Contacts of the helix formed by residues 351 - 360 (chain B) in PDB entry 1M6X
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 PRO 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B LEU* 3.6 24.0 - - + -
326B VAL* 4.8 10.3 - - + -
349B ALA 4.2 4.3 - - - +
350B ILE* 1.3 100.0 - - + +
352B ASP* 1.3 67.8 + - - +
353B HIS* 3.3 26.7 - - + -
354B TYR* 3.2 16.0 + - + +
355B PHE* 3.8 4.2 - - - -
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Residues in contact with ASP 352 (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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207B GLN 4.8 3.3 - - - +
208B ASN* 3.3 32.4 + - - +
209B LYS* 3.3 39.3 + - + +
210B TYR* 3.9 15.2 - - + -
350B ILE 3.6 2.2 + - - +
351B PRO* 1.3 72.9 - - - +
353B HIS* 1.3 65.4 + - - +
354B TYR 3.0 1.6 + - - -
355B PHE* 3.3 9.9 + - - -
356B ALA 3.6 4.0 + - - -
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Residues in contact with HIS 353 (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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210B TYR* 3.7 13.2 - - - +
320B LEU* 5.0 10.4 - - + +
322B GLU* 4.5 10.1 + - - -
323B LEU* 4.2 21.7 - - + +
351B PRO* 3.3 30.9 - - + +
352B ASP* 1.3 74.5 + - - +
354B TYR* 1.3 68.8 + - - +
355B PHE 3.2 0.4 - - - -
356B ALA* 3.1 10.8 + - - +
357B LEU* 3.1 17.0 + - - +
364B TYR* 5.4 4.5 - + - -
369B LYS 5.8 3.1 - - - -
371B MET* 3.2 36.8 - - + +
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Residues in contact with TYR 354 (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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187B ILE 2.6 29.8 + - - -
233B PHE* 5.3 0.9 - + - -
311B MET* 3.4 21.0 - - - +
315B LEU* 4.2 15.7 - - + -
323B LEU* 4.2 22.7 - - + -
327B VAL* 3.6 34.1 - - + +
350B ILE* 3.5 29.2 - - + -
351B PRO* 3.2 16.2 + - + +
352B ASP 3.0 1.0 + - - -
353B HIS* 1.3 84.2 + - - +
355B PHE* 1.3 87.3 + + - +
357B LEU* 3.2 7.0 + - + +
358B VAL* 3.1 43.0 + - + +
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Residues in contact with PHE 355 (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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187B ILE* 5.7 0.4 - - + -
188B ASN* 5.5 0.4 - - - -
208B ASN* 3.6 22.0 - - - +
211B LEU* 3.9 18.6 - - + -
214B ILE* 3.8 14.4 - - + -
231B TYR* 3.4 57.7 - + + -
233B PHE* 3.5 27.5 - + + -
350B ILE* 3.9 23.3 - - + -
351B PRO 3.8 12.8 - - - -
352B ASP* 3.7 6.5 - - - +
353B HIS 3.2 0.4 - - - -
354B TYR* 1.3 86.7 - + - +
356B ALA* 1.3 69.5 + - - +
358B VAL* 4.4 3.4 - - - +
359B SER* 2.8 27.8 + - - -
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Residues in contact with ALA 356 (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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210B TYR* 3.6 41.4 - - + +
211B LEU* 4.5 3.0 - - - +
352B ASP 3.6 2.4 + - - -
353B HIS* 3.1 16.9 + - - +
355B PHE* 1.3 78.3 - - - +
357B LEU* 1.3 60.3 + - - +
359B SER* 2.5 23.7 + - - -
360B ARG 3.5 3.1 + - - -
362B TYR* 3.8 20.6 + - + -
371B MET* 3.8 12.8 - - + -
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Residues in contact with LEU 357 (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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155B TRP* 5.2 1.6 + - - -
314B PHE* 3.5 37.8 - - + -
315B LEU* 5.5 2.2 - - + -
318B LYS* 4.6 13.9 - - + +
320B LEU* 3.8 28.9 - - + -
353B HIS 3.1 4.8 + - - +
354B TYR* 3.5 10.8 - - + +
355B PHE 3.1 0.2 - - - -
356B ALA* 1.3 80.6 - - - +
358B VAL* 1.3 65.0 + - + +
360B ARG* 3.0 18.7 + - - +
362B TYR 4.0 10.0 - - - +
363B ALA* 4.5 0.9 - - - -
364B TYR* 3.9 21.3 - - + +
371B MET* 3.2 23.0 - - + +
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Residues in contact with VAL 358 (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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155B TRP* 3.1 31.6 - - + +
187B ILE* 3.7 31.2 - - + -
233B PHE* 3.8 18.8 - - + -
235B ALA* 4.6 1.6 - - - +
311B MET* 4.1 18.6 - - + -
314B PHE* 4.7 11.7 - - + -
354B TYR* 3.1 48.8 + - + +
355B PHE 4.2 0.2 - - - +
357B LEU* 1.3 78.5 - - + +
359B SER* 1.3 58.8 + - - +
360B ARG* 3.4 0.7 - - - +
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Residues in contact with SER 359 (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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211B LEU* 3.3 27.9 - - - +
233B PHE* 3.7 10.3 - - - -
234B SER 3.5 19.5 - - - -
235B ALA* 3.2 6.1 - - - +
236B ARG 2.8 24.6 + - - -
355B PHE 2.8 13.5 + - - -
356B ALA 2.5 22.3 + - - -
358B VAL* 1.3 76.0 - - - +
360B ARG* 1.3 68.3 + - - +
361B TYR* 3.2 9.3 + - - +
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Residues in contact with ARG 360 (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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155B TRP* 3.4 68.0 - - - +
235B ALA* 5.1 2.5 - - - -
236B ARG* 3.6 33.7 + - + +
237B GLY* 4.9 6.3 - - - -
238B ARG 5.1 1.0 - - - +
239B ILE* 4.8 12.1 - - - +
356B ALA 3.5 0.4 + - - -
357B LEU 3.0 13.9 + - - +
358B VAL 3.4 10.1 - - - +
359B SER* 1.3 82.9 + - - +
361B TYR* 1.3 58.6 + - - +
362B TYR 3.0 11.4 - - - +
374B LEU* 3.3 19.4 - - - +
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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