Contacts of the helix formed by residues 441 - 456 (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 ILE 441 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A MET* 4.2 5.2 - - + -
377A VAL* 4.3 1.1 - - + +
378A GLU* 3.6 56.3 - - + +
382A TYR 3.4 23.8 - - - +
383A VAL* 4.1 5.5 - - + +
440A THR* 1.3 77.9 - - - +
442A LYS* 1.3 75.5 + - + +
443A SER 3.4 0.2 - - - -
444A ASP* 3.1 16.5 - - - +
445A VAL* 3.0 29.7 + - - +
509A PHE* 4.1 13.7 - - + -
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 5.3 1.0 + - - -
440A THR* 3.0 10.2 + - - +
441A ILE* 1.3 92.8 - - + +
443A SER* 1.3 56.5 + - - +
444A ASP 3.0 1.6 - - - -
445A VAL* 3.2 6.1 + - + +
446A TRP 3.0 17.0 + - - -
503A PRO* 3.2 49.4 - - + +
504A GLU* 4.4 11.0 - - + +
506A ARG* 2.4 49.5 + - + +
507A PRO 3.1 20.7 + - - +
508A THR* 4.0 11.3 - - - +
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 5.0 0.3 - - - +
429A THR* 5.9 0.4 - - - -
430A ALA* 3.8 13.1 + - - +
432A GLU* 3.7 13.4 + - - -
433A ALA* 4.2 8.3 - - - -
438A ARG 4.2 8.3 - - - -
439A PHE* 3.4 8.0 - - - +
440A THR* 2.6 42.4 + - - -
442A LYS* 1.3 77.7 - - - +
444A ASP* 1.3 58.2 + - - +
446A TRP* 3.2 4.3 + - - +
447A SER* 2.8 32.0 + - - -
506A ARG* 3.5 9.8 - - - +
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.5 9.3 - - - +
383A VAL* 3.5 6.8 - - - +
384A HIS* 2.7 37.9 + - - +
385A ARG* 3.2 24.3 + - - -
386A ASP 4.4 0.7 + - - -
387A LEU* 3.8 8.0 - - + +
440A THR 3.1 13.3 + - - +
441A ILE* 3.1 15.0 - - - +
443A SER* 1.3 76.1 + - - +
445A VAL* 1.3 59.6 + - - +
447A SER* 3.3 9.5 + - - -
448A PHE* 2.9 22.2 + - - +
509A PHE* 3.5 21.1 - - + -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 4.8 2.5 - - - +
441A ILE 3.0 21.9 + - - +
442A LYS* 3.2 13.0 + - + +
444A ASP* 1.3 74.3 - - - +
446A TRP* 1.3 68.1 + - - +
448A PHE* 2.9 14.0 + - - +
449A GLY 3.1 8.1 + - - -
498A CYS* 3.6 26.1 - - + +
506A ARG* 4.0 14.6 - - + -
507A PRO* 3.3 29.2 - - + +
509A PHE* 3.6 26.5 - - + +
512A LEU* 4.0 10.8 - - + -
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Residues in contact with TRP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS 4.9 1.4 + - - -
428A TRP 3.5 16.9 + - - -
429A THR 4.0 5.8 + - - -
430A ALA* 3.5 19.5 - - + +
431A PRO* 3.4 30.7 - - + -
442A LYS 3.0 6.9 + - - -
443A SER 3.2 9.9 - - - +
445A VAL* 1.3 75.9 - - - +
447A SER* 1.3 66.2 + - - +
449A GLY* 2.9 15.2 + - - -
450A ILE* 3.4 23.8 + - + +
463A TYR* 4.5 11.1 + - - -
475A VAL* 3.7 14.4 - - + -
480A ARG* 3.4 30.5 - - - -
498A CYS 3.3 12.5 + - - -
499A TRP* 2.9 46.2 + + + -
500A ARG 3.5 6.1 - - - -
506A ARG* 3.6 26.0 - - - +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG 6.0 1.0 - - - -
386A ASP* 5.8 0.7 - - - -
387A LEU* 3.6 32.5 + - - +
428A TRP* 2.9 29.4 + - - +
429A THR* 4.7 1.9 - - - -
443A SER* 2.8 16.6 + - - -
444A ASP* 3.4 12.3 + - - -
446A TRP* 1.3 76.3 - - - +
448A PHE* 1.3 56.8 + - - +
450A ILE* 3.0 8.8 + - - +
451A LEU* 3.0 24.9 + - - +
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA* 3.7 17.7 - - + -
370A ILE* 4.0 19.3 - - + -
371A ALA* 4.0 10.1 - - + -
387A LEU* 3.9 13.6 - - + +
444A ASP 2.9 12.9 + - - +
445A VAL* 2.9 11.5 + - - +
447A SER* 1.3 76.0 - - - +
449A GLY* 1.3 55.8 + - - +
451A LEU* 3.2 15.6 + - + +
452A LEU* 3.0 50.3 + - + +
498A CYS* 4.3 6.7 - - - -
509A PHE* 3.7 21.3 - + + -
512A LEU* 3.8 29.8 - - + -
516A LEU* 3.6 32.1 - - + -
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Residues in contact with GLY 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A VAL 3.1 5.5 + - - -
446A TRP 2.9 9.8 + - - -
