Contacts of the helix formed by residues 360 - 379 (chain A) in PDB entry 2PTK
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 LEU 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ARG* 1.3 68.6 - - - +
361A PRO* 1.3 66.3 - - + +
362A GLN 2.9 5.4 - - - -
363A LEU* 3.3 17.0 + - + -
364A VAL* 2.9 45.1 + - + +
456A THR* 4.9 5.6 - - + -
486A GLU 5.3 2.7 - - - +
487A CYS* 5.7 0.7 - - - -
488A PRO* 3.4 42.8 - - + -
491A LEU* 4.2 8.1 - - + -
519A TYR* 4.8 0.4 - - + -
520A PHE* 3.8 23.1 - - + -
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Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 5.1 0.7 + - - -
359A ARG* 3.5 15.5 - - + -
360A LEU* 1.3 94.4 - - + +
362A GLN* 1.3 60.7 + - - +
364A VAL* 4.0 1.2 - - - +
365A ASP* 3.1 26.5 + - - +
520A PHE* 3.2 31.4 - - + -
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR 3.9 3.5 - - - +
358A LEU* 3.5 18.3 - - + -
359A ARG* 2.8 54.2 + - - +
360A LEU 2.9 0.8 - - - -
361A PRO* 1.3 83.1 - - - +
363A LEU* 1.3 53.7 + - - +
365A ASP* 2.8 27.5 + - - +
366A MET* 2.8 22.9 + - - +
398A LEU* 3.2 31.8 - - + +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 4.1 10.8 - - + -
355A GLY 5.5 1.6 - - - +
358A LEU* 4.1 24.5 - - + +
359A ARG 3.3 15.9 + - - +
360A LEU* 4.0 20.4 - - + +
362A GLN* 1.3 75.0 - - - +
364A VAL* 1.3 57.3 + - + +
366A MET* 3.3 27.6 + - + +
367A ALA* 2.8 29.5 + - - +
455A LEU* 3.3 39.7 - - + +
456A THR* 4.6 11.0 - - + -
458A LYS* 6.3 0.7 - - - -
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 5.7 2.0 - - - +
360A LEU* 2.9 35.4 + - + +
363A LEU* 1.3 73.2 - - - +
365A ASP* 1.3 62.9 + - - +
367A ALA* 3.6 7.5 - - - +
368A ALA* 2.9 25.6 + - - +
491A LEU* 4.2 17.5 - - + -
516A LEU* 3.5 31.9 - - + +
519A TYR* 4.1 15.0 - - + -
520A PHE* 3.7 32.5 - - + -
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.8 37.1 + - - +
160A ARG* 3.0 39.4 + - - +
361A PRO 3.1 16.1 + - - +
362A GLN* 2.8 11.6 + - - +
364A VAL* 1.3 77.4 - - - +
366A MET* 1.3 56.9 + - - +
368A ALA* 2.9 18.2 + - - +
369A GLN* 3.0 24.8 + - - +
398A LEU* 4.0 9.8 - - + +
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Residues in contact with MET 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.4 22.9 - - + -
349A PHE* 4.2 13.5 - - - -
350A LEU* 4.1 5.4 - - + -
358A LEU* 4.1 24.0 - - - -
362A GLN 2.8 13.6 + - - +
363A LEU* 3.5 19.7 - - + +
365A ASP* 1.3 79.1 - - - +
367A ALA* 1.3 57.8 + - - +
369A GLN* 3.6 10.2 + - - +
370A ILE* 3.0 31.9 + - + +
394A VAL* 5.6 0.2 - - - -
398A LEU* 4.3 19.5 - - + +
400A CYS* 3.7 20.3 - - - +
455A LEU* 3.1 28.9 - - + -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU 2.8 16.4 + - - +
364A VAL* 3.6 9.0 - - - +
365A ASP 3.1 0.2 - - - -
366A MET* 1.3 74.8 - - - +
368A ALA* 1.3 60.6 + - - +
370A ILE* 3.6 4.5 + - - +
371A ALA* 3.1 27.9 + - - +
448A PHE* 3.7 7.0 - - + -
452A LEU* 3.8 18.4 - - + -
455A LEU* 3.7 22.9 - - + +
516A LEU* 3.8 13.2 - - + +
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Residues in contact with ALA 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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156A ARG* 4.3 8.3 - - - +
364A VAL 2.9 13.8 + - - +
365A ASP* 2.9 13.4 + - - +
367A ALA* 1.3 75.8 - - - +
369A GLN* 1.3 64.8 + - + +
371A ALA* 3.3 3.1 + - - +
372A SER* 3.0 22.9 + - - -
513A GLN* 4.0 6.9 - - - +
516A LEU* 4.1 23.3 - - + +
517A GLU* 4.2 23.0 - - + +
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 4.3 1.1 - - - +
160A ARG* 3.1 23.5 - - - +
321A LYS* 3.1 43.0 - - + +
365A ASP* 3.0 24.0 + - - +
366A MET* 3.8 15.0 - - - +
368A ALA* 1.3 75.8 - - - +
370A ILE* 1.3 58.2 + - - +
372A SER* 2.9 22.3 + - - -
373A GLY 3.0 11.1 + - - -
398A LEU 2.5 20.8 - - - +
399A VAL* 3.1 8.9 - - - +
400A CYS* 2.7 38.4 + - + +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.8 28.7 - - + -
366A MET 3.0 21.1 + - - +
367A ALA* 3.8 9.0 - - - +
368A ALA 3.3 0.2 - - - -
369A GLN* 1.3 76.8 - - - +
371A ALA* 1.3 56.3 + - - +
373A GLY* 3.5 0.7 + - - -
374A MET* 3.0 27.7 + - + +
387A LEU* 4.5 9.4 - - + -
392A ILE* 3.7 33.0 - - + -
400A CYS* 4.2 13.5 - - + -
402A VAL* 4.0 12.1 - - + +
448A PHE* 4.0 19.3 - - + -
451A LEU* 3.9 17.7 - - + -
455A LEU* 4.5 0.9 - - + -
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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
