Contacts of the helix formed by residues 281 - 300 (chain A) in PDB entry 4MYF
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 5.2 4.9 - + - -
54A PHE* 3.5 26.9 - + - -
279A GLU* 3.0 6.0 + - - +
280A GLU* 1.3 87.4 - - + +
282A ARG* 1.3 75.0 + - + +
283A SER 3.4 0.9 - - - -
284A PRO* 3.5 5.1 - - - +
285A ARG* 3.2 57.0 + - - +
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Residues in contact with ARG 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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234A SER 4.9 0.2 + - - -
235A SER 2.8 30.1 + - - -
236A ASP* 4.0 16.3 + - - +
238A PRO* 3.6 23.3 - - + +
279A GLU* 2.8 22.6 + - - +
281A TYR* 1.3 80.9 - - + +
283A SER* 1.3 64.9 + - - +
285A ARG* 3.4 9.7 + - - +
286A VAL* 3.1 26.2 + - + +
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A MET* 3.3 27.4 - - - +
238A PRO* 3.1 13.2 - - - +
239A GLY* 2.7 44.0 + - - -
274A LEU* 3.9 4.0 - - - -
279A GLU* 2.8 24.3 + - - -
282A ARG* 1.3 71.0 - - - +
284A PRO* 1.3 70.3 - - - +
286A VAL* 3.2 2.0 + - - -
287A ALA* 3.0 18.4 + - - +
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Residues in contact with PRO 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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50A ALA* 3.8 31.4 - - + +
51A PHE* 5.0 0.2 - - - -
54A PHE* 3.6 20.2 - - + -
274A LEU* 4.1 18.2 - - + -
276A PRO* 4.9 2.9 - - + -
279A GLU 4.1 3.6 - - - +
280A GLU* 3.3 31.2 - - - +
281A TYR 3.5 10.3 - - - +
283A SER* 1.3 94.9 - - - +
285A ARG* 1.3 55.4 + - - +
287A ALA* 3.3 2.1 + - - +
288A VAL* 3.0 32.9 + - - +
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Residues in contact with ARG 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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54A PHE* 3.6 26.5 - - + -
57A ARG* 6.1 0.2 - - - +
58A LEU* 3.6 31.3 - - + +
281A TYR* 3.2 53.5 + - - +
282A ARG* 3.4 10.3 + - - +
283A SER 3.2 0.6 - - - -
284A PRO* 1.3 75.7 - - - +
286A VAL* 1.3 60.2 + - + +
288A VAL* 3.2 2.8 + - - +
289A TYR* 2.9 65.9 + - + -
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Residues in contact with VAL 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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232A LEU* 3.9 22.0 - - + -
236A ASP* 3.6 21.1 - - + +
237A MET* 3.6 18.6 - - + -
250A ALA* 4.6 12.8 - - + -
254A PHE* 3.7 15.4 - - + -
282A ARG* 3.1 15.6 + - + +
283A SER 3.2 7.6 + - - +
285A ARG* 1.3 75.6 - - + +
287A ALA* 1.3 57.7 + - - +
289A TYR* 3.3 7.4 + - + -
290A MET* 2.9 33.9 + - - +
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Residues in contact with ALA 287 (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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51A PHE* 3.6 10.4 - - + -
237A MET* 4.0 8.3 - - + +
271A MET* 3.6 28.8 - - - +
274A LEU* 3.9 26.5 - - + -
283A SER 3.0 12.3 + - - +
284A PRO 3.5 7.9 - - - +
285A ARG 3.2 0.2 - - - -
286A VAL* 1.3 77.4 - - - +
288A VAL* 1.3 61.5 + - - +
290A MET* 3.3 8.4 + - - +
291A PHE 3.1 17.2 + - - -
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Residues in contact with VAL 288 (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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10A LEU* 4.2 13.5 - - + -
51A PHE* 3.3 46.2 - - + +
