Contacts of the helix formed by residues 351 - 360 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PRO* 5.2 6.5 - - + -
323D LEU* 3.8 25.4 - - + -
326D VAL* 4.6 12.1 - - + -
327D VAL* 5.4 1.1 - - + -
349D ALA* 3.1 12.5 - - + +
350D ILE* 1.3 94.5 - - + +
352D ASP* 1.3 66.3 + - - +
353D HIS* 3.3 27.1 - - + -
354D TYR* 3.1 18.1 + - + +
355D PHE* 3.8 2.6 - - - -
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Residues in contact with ASP 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D GLN 4.4 5.4 - - - +
208D ASN* 2.9 37.2 + - - +
209D LYS* 2.9 41.3 + - + +
210D TYR* 4.0 11.1 - - + -
350D ILE 3.7 2.0 + - - +
351D PRO* 1.3 71.9 - - - +
353D HIS* 1.3 64.3 + - - +
354D TYR 3.0 1.4 + - - -
355D PHE* 3.4 7.4 + - - -
356D ALA 3.6 3.6 + - - -
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Residues in contact with HIS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PRO* 4.0 23.3 - - + +
367A ILE* 4.5 30.1 + - + +
210D TYR* 3.6 30.9 - - + +
320D LEU* 5.0 10.0 - - + +
322D GLU* 4.6 6.4 + - - -
323D LEU* 4.1 24.9 - - + +
351D PRO* 3.3 30.3 - - + +
352D ASP* 1.3 74.3 + - - +
354D TYR* 1.3 66.1 + - - +
355D PHE 3.3 0.2 - - - -
356D ALA* 3.1 3.9 + - - +
357D LEU* 3.0 22.5 + - - +
364D TYR* 6.1 0.2 - + - -
371D MET* 4.0 16.4 - - + +
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Residues in contact with TYR 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ILE 2.7 29.3 + - - -
188D ASN* 5.6 0.2 - - - -
233D PHE* 5.3 0.7 - + - -
311D MET* 3.4 18.6 - - - +
315D LEU* 4.0 26.5 - - + -
323D LEU* 4.3 17.3 - - + -
327D VAL* 3.4 38.0 - - + +
350D ILE* 3.3 24.9 - - + -
351D PRO* 3.1 16.4 + - + +
352D ASP 3.0 1.0 + - - -
353D HIS* 1.3 83.8 + - - +
355D PHE* 1.3 83.4 + + - +
357D LEU* 3.1 5.5 + - + +
358D VAL* 3.1 44.8 + - + +
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Residues in contact with PHE 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D ILE* 5.7 0.4 - - + -
188D ASN* 5.5 0.7 - - - -
208D ASN* 3.5 22.2 - - - +
211D LEU* 3.9 18.4 - - + -
214D ILE* 3.8 13.9 - - + -
231D TYR* 3.4 55.9 - + + -
233D PHE* 3.4 27.1 - + + -
350D ILE* 3.5 34.1 - - + -
351D PRO 3.8 5.6 - - - -
352D ASP* 3.7 6.3 - - - +
353D HIS 3.3 0.2 - - - -
354D TYR* 1.3 85.2 - + - +
356D ALA* 1.3 68.9 + - - +
358D VAL* 4.4 3.6 - - - +
359D SER* 2.8 28.2 + - - -
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Residues in contact with ALA 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ASN* 4.7 0.6 + - - -
210D TYR* 3.3 48.9 - - + -
211D LEU* 4.5 2.8 - - - +
352D ASP 3.6 2.2 + - - -
353D HIS* 3.1 13.1 + - - +
355D PHE* 1.3 78.1 - - - +
357D LEU* 1.3 60.0 + - - +
359D SER* 2.6 23.5 + - - -
360D ARG 3.5 2.8 + - - -
362D TYR* 3.8 18.0 + - + -
371D MET* 4.1 10.5 - - + -
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D PHE* 3.7 33.2 - - + -
315D LEU* 4.7 7.6 - - + -
318D LYS* 4.5 19.3 - - + +
320D LEU* 3.5 30.1 - - + -
323D LEU* 6.2 0.2 - - + -
353D HIS 3.0 8.2 + - - +
354D TYR* 3.5 9.6 - - + +
356D ALA* 1.3 81.4 - - - +
358D VAL* 1.3 63.3 + - + +
360D ARG* 3.0 18.9 + - - +
362D TYR 4.0 14.9 - - - +
363D ALA* 4.3 1.6 - - - -
364D TYR* 4.1 16.8 - - + +
371D MET* 3.9 17.6 - - + +
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Residues in contact with VAL 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 3.1 29.5 - - + +
187D ILE* 3.7 29.6 - - + -
233D PHE* 3.7 18.9 - - + -
235D ALA* 4.6 1.7 - - - +
311D MET* 3.8 20.4 - - + -
314D PHE* 4.4 11.9 - - + -
354D TYR* 3.1 49.3 + - + +
355D PHE 4.2 0.4 - - - +
357D LEU* 1.3 77.5 - - + +
359D SER* 1.3 60.4 + - - +
360D ARG* 4.0 0.4 - - - -
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Residues in contact with SER 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.3 27.3 - - - +
233D PHE* 3.7 10.5 - - - -
234D SER 3.5 19.1 - - - -
235D ALA* 3.1 5.9 - - - +
236D ARG 2.8 24.9 + - - -
355D PHE 2.8 14.6 + - - -
356D ALA 2.6 21.7 + - - -
358D VAL* 1.3 74.4 - - - +
360D ARG* 1.3 68.0 + - - +
361D TYR* 3.2 9.8 + - - +
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 3.4 69.6 + - - +
235D ALA* 5.1 1.8 - - - -
236D ARG* 3.5 35.2 + - + +
237D GLY* 4.9 6.5 - - - -
238D ARG* 5.1 2.0 - - - +
239D ILE* 4.8 11.9 - - - +
356D ALA 3.5 0.4 + - - -
357D LEU 3.0 13.6 + - - +
358D VAL 3.4 10.1 - - - +
359D SER* 1.3 81.7 + - - +
361D TYR* 1.3 56.4 + - - +
362D TYR 3.0 10.5 - - - +
374D LEU* 3.2 23.2 - - - +
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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