Contacts of the helix formed by residues 281 - 299 (chain B) in PDB entry 4MXR
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 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 5.6 3.8 - + - -
54B PHE* 3.7 22.8 - + - -
279B GLU* 3.0 7.5 + - - +
280B GLU* 1.3 83.7 - - + +
282B ARG* 1.3 75.2 + - + +
283B SER 3.3 1.6 - - - -
284B PRO* 3.4 7.8 - - - +
285B ARG* 3.2 58.0 + - - +
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Residues in contact with ARG 282 (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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234B SER 4.9 0.4 + - - -
235B SER 2.7 30.5 + - - -
236B ASP* 4.0 16.3 + - - +
238B PRO* 3.9 21.9 - - + +
279B GLU* 2.8 21.4 + - - +
281B TYR* 1.3 84.0 - - + +
283B SER* 1.3 58.5 + - - +
285B ARG* 3.4 10.4 + - - +
286B VAL* 3.1 32.7 + - + +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B MET* 3.5 23.0 - - - +
238B PRO* 3.1 11.7 - - - +
239B GLY* 2.8 34.8 + - - -
274B LEU* 3.7 9.3 - - - +
279B GLU* 2.6 28.8 + - - -
282B ARG* 1.3 71.0 - - - +
284B PRO* 1.3 72.6 - - - +
286B VAL* 3.2 5.7 + - - +
287B ALA 3.0 17.5 + - - -
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Residues in contact with PRO 284 (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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50B ALA* 3.7 32.1 - - + +
51B PHE* 4.5 0.6 - - - +
54B PHE* 3.6 20.2 - - + -
274B LEU* 4.0 19.5 - - + -
276B PRO* 4.9 2.2 - - + -
279B GLU 4.0 3.6 - - - +
280B GLU* 3.3 28.3 - - - +
281B TYR 3.4 10.8 - - - +
283B SER* 1.3 96.1 - - - +
285B ARG* 1.3 54.2 + - - +
287B ALA* 3.3 2.3 + - - +
288B VAL* 2.9 33.3 + - - +
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Residues in contact with ARG 285 (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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54B PHE* 3.5 33.5 - - + -
57B ARG* 6.3 0.2 - - - +
58B LEU* 4.1 33.3 - - + +
281B TYR* 3.2 57.4 + - - +
282B ARG* 3.4 10.0 + - - +
283B SER 3.1 0.4 - - - -
284B PRO* 1.3 75.2 - - - +
286B VAL* 1.3 64.2 + - + +
288B VAL* 3.3 2.8 + - - +
289B TYR* 3.0 46.3 + - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.9 20.9 - - + -
236B ASP 3.7 21.3 - - - +
237B MET* 3.7 20.0 - - + -
250B ALA* 4.7 13.0 - - + -
254B PHE* 3.7 12.7 - - + -
282B ARG* 3.1 16.6 + - + +
283B SER 3.2 7.6 + - - +
285B ARG* 1.3 76.0 - - + +
287B ALA* 1.3 56.8 + - - +
289B TYR* 3.2 9.7 + - + +
290B MET* 2.9 33.3 + - - +
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Residues in contact with ALA 287 (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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51B PHE* 3.6 10.7 - - + -
237B MET* 4.2 8.1 - - + -
271B MET* 3.5 30.7 - - - +
274B LEU* 4.0 25.4 - - + -
283B SER 3.0 13.1 + - - +
284B PRO 3.5 8.3 - - - +
286B VAL* 1.3 76.0 - - - +
288B VAL* 1.3 62.6 + - - +
290B MET* 3.3 7.3 + - - +
291B PHE 3.1 17.5 + - - -
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Residues in contact with VAL 288 (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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10B LEU* 4.4 13.2 - - + -
51B PHE* 3.2 45.3 - - + +
54B PHE* 3.7 23.1 - - + +
55B LEU* 3.7 16.8 - - + +
58B LEU* 3.9 18.8 - - + -
284B PRO 2.9 20.3 + - - +
285B ARG 3.8 4.0 - - - +
286B VAL 3.3 0.2 - - - -
287B ALA* 1.3 75.9 - - - +
289B TYR* 1.3 58.3 + - - +
291B PHE* 3.3 3.1 + - - +
292B TYR* 2.8 27.6 + - + +
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Residues in contact with TYR 289 (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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58B LEU* 3.5 42.5 - - + +
59B GLY* 4.4 10.8 + - - -
254B PHE* 3.3 32.8 - + + -
285B ARG* 3.0 44.7 + - + +
286B VAL* 4.6 0.9 - - - -
288B VAL* 1.3 76.2 - - - +
290B MET* 1.3 58.0 + - - +
292B TYR* 3.4 22.2 - + + +
293B HIS* 2.8 41.2 + + - +
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Residues in contact with MET 290 (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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227B PHE* 3.5 52.9 - - + -
229B VAL* 4.1 17.7 - - + -
232B LEU* 4.4 4.9 - - - -
253B ALA* 4.1 13.2 - - + -
254B PHE* 3.9 20.2 - - + -
257B CYS* 3.2 27.1 - - - +
271B MET* 3.7 15.9 - - + -
286B VAL* 2.9 30.6 + - + +
287B ALA* 3.5 9.9 - - - +
288B VAL 3.2 0.2 - - - -
289B TYR* 1.3 74.3 - - - +
291B PHE* 1.3 66.2 + - - +
293B HIS* 3.3 1.4 + - - -
294B PHE* 3.1 17.0 + - - +
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Residues in contact with PHE 291 (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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10B LEU* 4.0 12.8 - - + -
