Contacts of the helix formed by residues 415 - 435 (chain A) in PDB entry 1HK8
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 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A PHE* 4.2 17.3 - - + -
407A LEU* 3.6 31.2 - - + -
408A ASN* 3.1 13.1 + - - +
411A VAL* 3.8 25.4 - - + -
413A ARG* 3.8 40.4 - - + +
414A ASP* 1.3 77.0 - - - +
416A GLY* 1.3 58.9 + - - +
418A GLU* 3.2 17.6 + - + +
419A ILE* 2.8 36.1 + - + +
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Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ILE* 4.0 20.2 - - - -
407A LEU* 5.5 0.4 - - - -
408A ASN* 3.7 2.6 + - - -
414A ASP* 3.2 9.0 + - - -
415A ILE* 1.3 76.5 - - - +
417A ARG* 1.3 61.1 + - - +
418A GLU* 3.6 0.2 + - - -
419A ILE* 3.4 8.1 - - - +
420A LEU* 3.2 29.1 + - - +
496A TYR* 3.5 19.5 - - - -
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 4.0 19.5 + - - +
416A GLY* 1.3 74.2 - - - +
418A GLU* 1.3 83.2 + - - +
420A LEU* 4.7 0.7 - - - -
421A THR* 2.8 35.2 + - - -
492A ARG 5.9 0.4 + - - -
495A PRO* 4.1 26.6 - - + +
496A TYR* 3.5 28.7 + - + +
499A ILE* 4.0 19.6 - - + +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 3.5 15.5 - - - +
415A ILE* 3.3 27.4 - - + +
416A GLY 3.1 0.6 + - - -
417A ARG* 1.3 106.6 + - - +
419A ILE* 1.3 64.0 + - - +
421A THR* 3.5 5.7 + - - -
422A LYS* 3.1 33.4 + - - +
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Residues in contact with ILE 419 (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 LEU* 4.5 13.9 - - + -
322A ILE* 5.8 0.2 - - + -
337A PHE* 3.6 34.1 - - + -
341A PHE* 3.6 30.3 - - + -
404A ILE* 5.2 0.9 - - + -
407A LEU* 4.1 24.9 - - + -
415A ILE* 2.8 24.9 + - + +
416A GLY* 3.4 9.6 - - - +
418A GLU* 1.3 73.6 - - - +
420A LEU* 1.3 74.5 + - + +
422A LYS* 3.2 10.7 + - + +
423A MET* 2.9 31.3 + - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.5 2.2 - - + -
401A TYR* 4.0 33.9 - - + +
404A ILE* 3.4 29.2 - - + -
416A GLY 3.2 12.0 + - - +
417A ARG 4.3 0.9 - - - +
419A ILE* 1.3 84.3 - - + +
421A THR* 1.3 63.2 + - - +
423A MET* 3.2 25.7 + - - +
424A ASN* 3.1 21.7 + - - +
440A LEU* 3.6 23.5 - - + +
496A TYR* 3.6 20.9 - - + -
499A ILE* 3.7 17.0 - - + -
500A ALA* 5.1 2.5 - - + -
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Residues in contact with THR 421 (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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417A ARG 2.8 25.1 + - - -
418A GLU* 3.7 7.0 - - - +
419A ILE 3.3 0.2 - - - -
420A LEU* 1.3 76.5 - - - +
422A LYS* 1.3 63.8 + - + +
424A ASN* 3.4 9.2 + - + +
425A ALA* 3.3 17.7 + - - +
499A ILE* 4.1 18.3 - - - +
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Residues in contact with LYS 422 (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 VAL* 5.2 12.3 - - - +
341A PHE* 4.5 19.5 - - + -
418A GLU* 3.1 21.2 + - - +
419A ILE* 3.2 12.1 + - - +
421A THR* 1.3 76.1 - - + +
423A MET* 1.3 65.9 + - - +
425A ALA* 3.1 17.3 + - - +
426A HIS* 3.2 21.7 + - + +
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Residues in contact with MET 423 (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* 4.0 21.8 - - + -
319A LEU* 4.2 15.7 - - + -
341A PHE* 3.7 20.4 - - + -
345A MET* 4.0 11.7 - - + -
399A LEU* 3.6 28.7 - - + -
400A GLY 4.5 1.1 - - - +
401A TYR* 4.3 12.6 - - + -
419A ILE* 2.9 17.5 + - - +
420A LEU* 3.2 33.6 + - - +
422A LYS* 1.3 75.8 - - - +
424A ASN* 1.3 61.8 + - - +
425A ALA 3.2 0.7 + - - -
426A HIS* 3.2 5.9 + - - +
427A LEU* 3.0 26.8 + - - +
440A LEU* 3.9 19.1 - - + -
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Residues in contact with ASN 424 (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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420A LEU 3.1 10.2 + - - +
421A THR* 3.6 11.8 - - + +
423A MET* 1.3 76.1 - - - +
425A ALA* 1.3 55.4 + - - +
427A LEU* 3.3 22.1 + - - +
428A LYS* 3.0 28.2 + - - +
439A SER* 5.3 0.7 - - - -
440A LEU* 3.7 13.0 + - - +
499A ILE* 2.7 43.3 + - - +
501A THR* 5.1 6.5 + - - +
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Residues in contact with ALA 425 (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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421A THR 3.3 10.5 + - - +
422A LYS* 3.1 15.2 + - - +
