Contacts of the helix formed by residues 363 - 376 (chain A) in PDB entry 3A4R
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 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A LEU* 4.6 1.1 - - - +
361A ASP 3.6 8.3 - - - +
362A SER* 1.3 87.8 - - - +
364A LEU* 1.3 67.2 + - - +
365A LYS* 3.1 4.7 - - + +
366A VAL* 2.9 29.6 + - + +
367A LEU 4.1 0.5 + - - -
393A GLY 3.5 14.6 - - - +
394A LYS* 4.5 7.9 - - - +
395A GLU 3.2 10.8 - - - +
396A LEU* 3.9 11.2 - - + -
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Residues in contact with LEU 364 (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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358A LEU* 4.2 7.6 - - + -
363A PRO* 1.3 72.5 - - - +
365A LYS* 1.3 62.2 + - - +
367A LEU* 3.0 41.2 + - + +
368A MET* 3.0 17.7 + - - +
391A LEU* 4.0 22.9 - - + -
393A GLY* 3.4 3.5 + - - -
395A GLU* 2.8 38.5 + - + +
396A LEU 3.9 2.5 - - - -
397A PRO* 3.8 31.2 - - + -
400A LEU* 3.9 22.4 - - + -
402A LEU* 4.2 11.0 - - + -
408A ILE* 4.8 3.1 - - + -
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Residues in contact with LYS 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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363A PRO* 3.0 4.7 + - + +
364A LEU* 1.3 76.2 - - - +
366A VAL* 1.3 58.3 + - + +
368A MET* 3.6 12.9 - - + +
369A SER* 2.9 39.2 + - - +
392A SER 5.9 1.6 - - - +
393A GLY* 2.9 24.7 + - - +
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Residues in contact with VAL 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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358A LEU* 4.0 13.9 - - + -
362A SER* 4.1 20.2 - - - +
363A PRO* 2.9 27.4 + - + +
365A LYS* 1.3 77.8 - - + +
367A LEU* 1.3 62.8 + - - +
369A SER* 3.4 5.2 + - - -
370A HIS* 3.0 49.2 + - + +
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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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343A LEU* 3.8 29.4 - - + -
345A VAL* 3.9 26.7 - - + -
354A LEU* 4.8 0.9 - - + +
356A ILE* 3.8 32.1 - - + -
358A LEU* 4.2 8.9 - - + +
363A PRO 4.1 0.4 + - - -
364A LEU* 3.0 24.8 + - + +
366A VAL* 1.3 79.2 - - - +
368A MET* 1.3 65.6 + - + +
370A HIS* 3.3 2.3 + - - +
371A TYR* 2.9 27.0 + - - +
384A PHE* 4.3 17.3 - - + -
391A LEU* 5.6 0.4 - - + -
408A ILE* 4.1 16.8 - - + -
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Residues in contact with MET 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.0 13.1 + - + +
365A LYS* 3.6 9.9 - - + +
367A LEU* 1.3 80.6 - - + +
369A SER* 1.3 56.2 + - - +
371A TYR* 3.4 2.3 + - - +
372A GLU* 3.1 37.8 + - - +
384A PHE* 3.4 54.9 - - + -
391A LEU* 3.1 51.1 - - + +
392A SER 4.3 2.5 - - - +
393A GLY* 3.5 25.4 - - - +
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Residues in contact with SER 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 2.9 30.4 + - - +
366A VAL* 3.7 6.5 - - - -
368A MET* 1.3 74.1 - - - +
370A HIS* 1.3 66.2 + - - +
372A GLU* 3.4 12.8 + - - +
373A GLU* 3.0 24.6 + - - +
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Residues in contact with HIS 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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3A EDO 2.5 53.3 + - - +
354A LEU* 3.9 4.0 - - + -
356A ILE* 3.7 21.8 - - + -
366A VAL* 3.0 45.7 + - + +
367A LEU 3.7 3.6 - - - +
369A SER* 1.3 76.7 - - - +
371A TYR* 1.3 57.3 + - - +
373A GLU* 4.5 1.1 - - - -
374A ALA* 2.9 26.9 + - - +
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Residues in contact with TYR 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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345A VAL* 3.4 41.7 - - + -
347A GLY* 3.2 25.3 + - - -
352A GLN* 3.6 19.8 + - - +
354A LEU* 3.7 19.9 - - + +
367A LEU 2.9 16.9 + - - +
368A MET 3.7 3.6 - - - +
369A SER 3.2 0.2 - - - -
370A HIS* 1.3 77.6 - - - +
372A GLU* 1.3 66.3 + - - +
374A ALA* 3.3 0.6 + - - -
375A MET* 3.0 46.6 + - + +
377A LEU* 3.9 20.1 - - + +
382A LEU* 4.2 5.6 - - + -
384A PHE* 3.9 22.0 - + + -
410A VAL* 3.9 22.9 - - + +
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Residues in contact with GLU 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 MET* 3.1 21.9 + - - +
369A SER* 3.7 11.2 + - - +
371A TYR* 1.3 78.6 - - - +
373A GLU* 1.3 61.8 + - - +
376A GLY* 3.0 4.9 + - - -
377A LEU* 2.8 39.8 + - - +
378A SER* 3.8 24.0 + - - +
379A GLY 4.6 3.7 + - - -
380A HIS 4.5 6.2 - - - +
382A LEU* 4.0 26.8 - - + +
384A PHE* 4.5 9.3 - - + -
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Residues in contact with GLU 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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3A EDO 3.9 19.1 - - - +
369A SER 3.0 16.0 + - - +
370A HIS* 3.7 3.1 - - - +
372A GLU* 1.3 77.1 - - - +
374A ALA* 1.3 68.1 + - - +
375A MET 3.2 0.5 + - - -
376A GLY* 3.4 7.6 + - - -
378A SER* 6.1 1.1 - - - -
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Residues in contact with ALA 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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3A EDO 4.0 9.2 - - - -
354A LEU* 3.9 26.2 - - + -
370A HIS 2.9 17.2 + - - +
371A TYR 3.7 4.0 - - - +
373A GLU* 1.3 79.1 - - - +
375A MET* 1.3 74.7 + - + +
376A GLY 3.7 0.2 + - - -
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Residues in contact with MET 375 (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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351A HIS* 4.6 4.0 - - - +
352A GLN* 3.9 24.0 - - + +
353A MET 3.1 42.6 - - - +
354A LEU* 3.7 14.8 - - + +
371A TYR* 3.0 38.1 + - + +
374A ALA* 1.3 88.9 - - + +
376A GLY* 1.3 61.6 - - - +
377A LEU* 3.6 26.4 - - + +
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Residues in contact with GLY 376 (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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372A GLU 3.0 5.8 + - - -
373A GLU* 3.4 6.9 + - - -
374A ALA 3.4 3.6 + - - -
375A MET* 1.3 78.8 - - - +
377A LEU* 1.3 63.6 + - - +
378A SER 3.7 3.0 + - - +
380A HIS* 4.2 7.3 - - - -
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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