54A PHE* 3.8 22.7 - - + +
55A LEU* 3.7 17.0 - - + +
58A LEU* 4.0 19.5 - - + -
284A PRO 3.0 20.4 + - - +
285A ARG 3.8 3.4 - - - +
287A ALA* 1.3 74.6 - - - +
289A TYR* 1.3 58.4 + - - +
291A PHE* 3.2 3.3 + - + +
292A TYR* 2.8 27.1 + - + +
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Residues in contact with TYR 289 (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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9A ARG* 5.5 2.3 + - - -
58A LEU* 3.7 36.8 - - + +
59A GLY* 4.3 11.4 + - - -
254A PHE* 3.4 33.4 - + + -
285A ARG* 2.9 51.3 + - + +
286A VAL* 3.7 1.1 - - + +
288A VAL* 1.3 78.0 - - - +
290A MET* 1.3 57.8 + - - +
292A TYR* 3.4 21.0 - + + +
293A HIS* 2.8 38.8 + + - +
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Residues in contact with MET 290 (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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227A PHE* 3.5 54.1 - - + -
229A VAL* 3.9 24.0 - - + -
232A LEU* 4.2 3.6 - - - -
253A ALA* 4.0 15.9 - - + -
254A PHE* 3.8 19.3 - - + -
257A CYS* 3.2 24.4 - - - +
271A MET* 3.8 12.8 - - + -
286A VAL* 2.9 30.2 + - - +
287A ALA* 3.4 9.9 - - - +
288A VAL 3.2 0.2 - - - -
289A TYR* 1.3 74.7 - - - +
291A PHE* 1.3 65.0 + - - +
293A HIS 3.3 1.4 + - - -
294A PHE* 3.1 18.2 + - - +
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Residues in contact with PHE 291 (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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10A LEU* 4.1 13.9 - - + -
24A ILE* 4.2 11.4 - - + -
26A ILE* 3.7 28.7 - - + -
51A PHE* 3.7 26.9 - + + -
55A LEU* 4.0 12.1 - - + -
75A LEU* 4.1 13.7 - - + -
108A PHE* 3.7 50.7 - + + -
257A CYS* 5.6 0.2 - - - -
269A MET* 5.7 0.4 - - - -
271A MET* 4.2 3.7 - - - +
287A ALA 3.1 5.5 + - - +
288A VAL 3.5 6.5 - - - +
290A MET* 1.3 78.6 - - - +
292A TYR* 1.3 59.5 + - - +
294A PHE* 3.1 14.1 + + - +
295A VAL* 2.9 52.7 + - + +
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Residues in contact with TYR 292 (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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10A LEU* 3.9 28.0 - - + -
59A GLY* 3.4 26.5 - - - -
60A SER* 2.4 40.2 + - - -
61A VAL* 4.7 0.9 - - - -
63A ASN* 3.3 26.7 + - - +
288A VAL* 2.8 17.7 + - + +
289A TYR* 3.4 20.2 - + + +
291A PHE* 1.3 77.7 - - - +
293A HIS* 1.3 78.4 + + - +
295A VAL* 3.1 7.8 + - + +
296A LEU* 3.0 52.8 + - + +
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Residues in contact with HIS 293 (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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63A ASN* 5.2 2.0 + - - -
66A LEU* 4.0 27.6 - - + +
251A GLN* 5.0 4.2 + - - -
254A PHE* 3.3 65.3 - + + +
255A ASP* 5.4 3.1 - - - -
258A PHE* 3.4 19.6 - - + +
289A TYR* 2.8 32.2 + + + +
290A MET 3.8 4.7 - - - +
292A TYR* 1.3 90.9 - + - +
294A PHE* 1.3 66.6 + - - +
296A LEU* 3.3 5.9 + - + +
297A GLY 3.0 18.5 + - - -
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Residues in contact with PHE 294 (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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24A ILE* 4.1 13.2 - - + -
106A PHE* 3.0 52.7 - + - -
108A PHE* 5.6 0.9 - + + -
257A CYS* 3.3 19.6 + - + +
260A ALA* 3.9 9.9 - - + -