24B ILE* 4.2 12.8 - - + -
26B ILE* 3.8 26.9 - - + -
51B PHE* 3.7 28.0 - + + -
55B LEU* 4.2 8.7 - - + -
75B LEU* 4.1 16.4 - - + -
108B PHE* 3.6 51.1 - + + -
269B MET* 5.5 0.7 - - - -
271B MET* 4.2 3.9 - - - +
287B ALA 3.1 5.2 + - - +
288B VAL 3.6 6.5 - - - +
290B MET* 1.3 78.7 - - - +
292B TYR* 1.3 59.2 + - - +
294B PHE* 3.0 14.8 + + - +
295B VAL* 2.8 52.0 + - + +
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Residues in contact with TYR 292 (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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10B LEU* 3.8 28.7 - - + -
58B LEU* 6.4 0.2 - - + -
59B GLY* 3.3 26.2 - - - -
60B SER* 2.6 39.0 + - - -
61B VAL* 4.6 1.1 - - - -
63B ASN* 3.1 28.7 + - - +
288B VAL* 2.8 18.6 + - + +
289B TYR* 3.4 20.6 - + + +
291B PHE* 1.3 75.2 - - - +
293B HIS* 1.3 78.5 + + - +
295B VAL* 3.1 7.1 + - + +
296B LEU* 2.9 52.6 + - + +
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Residues in contact with HIS 293 (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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63B ASN* 5.3 2.0 + - - -
66B LEU* 4.1 26.5 - - + +
251B GLN* 5.0 4.6 + - - -
254B PHE* 3.3 64.6 - + + +
255B ASP* 5.3 2.5 - - - -
257B CYS* 4.2 0.2 - - + -
258B PHE* 3.2 22.3 - - + +
289B TYR* 2.8 32.8 + + + +
290B MET 3.3 4.7 + - - +
292B TYR* 1.3 91.4 - + - +
294B PHE* 1.3 65.2 + - - +
296B LEU* 3.5 6.9 + - + -
297B GLY 3.1 17.5 + - - -
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Residues in contact with PHE 294 (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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24B ILE* 3.9 24.0 - - + -
106B PHE* 3.0 50.7 - + - -
108B PHE* 5.6 0.4 - + - -
257B CYS* 3.2 19.2 + - + +
260B ALA* 3.9 13.5 - - + -
261B GLY* 3.4 31.2 - - - -
266B VAL* 4.6 2.2 - - + -
269B MET* 4.3 20.4 - - + -
290B MET 3.1 11.7 + - - +
291B PHE* 3.0 20.6 + + - +
293B HIS* 1.3 77.9 - - - +
295B VAL* 1.3 63.5 + - + +
297B GLY 3.1 1.4 + - - -
298B PHE* 2.8 40.2 + + - +
301B ARG* 4.2 0.7 - - - -
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Residues in contact with VAL 295 (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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10B LEU* 4.1 9.6 - - + -
13B LEU* 4.1 23.3 - - + -
24B ILE* 4.3 10.3 - - + -
70B ALA* 4.2 7.0 - - + -
73B LEU* 3.4 21.1 - - + +
75B LEU* 4.5 5.4 - - + -
291B PHE* 2.8 53.9 + - + +
292B TYR* 3.1 10.3 + - + +
294B PHE* 1.3 79.3 - - + +
296B LEU* 1.3 64.3 + - + +
298B PHE* 3.2 4.6 + - - -
299B ALA* 3.0 18.5 + - - +
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Residues in contact with LEU 296 (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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61B VAL 3.9 20.9 - - - +
63B ASN* 3.7 17.0 - - + +
66B LEU* 3.9 16.4 - - + -
68B VAL* 3.2 36.6 - - + +
70B ALA* 4.1 10.8 - - + -
258B PHE* 3.8 11.9 - - + -
292B TYR* 2.9 60.4 + - + +
293B HIS* 3.7 11.0 - - + +
294B PHE 3.3 0.2 - - - -
295B VAL* 1.3 76.3 - - + +
297B GLY* 1.3 64.3 + - - +
299B ALA* 3.1 12.0 + - - +
300B THR* 3.6 2.8 - - - +
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Residues in contact with GLY 297 (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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258B PHE* 3.5 38.7 - - - -
261B GLY 3.2 6.7 - - - -
262B LYS* 3.3 8.4 - - - -
293B HIS 3.1 11.3 + - - -
294B PHE 3.6 1.8 - - - -
296B LEU* 1.3 75.9 - - - +
298B PHE* 1.3 62.4 + - - +
300B THR* 2.7 25.2 + - - -
301B ARG 3.8 0.5 + - - -
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Residues in contact with PHE 298 (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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23B ASP* 4.0 19.5 - - + -
24B ILE* 3.8 16.6 - - + -
72B HIS* 5.3 0.2 + - - -
73B LEU* 3.7 29.0 - - + +
106B PHE* 4.0 25.8 - + + -
261B GLY 3.1 11.9 + - - +
294B PHE* 2.8 32.5 + + + +
295B VAL 3.2 5.6 + - - +
297B GLY* 1.3 75.0 - - - +
299B ALA* 1.3 58.2 + - - +
301B ARG* 3.0 65.0 + - + +
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Residues in contact with ALA 299 (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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68B VAL* 4.0 5.2 - - + -
69B ASP 3.9 4.0 - - - +
70B ALA* 3.8 24.5 - - + -
72B HIS* 3.2 29.7 + - + -
73B LEU* 3.7 22.0 - - + -
295B VAL 3.0 7.9 + - - +
296B LEU 3.1 12.5 + - - +
298B PHE* 1.3 76.3 - - - +
300B THR* 1.3 59.1 + - - +
301B ARG 3.4 3.7 + - - +
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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