Contacts of the helix formed by residues 361 - 373 (chain A) in PDB entry 1PJR
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 ASN 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A TYR* 3.7 18.6 - - + +
360A THR* 1.3 72.1 - - - +
362A ALA* 1.3 68.4 + - - +
363A GLN 3.0 2.7 - - - -
364A SER* 2.9 11.6 + - - -
389A ARG* 2.8 47.2 + - - +
507A SER* 3.0 25.5 + - - -
510A GLU* 5.5 0.3 - - - +
511A ASN* 3.3 8.5 + - - +
563A THR* 5.0 7.6 + - - -
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Residues in contact with ALA 362 (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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360A THR* 3.3 2.3 - - - +
361A ASN* 1.3 81.2 + - - +
363A GLN* 1.3 61.1 + - - +
364A SER 3.0 1.9 + - - -
365A ARG* 3.1 21.3 + - - +
366A VAL* 4.9 0.3 + - - +
386A PHE* 5.1 0.2 - - - -
510A GLU* 4.2 16.2 - - + +
511A ASN* 4.1 14.8 - - - +
514A GLU* 3.9 21.1 - - + +
625A LEU* 4.5 3.4 - - + -
626A PHE* 3.7 35.2 - - + -
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Residues in contact with GLN 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 3.5 24.2 - - + +
359A ARG 3.6 4.2 + - - +
360A THR* 3.0 44.9 + - - +
361A ASN 3.0 0.4 - - - -
362A ALA* 1.3 76.8 - - - +
364A SER* 1.3 60.1 + - - +
365A ARG 3.2 0.8 + - - -
366A VAL* 4.1 10.9 - - - +
367A MET* 4.0 14.0 + - - +
578A ILE* 4.1 23.1 + - + +
579A GLY* 4.2 5.9 - - - -
584A ILE* 3.6 28.6 - - - +
623A ARG* 5.4 9.2 - - - +
625A LEU* 4.0 25.9 - - + +
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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
----------------------------------------------------------
358A TYR* 3.4 36.8 - - - -
361A ASN 2.9 13.7 + - - -
363A GLN* 1.3 76.7 - - - +
365A ARG* 1.3 56.5 + - - +
367A MET* 3.0 6.8 + - - +
368A GLU* 2.7 54.1 + - - +
380A ILE* 4.2 2.0 - - - -
386A PHE* 4.9 0.2 - - - +
389A ARG* 2.8 29.7 + - - -
561A LEU* 4.6 1.3 - - - -
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Residues in contact with ARG 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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362A ALA 3.1 15.5 + - - +
364A SER* 1.3 80.4 + - - +
366A VAL* 1.3 80.1 + - - +
368A GLU* 3.1 8.2 + - - +
369A GLU* 2.9 60.8 + - + +
386A PHE* 3.8 37.2 - - + -
387A TYR* 5.9 1.8 - - + +
514A GLU* 2.7 51.9 + - - +
517A SER* 3.9 20.3 - - - -
518A VAL* 3.6 19.3 - - + +
521A HIS* 6.2 1.6 - - - +
624A THR 5.8 1.2 + - - -
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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
----------------------------------------------------------
329A GLU* 4.4 35.9 - - + +
330A ALA* 4.6 15.7 - - + -
332A GLU* 6.0 0.9 - - - +
333A ALA* 4.4 4.5 - - + -
362A ALA 4.9 0.2 + - - -
363A GLN* 4.1 12.8 + - - +
365A ARG* 1.3 99.5 - - - +
367A MET* 1.3 63.2 + - + +
369A GLU* 3.5 9.3 + - + +
370A MET* 3.3 33.4 + - + +
514A GLU* 4.9 2.7 + - - +
578A ILE* 6.6 0.2 - - + -
623A ARG* 5.6 2.9 - - - +
625A LEU* 6.5 0.9 - - + -
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Residues in contact with MET 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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333A ALA* 3.6 38.8 - - + +