261A GLY* 3.4 31.1 - - - -
266A VAL* 4.6 4.5 - - + -
269A MET* 4.3 20.4 - - - -
290A MET 3.1 13.2 + - - +
291A PHE* 3.1 21.1 + + - +
293A HIS* 1.3 75.8 - - - +
295A VAL* 1.3 66.1 + - + +
297A GLY 3.2 1.0 + - - -
298A PHE* 2.8 47.0 + + - +
301A ARG* 4.1 0.9 - - - -
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Residues in contact with VAL 295 (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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10A LEU* 4.3 11.2 - - + -
13A LEU* 4.2 16.2 - - + -
24A ILE* 4.2 11.7 - - + -
70A ALA* 4.2 12.8 - - + -
73A LEU* 3.4 22.7 - - + +
75A LEU* 4.6 6.1 - - + -
291A PHE* 2.9 51.5 + - + +
292A TYR* 3.1 9.4 + - + +
294A PHE* 1.3 79.5 - - + +
296A LEU* 1.3 57.5 + - + +
298A PHE* 3.3 4.3 + - - +
299A ALA* 2.9 23.6 + - - +
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Residues in contact with LEU 296 (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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60A SER 4.4 0.2 - - - +
61A VAL* 4.0 12.8 - - - +
63A ASN* 3.6 22.4 - - + +
66A LEU* 3.9 17.5 - - + -
68A VAL* 3.3 28.4 - - + +
70A ALA* 4.0 19.5 - - + -
258A PHE* 3.8 11.2 - - + -
292A TYR* 3.0 55.7 + - + +
293A HIS* 3.7 9.6 - - + +
295A VAL* 1.3 73.0 - - + +
297A GLY* 1.3 68.0 + - - +
299A ALA* 3.2 17.9 + - - +
300A THR* 3.6 3.3 + - - +
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Residues in contact with GLY 297 (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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258A PHE* 3.5 39.4 - - - -
261A GLY 3.3 6.7 - - - -
262A LYS* 3.3 9.0 - - - -
293A HIS 3.0 11.1 + - - -
294A PHE 3.7 2.0 - - - -
296A LEU* 1.3 75.6 - - - +
298A PHE* 1.3 60.6 + - - +
300A THR* 2.7 24.5 + - - -
301A ARG 3.7 0.5 + - - -
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Residues in contact with PHE 298 (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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23A ASP* 4.1 18.4 - - + -
24A ILE* 3.7 16.2 - - + -
72A HIS* 5.4 0.3 + - - -
73A LEU* 3.8 22.7 - - + +
106A PHE* 3.9 28.9 - + + -
261A GLY 3.1 11.1 + - - +
294A PHE* 2.8 37.6 + + + +
295A VAL* 3.5 7.2 - - - +
297A GLY* 1.3 75.6 - - - +
299A ALA* 1.3 63.7 + - - +
301A ARG* 3.0 63.7 + - + +
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Residues in contact with ALA 299 (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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68A VAL* 4.0 8.7 - - + -
69A ASP 4.1 4.0 - - - +
70A ALA* 3.8 24.2 - - + -
72A HIS* 3.2 24.6 + - + -
73A LEU* 3.7 17.6 - - + +
295A VAL 2.9 13.6 + - - +
296A LEU 3.2 13.5 - - - +
297A GLY 3.1 0.4 - - - -
298A PHE* 1.3 77.6 - - - +
300A THR* 1.3 57.8 + - - +
301A ARG 3.6 4.2 + - - +
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Residues in contact with THR 300 (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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68A VAL* 3.7 27.6 - - + -
258A PHE* 4.6 6.7 - - + -
262A LYS* 3.4 18.9 - - - +
296A LEU 3.6 14.4 - - - +
297A GLY* 2.7 17.7 + - - -
299A ALA* 1.3 76.4 - - - +
301A ARG* 1.3 64.7 + - - +
302A PRO* 3.4 6.2 - - - +
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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