
279A PHE* 1.3 73.3 + - + +
281A MET 4.0 0.5 - - - -
282A MET* 3.1 41.0 + - + +
701A 3PE 5.6 2.5 - - + -
209B ILE* 6.2 2.9 - - + -
248B VAL* 3.8 22.0 - - + +
251B LEU* 3.9 31.9 - - + +
252B TYR* 3.9 9.9 - - + +
255B ILE* 3.9 27.5 - - + +
701B 3PE 5.9 2.9 - - + -
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Residues in contact with PHE 279 (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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275A LEU* 3.2 43.2 + - + +
276A PHE* 4.1 10.3 - + + +
278A ILE* 1.3 84.1 - - + +
280A PHE* 1.3 59.1 + - - +
282A MET* 3.8 25.5 - - + +
283A PHE* 3.7 17.0 + - - +
701B 3PE 6.5 1.3 - - + -
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Residues in contact with PHE 280 (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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208A ALA 4.4 4.3 - - - -
212A ALA* 3.6 33.2 - - + -
253A TRP* 4.0 24.9 - + - -
254A SER* 4.4 8.1 - - - -
257A THR* 3.2 27.4 - - - -
258A LEU* 4.2 16.2 - - + -
276A PHE* 2.9 29.7 + + + +
277A ASP* 4.1 5.2 - - - +
279A PHE* 1.3 77.0 - - - +
281A MET* 1.3 63.6 + - + +
282A MET 3.2 1.8 - - - -
283A PHE* 3.1 18.7 + + + +
284A ASN* 2.9 55.2 + - - +
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Residues in contact with MET 281 (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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257A THR* 5.0 11.0 - - - +
277A ASP* 2.9 45.4 + - + +
278A ILE 4.0 0.2 - - - -
280A PHE* 1.3 78.0 - - + +
282A MET* 1.3 59.8 + - - +
284A ASN* 3.9 14.6 - - + +
285A LEU* 3.7 10.0 + - - +
252B TYR* 4.1 8.5 - - + -
255B ILE* 3.7 36.5 - - + +
256B THR* 3.9 14.6 - - - +
259B THR* 3.4 28.3 - - + +
261B THR* 3.6 29.4 - - - +
263B TYR* 4.3 14.1 - - + +
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Residues in contact with MET 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 3.1 20.8 + - + +
279A PHE* 3.8 35.7 - - + +
281A MET* 1.3 75.2 - - - +
283A PHE* 1.3 64.6 + - - +
284A ASN 3.3 0.2 - - - -
285A LEU* 3.6 10.2 + - + +
286A GLY 3.6 12.8 + - - -
701A 3PE 1.8 110.8 - - + +
206B LEU* 4.9 0.2 - - + -
209B ILE* 4.5 2.5 - - + -
255B ILE* 3.8 18.4 - - + -
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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