Contacts of the helix formed by residues 270 - 286 (chain A) in PDB entry 4MCA
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 TYR 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A SER* 5.8 0.9 - - - -
163A ARG* 3.5 44.7 + - + -
164A LEU* 3.6 32.4 - - + +
167A ALA* 3.9 24.0 - - + -
268A HIS 4.1 8.1 - - - -
269A LEU* 1.3 76.5 - - - +
271A HIS* 1.3 68.5 + - - +
272A GLY 3.2 0.7 - - - +
273A GLU* 2.9 40.3 + - - +
274A LYS* 3.2 10.8 + - - +
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 4.1 22.9 - - + -
129A VAL* 6.0 1.6 - - + -
131A TYR* 3.9 9.4 + - - +
171A ASP* 3.3 16.4 + - - -
254A HIS* 3.3 7.1 + + - -
257A HIS* 2.9 42.5 + + - +
269A LEU 3.8 1.6 + - - -
270A TYR* 1.3 71.3 - - - +
272A GLY* 1.3 58.2 + - - +
274A LYS* 3.1 9.3 + - - +
275A VAL* 3.0 34.8 + - + +
1000A ZN 2.2 32.5 - - - -
1002A GOL 2.8 17.0 + - - -
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Residues in contact with GLY 272 (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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119A SER 4.8 2.6 + - - -
167A ALA* 3.2 29.6 + - - +
170A GLY* 3.4 15.0 - - - -
171A ASP* 3.7 15.5 - - - -
270A TYR* 3.2 3.4 - - - +
271A HIS* 1.3 76.4 - - - +
273A GLU* 1.4 58.3 + - - +
275A VAL* 4.2 2.7 - - - -
276A ALA* 3.0 23.2 + - - +
305A LEU* 4.7 0.2 - - - -
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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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163A ARG* 2.8 49.0 + - - +
166A VAL* 5.8 2.3 - - + +
167A ALA* 4.3 9.1 + - + +
269A LEU* 3.7 17.7 - - + +
270A TYR* 2.9 39.2 + - + +
272A GLY* 1.4 74.6 - - - +
274A LYS* 1.3 63.7 + - - +
276A ALA* 3.4 8.1 + - - +
277A PHE* 3.5 4.9 + - - +
304A GLY 5.5 4.1 - - - +
305A LEU* 4.3 14.4 - - + -
306A PRO* 3.3 40.4 - - + +
312A MET* 4.7 0.2 - - - -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS* 3.7 36.7 - - + +
260A PHE* 4.5 18.5 - - + -
261A THR* 4.9 9.2 - - - -
266A CYS* 3.5 31.6 + - + +
267A HIS* 4.1 9.7 + - - +
269A LEU* 2.7 38.2 + - + +
270A TYR 3.2 8.6 + - - +
271A HIS* 3.1 7.3 + - - +
273A GLU* 1.3 77.0 - - - +
275A VAL* 1.3 57.6 + - - +
277A PHE* 3.3 5.9 + - - +
278A GLY* 3.0 23.4 + - - -
312A MET* 3.8 23.4 - - + +
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Residues in contact with VAL 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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170A GLY 3.6 14.6 - - - +
171A ASP* 3.8 10.3 - - - +
174A SER* 3.5 29.4 - - - +
253A ALA* 4.4 4.1 - - + +
254A HIS* 3.7 14.1 - - + +
257A HIS* 3.8 18.4 - - + -
271A HIS* 3.0 46.2 + - + +
272A GLY* 3.9 5.2 - - - +
273A GLU 3.3 0.2 - - - -
274A LYS* 1.3 74.3 - - - +
276A ALA* 1.3 59.4 + - - +
278A GLY* 3.2 2.8 + - - +
279A THR* 2.9 31.7 + - - -
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Residues in contact with ALA 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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170A GLY* 3.9 8.5 + - - +
173A LEU* 4.4 6.9 - - + +
272A GLY 3.0 16.9 + - - +
273A GLU 3.6 6.7 - - - +
275A VAL* 1.3 76.5 - - - +
277A PHE* 1.3 61.9 + - - +
279A THR* 3.2 9.1 + - - -
280A LEU* 3.2 19.1 + - - +
296A VAL* 5.6 0.7 - - - +
300A CYS* 4.3 10.7 - - - -
305A LEU* 3.8 36.8 - - + -
306A PRO* 4.6 3.1 - - + +
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Residues in contact with PHE 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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260A PHE* 4.0 13.0 - + - -
273A GLU 3.5 3.1 + - - +
274A LYS 3.3 6.9 + - - +
276A ALA* 1.3 75.8 - - - +
278A GLY* 1.3 63.5 + - - +
280A LEU* 3.1 19.7 + - + +
281A ALA* 2.8 26.1 + - + +
306A PRO 3.9 12.7 + - - +
307A ILE* 3.8 34.8 - - - -
308A THR* 3.8 9.0 - - - -
309A LEU* 4.1 21.1 - - + -
312A MET* 3.6 31.4 - - + -
352A ILE* 4.0 40.8 - - + -
355A ALA* 4.2 5.4 - - + -
356A ASP 4.0 8.3 - - - -
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Residues in contact with GLY 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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253A ALA* 3.7 21.2 - - - -
256A ILE* 3.9 27.4 - - - +
257A HIS 5.0 0.4 - - - -
260A PHE* 5.6 0.4 - - - -
274A LYS 3.0 13.9 + - - -
275A VAL 3.2 4.0 + - - -
277A PHE* 1.3 76.5 - - - +