336A VAL* 3.8 20.9 - - + -
356A VAL* 4.1 27.6 - - + -
358A TYR* 5.7 0.7 - - + -
363A GLN 4.0 10.3 - - - +
364A SER* 3.0 11.7 + - - +
366A VAL* 1.3 82.4 - - + +
368A GLU* 1.3 63.4 + - - +
370A MET* 3.6 2.1 + - + -
371A LEU* 3.1 46.7 + - + +
561A LEU* 4.0 19.5 - - + -
578A ILE* 4.2 15.3 - - + -
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Residues in contact with GLU 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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364A SER* 2.7 46.1 + - - +
365A ARG* 3.5 4.5 - - - +
367A MET* 1.3 71.3 - - - +
369A GLU* 1.4 61.9 + - + +
371A LEU* 3.3 4.1 + - - +
372A LEU* 2.9 27.1 + - - +
378A TYR* 2.9 49.7 + - + +
380A ILE* 3.6 5.4 - - - +
385A LYS* 3.5 5.4 - - - +
386A PHE* 3.0 37.3 + - + +
387A TYR* 6.0 0.5 - - - -
389A ARG* 3.4 2.8 + - - -
561A LEU* 4.1 11.0 - - + -
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Residues in contact with GLU 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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365A ARG* 2.9 58.0 + - + +
366A VAL* 3.7 13.0 - - + +
367A MET 3.4 0.2 - - - -
368A GLU* 1.4 74.2 - - - +
370A MET* 1.3 59.4 + - + +
372A LEU* 3.2 8.5 + - - +
373A LYS* 3.0 43.2 + - - +
387A TYR* 4.5 4.4 + - + -
518A VAL* 4.1 10.4 - - - +
521A HIS* 5.8 1.7 + - - -
541A ILE* 3.9 33.8 - - + +
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Residues in contact with MET 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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330A ALA* 3.8 35.0 - - + +
333A ALA* 3.5 38.4 - - + +
334A GLN* 3.9 20.6 - - + +
337A ALA* 4.5 7.4 - - + +
366A VAL* 3.3 16.6 + - + +
367A MET* 4.1 3.6 - - + +
369A GLU* 1.3 74.8 - - + +
371A LEU* 1.3 67.3 + - - +
373A LYS* 3.3 32.5 + - - +
374A ALA* 3.1 25.8 + - - +
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Residues in contact with LEU 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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337A ALA* 4.1 8.5 - - + -
340A ILE* 4.4 7.9 - - + -
356A VAL* 6.0 0.2 - - + -
367A MET* 3.1 46.4 + - + +
368A GLU* 3.7 4.5 - - - +
370A MET* 1.3 75.2 - - - +
372A LEU* 1.3 60.0 + - - +
374A ALA 3.7 0.3 + - - -
375A ASN 3.3 3.5 + - - -
376A ILE* 3.0 74.0 + - + +
378A TYR* 3.5 37.9 - - + -
559A VAL* 4.1 12.6 - - + -
561A LEU* 4.2 8.3 - - + -
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Residues in contact with LEU 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 GLU 2.9 18.9 + - - +
369A GLU* 3.5 6.1 - - - +
371A LEU* 1.3 76.3 - - - +
373A LYS* 1.3 66.3 + - - +
375A ASN* 3.3 18.7 + - - -
376A ILE 5.3 3.6 - - - +
378A TYR* 4.7 21.7 - - + +
540A LEU 5.2 2.9 - - - +
541A ILE* 4.5 31.4 - - + +
542A SER* 4.7 6.1 - - - +
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Residues in contact with LYS 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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369A GLU* 3.0 30.3 + - - +
370A MET* 3.3 35.4 + - - +
372A LEU* 1.3 74.8 - - - +
374A ALA* 1.3 60.2 + - - +
375A ASN* 3.0 14.9 + - - -
521A HIS* 6.2 2.2 - - - -
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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