Contacts of the helix formed by residues 354 - 365 (chain A) in PDB entry 1M2V
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 GLY 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ILE* 4.0 12.3 - - - +
309A ARG* 3.9 6.7 - - - -
352A GLN* 3.5 2.2 - - - +
353A ILE* 1.3 81.5 - - - +
355A MET* 1.3 62.0 + - - +
356A SER 3.0 2.7 - - - -
357A GLU* 3.1 19.9 + - - +
358A MET* 2.8 36.1 + - - +
604A ASP* 3.1 3.9 + - - -
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.0 8.3 - - + -
347A ALA* 3.5 22.0 - - + +
353A ILE* 3.7 12.3 - - + -
354A GLY* 1.3 77.9 - - - +
356A SER* 1.3 56.5 + - - +
358A MET* 3.7 7.4 - - - +
359A LYS* 2.7 35.0 + - - +
369A LEU* 3.6 35.4 - - + -
370A LEU 3.2 35.0 - - - +
371A LEU* 3.8 24.9 - - - +
604A ASP* 2.9 26.1 + - + +
607A ALA* 3.9 10.1 - - + +
608A PHE* 4.8 3.1 - - - -
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Residues in contact with SER 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ARG* 3.7 12.6 - - - -
311A HIS* 5.6 1.9 - - - -
314A ILE* 4.5 1.2 - - - +
322A TYR* 2.8 33.5 + - - -
326A CYS* 4.6 2.1 - - - -
354A GLY 3.0 0.4 - - - -
355A MET* 1.3 81.3 - - - +
357A GLU* 1.3 69.6 + - - +
359A LYS* 3.8 11.0 - - - +
603A PRO* 3.9 21.0 + - - +
604A ASP* 3.4 6.4 + - - -
607A ALA* 4.0 11.2 - - - +
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.7 28.1 - - + +
309A ARG* 2.8 43.1 + - - -
322A TYR* 3.1 36.1 - - + -
325A ALA* 3.8 19.7 - - + -
326A CYS* 3.6 25.7 - - - +
329A TYR* 3.5 18.2 - - + +
330A ASN* 4.5 6.8 - - - +
354A GLY* 3.3 10.9 - - - +
356A SER* 1.3 78.1 - - - +
358A MET* 1.3 60.7 + - - +
359A LYS 3.6 0.3 + - - -
360A GLN* 4.7 1.9 + - - +
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Residues in contact with MET 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 4.4 16.4 - - + -
266A LEU* 4.4 3.8 - - - -
286A LEU* 4.6 2.9 - - + -
288A ALA* 5.8 1.3 - - + -
299A ILE* 5.2 0.7 - - + -
329A TYR* 3.6 49.8 - - + -
345A ILE* 3.8 26.7 - - + +
353A ILE* 3.4 50.0 - - + +
354A GLY* 2.8 26.2 + - - +
355A MET* 4.0 3.4 - - - +
357A GLU* 1.3 70.3 - - - +
359A LYS* 1.3 65.3 + - - +
360A GLN 3.3 2.0 - - - -
361A LEU* 2.9 26.9 + - + +
362A THR 4.1 0.5 + - - -
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 2.7 20.4 + - - +
356A SER 3.8 11.2 - - - +
357A GLU 3.4 1.4 - - - -
358A MET* 1.3 70.0 - - - +
360A GLN* 1.3 66.2 + - - +
362A THR* 2.7 28.6 + - - -
363A ASP* 2.8 38.0 + - - +
369A LEU* 4.3 11.9 - - + -
537A VAL* 5.9 0.8 - - - +
541A GLU* 3.3 38.6 + - - +
607A ALA* 3.1 48.0 - - + +
610A ARG* 4.0 12.6 - - - +
611A HIS* 4.1 5.2 - - - +
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Residues in contact with GLN 360 (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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329A TYR 5.3 1.1 - - - +
330A ASN* 3.4 29.4 - - + +
333A ALA* 3.8 11.2 - - + -
334A GLN* 6.4 0.9 - - + -
357A GLU 4.7 1.9 + - - +
358A MET 3.2 2.1 + - - -
359A LYS* 1.3 80.0 + - - +
361A LEU* 1.3 65.2 + - - +
363A ASP* 4.2 13.5 - - - +
364A SER* 2.9 59.0 + - - +
541A GLU* 5.9 2.6 - - - +
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Residues in contact with LEU 361 (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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266A LEU* 3.4 33.4 - - + -
329A TYR* 3.4 38.1 - - + +
332A ILE* 3.6 17.3 - - + -
333A ALA* 3.4 20.6 - - - +
343A VAL* 4.0 33.0 - - + +
345A ILE* 4.2 7.4 - - + -
358A MET* 2.9 20.1 + - + +
360A GLN* 1.3 79.6 - - - +
362A THR* 1.3 62.3 + - + +
364A SER* 4.5 0.2 - - - -
365A THR* 2.8 28.6 + - - +
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Residues in contact with THR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A VAL 3.5 17.3 - - - +
345A ILE* 4.1 24.2 - - + -
358A MET 4.9 0.4 - - - +
359A LYS 2.7 19.8 + - - +
361A LEU* 1.3 77.2 - - - +
363A ASP* 1.3 53.4 + - - -
365A THR* 2.3 27.4 - - - +
366A GLY 4.1 0.2 - - - -
367A GLY* 3.3 8.7 + - - -
368A VAL 3.4 22.2 - - - +
369A LEU* 3.6 17.5 - - + +
420A HIS* 4.5 0.9 - - - +
611A HIS* 3.3 32.1 + - - -
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Residues in contact with ASP 363 (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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359A LYS* 2.8 51.2 + - - +
360A GLN* 4.2 16.2 + - - +
362A THR* 1.3 76.7 - - - +
364A SER* 1.3 61.0 + - - +
365A THR 3.2 0.7 - - - -
419A GLY 4.1 2.6 - - - +
420A HIS* 3.0 48.8 + - + -
421A ALA 3.4 2.4 + - - +
611A HIS* 2.7 30.3 + - - -
614A THR* 4.4 1.8 + - - -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 4.2 10.1 + - - +
334A GLN* 5.7 0.9 - - - +
337A ALA* 3.9 20.9 - - - +
360A GLN* 2.9 43.8 + - - +
361A LEU 4.5 0.2 - - - -
363A ASP* 1.3 77.1 - - - +
365A THR* 1.3 63.7 + - - +
421A ALA* 3.6 16.8 - - - -
422A SER* 3.0 25.6 + - - -
446A LYS 4.3 2.9 - - - +
448A ALA 5.2 0.7 + - - -
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Residues in contact with THR 365 (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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336A VAL* 3.7 21.3 - - + -
337A ALA* 3.9 14.8 - - + -
341A HIS 3.1 28.0 - - - +
342A THR* 4.0 2.7 - - - -
343A VAL 3.5 13.7 + - - -
361A LEU 2.8 19.5 + - - +
362A THR* 2.3 27.9 - - - +
363A ASP 3.5 4.5 - - - +
364A SER* 1.3 82.3 - - - +
366A GLY* 1.3 57.4 + - - +
367A GLY 3.1 5.0 + - - -
420A HIS* 3.7 6.5 - - - +
448A ALA* 3.8 13.7 - - + +
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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