----------------------------------------------------------
367A ALA 3.1 17.8 + - - +
368A ALA 3.8 4.3 - - - +
369A GLN 3.2 0.2 - - - -
370A ILE* 1.3 74.2 - - - +
372A SER* 1.3 56.7 + - - +
374A MET 3.5 0.3 - - - -
375A ALA* 2.7 35.5 + - - +
448A PHE* 4.0 16.8 - - + -
509A PHE* 3.7 15.9 - - + +
512A LEU* 4.2 4.0 - - + -
513A GLN* 3.8 28.7 - - - +
516A LEU* 4.0 3.6 - - + -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A HIS* 3.2 23.3 + - - -
321A LYS* 3.7 6.5 - - - +
368A ALA 3.0 12.5 + - - -
369A GLN* 2.9 16.1 + - - -
371A ALA* 1.3 75.7 - - - +
373A GLY* 1.3 63.0 + - - +
375A ALA* 2.9 4.0 + - - +
376A TYR* 2.9 22.3 + - - +
379A ARG* 4.9 1.2 + - - -
513A GLN* 3.6 28.4 + - - +
517A GLU* 5.1 1.6 - - - -
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Residues in contact with GLY 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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319A HIS* 4.0 8.3 - - - -
321A LYS* 3.5 29.5 - - - +
322A LEU* 3.8 10.1 - - - +
369A GLN 3.0 10.3 + - - -
370A ILE 3.9 2.5 - - - -
372A SER* 1.3 76.8 + - - +
374A MET* 1.3 55.9 + - - +
376A TYR* 3.0 7.1 + - - +
377A VAL* 2.9 27.2 + - - +
402A VAL* 4.4 1.1 - - - -
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Residues in contact with MET 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 ILE* 3.0 20.2 + - + +
371A ALA 3.5 0.2 - - - -
373A GLY* 1.3 71.0 - - - +
375A ALA* 1.3 60.0 + - - +
376A TYR 3.1 1.6 - - - -
377A VAL* 3.7 28.4 - - + +
378A GLU* 2.9 27.5 + - - +
384A HIS* 4.0 13.5 - - + -
387A LEU* 3.9 37.2 - - + -
402A VAL* 4.2 6.7 - - + +
441A ILE* 4.2 2.5 - - + -
444A ASP* 3.5 23.8 - - + +
509A PHE* 3.4 48.6 - - + -
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Residues in contact with ALA 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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371A ALA 2.7 22.9 + - - +
372A SER 2.9 6.7 + - - +
374A MET* 1.3 73.1 - - - +
376A TYR* 1.3 59.7 + - - +
378A GLU* 3.4 5.6 - - - +
379A ARG* 3.1 37.3 + - - +
509A PHE* 3.5 22.2 - - - +
510A GLU* 4.1 7.0 - - + +
513A GLN* 3.4 21.8 - - - +
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Residues in contact with TYR 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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316A LYS 4.2 1.9 + - - -
317A LEU* 3.6 10.6 - - + -
318A ARG* 3.0 42.7 + - - +
319A HIS* 3.3 39.3 - + + -
322A LEU* 3.5 20.0 - - + -
372A SER 2.9 6.0 + - - +
373A GLY 3.2 7.4 - - - +
375A ALA* 1.3 74.8 - - - +
377A VAL* 1.3 65.2 + - - +
378A GLU 2.8 5.0 + - - -
379A ARG* 3.1 31.6 + - - +
380A MET* 3.0 62.6 + - + +
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Residues in contact with VAL 377 (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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317A LEU* 5.8 1.8 - - + -
322A LEU* 3.7 27.4 - - + -
373A GLY 2.9 19.4 + - - +
374A MET* 3.5 35.0 + - + +
376A TYR* 1.3 77.4 - - - +
378A GLU* 1.3 58.7 + - - +
380A MET* 3.5 8.0 + - - -
382A TYR* 3.0 60.7 + - + +
383A VAL* 3.9 5.8 - - - +
384A HIS* 4.3 4.0 - - - +
405A PHE* 4.8 11.2 - - + -
441A ILE* 4.5 0.4 - - + -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET 2.9 17.9 + - - +
375A ALA* 3.4 6.6 - - - +
376A TYR 2.8 1.6 + - - -
377A VAL* 1.3 74.6 - - - +
379A ARG* 1.3 57.2 + - - +
380A MET 3.0 4.3 - - - -
381A ASN* 2.9 23.7 + - - -
441A ILE* 3.6 40.1 - - + +
442A LYS* 5.3 1.2 + - - -
445A VAL* 4.8 1.2 - - - +
507A PRO 4.7 0.7 - - - +
508A THR* 3.4 19.9 - - - +
509A PHE* 2.9 34.1 + - - +
510A GLU* 3.3 15.8 + - - +
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Residues in contact with ARG 379 (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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319A HIS* 3.9 14.3 + - - -
372A SER 4.9 0.8 + - - -
375A ALA* 3.1 30.9 + - - +
376A TYR* 3.1 39.2 + - - +
378A GLU* 1.3 78.8 - - - +
380A MET* 1.3 74.1 + - + +
381A ASN* 3.0 15.6 + - - +
510A GLU* 6.3 0.2 - - - +
513A GLN* 5.0 4.6 - - - +
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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
------------------------------------------------------------
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