279A THR* 1.3 56.1 + - - +
281A ALA* 3.3 3.7 + - - +
282A GLN* 2.9 27.9 + - - +
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Residues in contact with THR 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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173A LEU* 4.2 14.4 - - + +
174A SER* 3.1 31.9 + - - -
177A PHE* 3.8 35.4 - - + -
253A ALA* 3.6 6.6 - - + +
275A VAL 2.9 13.6 + - - -
276A ALA* 3.3 12.4 - - - -
278A GLY* 1.3 71.3 - - - +
280A LEU* 1.3 65.6 + - - +
282A GLN* 3.1 6.2 + - + +
283A LEU* 2.9 29.3 + - + +
296A VAL* 5.2 3.6 - - + -
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Residues in contact with LEU 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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276A ALA 3.2 11.0 + - - +
277A PHE* 3.1 18.7 + - + +
279A THR* 1.3 76.2 - - - +
281A ALA* 1.3 63.4 + - - +
283A LEU* 3.1 26.6 + - + +
284A VAL* 3.3 16.0 + - + +
293A ILE* 4.2 17.5 - - + -
296A VAL* 5.0 9.7 - - + +
297A LEU* 3.6 39.0 - - + -
306A PRO 5.5 0.4 - - - +
307A ILE* 3.8 17.7 - - + +
355A ALA* 3.7 34.3 - - + +
358A LEU* 5.3 1.8 - - + -
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Residues in contact with ALA 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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256A ILE* 3.9 19.3 - - + -
277A PHE* 2.8 15.1 + - + +
278A GLY* 3.6 9.4 - - - +
279A THR 3.3 0.2 - - - -
280A LEU* 1.3 78.6 - - - +
282A GLN* 1.3 54.9 + - - +
284A VAL* 3.3 2.1 + - - +
285A LEU* 2.9 24.2 + - - +
351A ALA* 3.4 12.1 - - + +
352A ILE* 3.9 29.2 - - + +
355A ALA* 4.0 11.4 - - + +
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Residues in contact with GLN 282 (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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177A PHE* 3.1 38.6 + - + +
178A GLU* 3.5 12.6 - - - +
181A ALA* 3.9 8.5 - - - +
251A ALA* 4.1 0.2 - - - +
252A ALA* 3.2 22.7 + - + -
253A ALA* 3.1 22.6 + - - +
256A ILE* 4.5 1.2 - - - +
278A GLY 2.9 14.3 + - - +
279A THR* 3.1 12.1 + - + +
281A ALA* 1.3 73.8 - - - +
283A LEU* 1.3 63.9 + - + +
285A LEU* 3.1 7.2 + - - +
286A GLN* 2.9 45.7 + - - +
339A MET* 3.9 12.3 - - + -
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Residues in contact with LEU 283 (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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177A PHE* 3.7 39.5 - - + -
279A THR* 2.9 20.4 + - + +
280A LEU* 3.1 12.5 + - + +
282A GLN* 1.3 76.2 - - - +
284A VAL* 1.3 60.7 + - - +
286A GLN* 3.8 5.3 - - - +
287A ASN* 3.1 2.9 + - - -
288A SER* 2.9 52.2 + - - +
292A GLN* 4.3 3.8 - - + +
293A ILE* 4.1 27.0 - - + +
296A VAL* 3.9 38.4 - - + -
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Residues in contact with VAL 284 (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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280A LEU* 3.3 15.0 + - + +
281A ALA 3.3 6.6 + - - +
283A LEU* 1.3 73.1 - - + +
285A LEU* 1.3 67.0 + - - +
287A ASN* 3.1 15.4 + - - +
293A ILE* 4.8 7.0 - - + -
350A ALA 5.1 0.2 - - - -
351A ALA* 3.7 23.6 - - - +
354A THR* 3.9 20.0 - - + -
355A ALA* 4.0 15.7 - - + +
358A LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 285 (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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252A ALA* 3.9 26.7 - - + -
256A ILE* 5.3 3.4 - - + -
281A ALA 2.9 14.5 + - - +
282A GLN* 3.1 9.8 + - + +
284A VAL* 1.3 78.0 - - - +
286A GLN* 1.3 58.6 + - - +
287A ASN* 3.5 1.6 + - - +
336A ILE* 4.3 4.5 - - + -
339A MET* 4.5 2.9 - - + -
341A PHE* 3.8 21.3 - - + -
343A VAL* 4.2 30.3 - - + -
347A GLY* 3.5 35.4 - - - +
348A VAL* 4.1 7.0 - - + +
351A ALA* 3.9 8.5 - - + +
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Residues in contact with GLN 286 (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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177A PHE* 4.5 11.5 + - - +
181A ALA* 4.4 4.5 - - - +
282A GLN* 2.9 47.1 + - - +
283A LEU* 3.8 9.3 - - - +
285A LEU* 1.3 74.3 - - - +
287A ASN* 1.3 67.5 + - - +
288A SER* 3.5 23.8 + - - +
292A GLN* 5.8 1.4 - - - +
339A MET* 3.3 10.5 - - + +
341A PHE* 3.9 24.6 - - + -
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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