424A ASN* 1.3 72.3 - - - +
426A HIS* 1.3 68.4 + - + +
428A LYS* 3.5 9.1 + - - +
429A GLN* 3.4 26.6 + - - +
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Residues in contact with HIS 426 (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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341A PHE* 3.9 17.4 - + - -
342A ASN* 4.2 19.5 + - + -
345A MET* 3.5 46.2 - - + +
346A ASP* 4.7 10.0 + - - -
422A LYS* 3.2 26.1 + - + +
423A MET 3.2 2.1 + - - +
425A ALA* 1.3 80.0 - - + +
427A LEU* 1.3 61.7 + - - +
429A GLN* 3.0 28.7 + - - +
430A TRP* 2.9 36.2 + - + +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A MET* 4.6 0.7 - - + -
399A LEU* 3.5 31.0 - - + -
423A MET 3.0 15.0 + - - +
424A ASN* 3.3 29.8 + - - +
426A HIS* 1.3 74.9 - - - +
428A LYS* 1.3 58.7 + - - +
430A TRP* 3.2 29.3 + - + +
431A THR* 2.9 33.8 + - - -
438A PHE* 4.0 22.0 - - + +
439A SER* 3.7 4.7 - - - +
440A LEU* 3.6 33.9 - - + +
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Residues in contact with LYS 428 (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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424A ASN 3.0 16.7 + - - +
425A ALA* 3.7 9.0 - - - +
426A HIS 3.3 0.2 - - - -
427A LEU* 1.3 75.3 - - - +
429A GLN* 1.3 62.5 + - + +
431A THR* 3.5 6.7 + - - -
432A GLU* 3.2 55.0 + - + +
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Residues in contact with GLN 429 (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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425A ALA 3.4 13.1 + - - +
426A HIS* 3.0 31.1 + - - +
428A LYS* 1.3 76.5 - - + +
430A TRP* 1.3 64.2 + - + +
432A GLU* 3.4 12.1 + - - +
433A ARG* 3.0 29.7 + - - +
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Residues in contact with TRP 430 (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 MET* 3.0 52.3 - - + -
346A ASP* 5.4 4.0 + - - +
348A CYS* 4.3 3.4 - - + -
349A PHE* 3.5 48.6 - + + +
352A LEU* 4.4 9.9 - - + -
399A LEU* 4.3 8.7 - - + -
426A HIS* 2.9 37.9 + - + +
427A LEU* 3.5 27.8 - - + +
429A GLN* 1.3 79.8 - - + +
431A THR* 1.3 61.3 + - - +
433A ARG* 3.4 3.4 + - - -
434A THR* 2.8 37.8 + - - +
438A PHE* 3.6 36.6 - + + -
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Residues in contact with THR 431 (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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393A GLY* 6.4 0.4 - - - -
427A LEU 2.9 18.9 + - - -
428A LYS* 3.6 9.1 - - - -
430A TRP* 1.3 78.2 - - - +
432A GLU* 1.3 60.0 + - + +
435A GLY* 2.9 30.7 + - - +
436A PHE 3.2 18.6 - - - +
437A ALA* 4.0 10.3 - - + -
438A PHE* 3.2 25.1 + - - +
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Residues in contact with GLU 432 (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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428A LYS* 3.2 52.7 + - + +
429A GLN* 3.9 11.6 - - - +
431A THR* 1.3 80.3 - - + +
433A ARG* 1.3 62.1 + - - +
435A GLY* 4.5 2.1 + - - -
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Residues in contact with ARG 433 (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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349A PHE* 4.1 30.1 - - - -
429A GLN 3.0 17.1 + - - +
430A TRP* 3.4 6.3 + - - +
432A GLU* 1.3 79.0 - - - +
434A THR* 1.3 68.5 + - + +
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Residues in contact with THR 434 (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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349A PHE* 3.9 29.4 - - + -
353A MET* 4.1 16.4 - - + -
391A LYS* 5.7 4.5 - - - +
392A ASN* 5.4 0.2 + - - -
430A TRP 2.8 20.7 + - - +
433A ARG* 1.3 90.5 - - - +
435A GLY* 1.3 57.7 + - - +
436A PHE* 3.2 37.5 + - - -
438A PHE* 3.5 11.1 - - - -
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Residues in contact with GLY 435 (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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391A LYS* 5.3 0.4 - - - -
392A ASN* 3.1 41.3 + - - -
393A GLY* 3.1 11.3 + - - -
431A THR* 2.9 17.2 + - - +
432A GLU 4.5 2.2 + - - -
433A ARG 3.9 0.8 - - - -
434A THR* 1.3 75.9 - - - +
436A PHE* 1.3 61.0 + - - +
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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