448A PHE* 1.3 77.5 - - - +
450A ILE* 1.3 61.3 + - - +
452A LEU* 3.2 23.8 + - - +
453A THR* 3.5 4.2 - - - +
495A MET* 4.0 5.0 - - - +
498A CYS* 3.9 18.4 - - - -
499A TRP* 3.4 24.6 - - - -
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Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS 3.6 19.7 - - - +
428A TRP* 3.7 16.2 - - + -
446A TRP* 3.7 27.4 - - + +
447A SER 3.0 7.6 + - - +
449A GLY* 1.3 74.6 - - - +
451A LEU* 1.3 64.3 + - - +
453A THR* 2.6 26.1 + - - -
454A GLU* 3.3 5.1 + - - +
462A PRO* 3.4 35.2 - - + -
463A TYR* 4.1 8.5 - - - +
481A MET* 3.6 12.1 - - + -
499A TRP* 3.0 38.6 - - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.2 7.6 - - + -
370A ILE* 3.9 21.3 - - + -
387A LEU* 4.0 18.6 - - + -
388A ARG* 3.6 31.2 - - - +
389A ALA* 3.6 13.5 - - + +
392A ILE* 4.2 10.8 - - + -
428A TRP* 4.4 0.2 - - - +
447A SER 3.0 11.0 + - - +
448A PHE* 3.3 15.5 - - + +
450A ILE* 1.3 78.7 - - - +
452A LEU* 1.3 56.4 + - - +
454A GLU* 3.3 13.0 + - - +
455A LEU* 3.0 49.8 + - + +
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Residues in contact with LEU 452 (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 ALA* 3.8 28.9 - - + -
448A PHE* 3.0 37.7 + - + +
449A GLY* 3.2 15.5 - - - +
450A ILE 3.0 0.6 - - - -
451A LEU* 1.3 79.3 - - - +
453A THR* 1.3 48.9 + - - +
455A LEU* 3.5 10.9 - - + +
456A THR* 2.4 40.6 + - + +
491A LEU* 4.5 12.8 - - + +
494A LEU* 4.0 28.5 - - + -
495A MET* 3.8 29.6 - - + +
498A CYS* 5.3 0.9 - - - -
516A LEU* 5.2 2.9 - - + -
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Residues in contact with THR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLY 3.5 15.5 - - - +
450A ILE 2.6 17.0 + - - +
452A LEU* 1.3 75.4 - - - +
454A GLU* 1.3 56.9 + - - +
456A THR* 3.3 6.2 + - - -
457A THR* 2.4 44.9 + - - +
460A ARG* 5.0 2.8 + - - -
462A PRO* 4.3 7.3 - - - +
481A MET* 3.7 38.7 - - + +
484A PRO* 4.7 9.2 - - + -
495A MET* 3.8 9.9 - - - -
499A TRP* 3.7 15.5 - - + -
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Residues in contact with GLU 454 (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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347A LEU* 4.2 13.7 - - - +
350A LEU* 4.0 2.7 - - + +
389A ALA* 3.2 40.6 + - + +
390A ALA 4.8 0.5 + - - -
428A TRP* 2.5 48.2 + - + -
450A ILE 3.5 10.5 - - - +
451A LEU* 3.6 11.0 - - - +
453A THR* 1.3 78.4 + - - +
455A LEU* 1.3 65.9 + - - +
457A THR* 3.0 11.7 + - - -
459A GLY* 3.0 31.6 + - - +
460A ARG 3.8 15.9 - - - +
462A PRO* 4.3 2.8 - - + +
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.2 9.6 - - + -
350A LEU* 4.4 9.1 - - + +
363A LEU* 3.3 44.6 - - + +
366A MET* 3.1 38.4 - - + -
367A ALA* 3.7 32.8 - - + -
370A ILE* 4.5 2.0 - - + -
448A PHE* 5.8 0.2 - - + -
451A LEU* 3.0 41.9 + - + +
452A LEU* 3.5 15.3 - - + +
454A GLU* 1.3 78.3 - - - +
456A THR* 1.3 61.8 + - + +
457A THR 3.6 0.2 + - - -
458A LYS 4.2 4.3 + - - -
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Residues in contact with THR 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.9 9.0 - - + -
363A LEU* 4.6 11.7 - - + -
452A LEU* 2.4 28.2 + - + +
453A THR* 3.3 10.6 + - - -
455A LEU* 1.3 77.1 - - + +
457A THR* 1.3 61.9 + - - +
458A LYS 3.6 1.6 - - - -
484A PRO* 3.9 8.4 - - - +
485A PRO* 4.6 9.0 - - - +
487A CYS* 3.9 33.4 - - + +
491A LEU* 4.0 19.3 - - + -
495A MET* 3.7 8.3 - - + +
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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
------------------------------------------------------------
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