Contacts of the helix formed by residues 365 - 374 (chain A) in PDB entry 6MOL
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 THR 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A HIS* 4.0 2.5 - - - -
356A VAL 4.7 4.9 - - - -
357A ASN* 4.2 15.5 - - + +
358A ALA 3.4 9.6 - - - +
359A SER* 4.3 6.5 - - - -
363A GLY 4.3 5.2 - - - +
364A THR* 1.3 77.4 - - - +
366A PRO* 1.3 75.3 - - - +
367A LEU* 3.6 8.7 + - - +
368A HIS* 2.9 42.1 + - - +
369A LEU* 3.2 12.5 + - - +
388A ASP* 5.2 2.5 + - + -
391A ALA* 4.2 21.0 - - + +
392A TYR 6.0 0.2 - - - +
399A PRO* 5.1 1.2 - - - +
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Residues in contact with PRO 366 (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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334A LEU* 4.0 40.6 - - + +
335A HIS* 3.4 26.2 - - + +
338A ALA* 3.8 8.0 - - + +
355A ASP 4.5 2.2 - - - +
356A VAL 3.7 14.4 - - - +
358A ALA 3.2 16.4 - - - +
365A THR* 1.3 86.8 - - - +
367A LEU* 1.3 55.7 + - - +
369A LEU* 3.5 5.4 + - + +
370A ALA* 3.0 29.1 + - - +
382A LEU* 3.6 16.6 - - + +
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Residues in contact with LEU 367 (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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356A VAL 5.1 1.8 + - - +
365A THR* 3.1 8.5 + - - +
366A PRO* 1.3 75.8 - - - +
368A HIS* 1.3 65.8 + - - +
370A ALA* 4.3 0.7 - - - -
371A ALA* 3.1 24.3 + - + +
379A VAL* 3.7 30.5 - - + -
382A LEU* 3.8 27.5 - - + +
383A LEU* 3.7 29.4 - - + -
387A ALA* 3.9 17.5 - - + +
388A ASP 3.9 16.8 - - - +
389A VAL* 4.3 1.6 - - - -
399A PRO* 3.9 19.4 - - + +
415A LEU* 4.0 9.9 - - + -
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Residues in contact with HIS 368 (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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363A GLY 4.0 3.8 - - - -
364A THR* 3.6 16.2 - - + -
365A THR* 2.9 37.8 + - + +
367A LEU* 1.3 77.2 - - - +
369A LEU* 1.3 60.8 + - - +
371A ALA* 3.5 1.2 + - - +
372A THR* 2.9 28.9 + - - -
391A ALA* 3.0 32.8 + - + -
392A TYR 3.8 12.3 - - - -
393A ASP* 3.9 5.5 + - - -
397A ALA 2.9 23.3 + - - -
398A THR 3.7 3.6 - - - -
399A PRO* 3.3 30.5 - - + +
402A LEU* 3.7 17.6 - - + +
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Residues in contact with LEU 369 (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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335A HIS* 3.8 50.5 - - + +
338A ALA 4.8 1.6 - - - -
339A LEU* 4.5 23.3 - - + +
364A THR* 4.3 22.7 - - + +
365A THR 3.2 8.5 + - - +
366A PRO* 4.0 5.8 - - + +
368A HIS* 1.3 77.3 - - - +
370A ALA* 1.3 61.6 + - - +
372A THR* 3.4 5.3 + - - +
373A MET* 3.3 30.2 + - - +
110B HIS* 4.2 35.0 - - + +
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Residues in contact with ALA 370 (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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338A ALA* 4.2 12.1 + - + +
366A PRO 3.0 18.2 + - - +
367A LEU 4.0 2.7 - - - +
369A LEU* 1.3 78.3 - - - +
371A ALA* 1.3 57.2 + - - +
373A MET* 4.3 0.2 - - - -
374A GLY* 3.1 21.8 + - - -
375A HIS* 3.3 14.0 + - + +
378A ILE* 3.9 24.2 - - + -
379A VAL* 3.6 22.7 - - + +
382A LEU* 4.0 4.7 - - + -
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Residues in contact with ALA 371 (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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367A LEU* 3.1 19.1 + - + +
368A HIS 4.1 2.7 - - - +
370A ALA* 1.3 75.2 - - - +
372A THR* 1.3 65.9 + - - +
374A GLY* 3.7 2.8 + - - -
379A VAL* 4.1 2.9 - - + +
399A PRO* 3.7 29.8 - - + +
402A LEU* 5.1 0.9 - - + -
403A ALA* 4.0 17.7 - - + +
408A HIS* 3.4 19.6 + - - -
411A ILE* 4.2 19.8 - - + +
415A LEU* 4.7 1.1 - - + -
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Residues in contact with THR 372 (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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368A HIS 2.9 19.0 + - - -
369A LEU* 3.9 7.5 - - - +
370A ALA 3.4 0.2 - - - -
371A ALA* 1.3 77.1 - - - +
373A MET* 1.3 69.4 + - - +
402A LEU* 3.3 29.1 - - + +
405A ARG* 5.6 3.6 - - - +
406A MET* 3.4 39.0 - - + +
408A HIS* 3.3 14.2 - - - -
109B TYR* 6.5 0.9 - - + -
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Residues in contact with MET 373 (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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339A LEU* 3.7 39.3 - - + +
369A LEU 3.3 16.6 + - - +
372A THR* 1.3 86.9 - - - +
374A GLY* 1.3 59.3 + - - +
375A HIS* 3.4 28.0 - - + +
406A MET* 5.4 4.4 - - - +
408A HIS* 3.3 11.4 + - - -
110B HIS 4.4 7.4 - - - +
111B ARG* 4.4 23.1 - - + +
112B VAL 6.1 0.7 - - - +
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Residues in contact with GLY 374 (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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370A ALA 3.1 5.7 + - - -
371A ALA 3.7 0.2 + - - -
372A THR 3.5 1.2 - - - -
373A MET* 1.3 78.9 - - - +
375A HIS* 1.3 62.9 + - - +
376A LEU* 3.1 9.8 + - - +
408A HIS* 3.5 21.7 - - - -
411A ILE* 3.5 19.8 - - - +
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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