Contacts of the helix formed by residues 421 - 440 (chain A) in PDB entry 4HPF
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 ASP 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A CYS* 3.7 13.1 - - - +
420A SER* 1.3 78.0 - - - +
422A SER* 1.3 66.9 + - - +
423A HIS* 3.1 21.1 + - - +
424A ALA* 3.5 31.1 + - + +
425A GLU 3.4 13.5 + - - -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A CYS* 4.1 13.6 + - - -
420A SER 4.0 2.8 + - - -
421A ASP* 1.3 71.0 + - - +
423A HIS* 1.3 66.8 + - - +
425A GLU* 3.1 13.2 + - - +
426A ASP* 3.4 14.0 + - - -
450A LEU* 3.6 25.5 - - - +
451A GLN* 3.5 23.3 + - - +
728A PRO* 4.7 18.0 - - - +
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Residues in contact with HIS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASP* 3.1 17.0 + - - +
422A SER* 1.3 77.3 - - - +
424A ALA* 1.3 64.3 + - - +
426A ASP* 3.1 13.2 + - - +
427A ILE* 3.1 44.8 + - + +
451A GLN* 3.7 20.7 + - - +
453A HIS* 5.4 6.0 - + - -
454A ASN* 3.9 17.6 + - - +
457A TYR* 5.1 5.6 + - - -
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASP* 3.5 29.3 + - + +
422A SER 3.3 0.4 - - - -
423A HIS* 1.3 79.6 - - - +
425A GLU* 1.3 57.6 + - - +
427A ILE* 3.8 7.8 - - - +
428A SER* 2.9 30.7 + - - -
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY 4.4 5.2 - - - +
414A ILE 4.4 2.1 - - - +
415A ALA* 3.8 4.1 - - + -
416A ASN 3.6 23.2 + - - +
417A PRO* 3.8 15.0 - - - +
419A CYS* 3.7 31.8 - - + +
421A ASP 3.4 4.3 + - - +
422A SER 3.1 11.3 + - - +
424A ALA* 1.3 77.6 - - - +
426A ASP* 1.3 59.6 + - - +
428A SER* 3.2 10.4 + - - -
429A ASN* 2.8 55.4 + - - +
432A ARG* 5.4 0.9 + - - -
450A LEU* 4.1 8.1 - - + -
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Residues in contact with ASP 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER 3.4 6.5 + - - -
423A HIS 3.1 3.2 + - - +
425A GLU* 1.3 77.4 - - - +
427A ILE* 1.3 58.4 + - + +
429A ASN* 2.8 7.9 + - - +
430A ILE* 2.6 39.8 + - + +
448A GLN 4.3 3.6 - - - +
449A ILE* 3.3 19.6 - - + +
450A LEU* 3.0 29.9 + - - +
451A GLN* 3.1 23.2 + - - +
454A ASN* 2.9 39.6 + - + +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A HIS* 3.1 43.4 + - + +
424A ALA* 3.8 11.7 - - - +
426A ASP* 1.3 76.9 - - + +
428A SER* 1.3 66.6 + - - +
430A ILE* 3.3 12.6 + - + +
431A MET* 2.9 38.5 + - + +
454A ASN* 4.5 7.2 - - - +
457A TYR* 5.3 7.2 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.7 5.0 - - - +
424A ALA 2.9 20.4 + - - -
425A GLU* 3.2 12.4 + - - -
427A ILE* 1.3 79.5 - - - +
429A ASN* 1.3 58.5 + - - +
431A MET* 3.0 26.0 - - - +
432A ARG* 3.1 29.4 + - - -
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Residues in contact with ASN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY* 4.8 2.3 - - - +
413A ILE* 3.4 21.1 - - + +
414A ILE 4.1 5.6 + - - +
415A ALA* 3.7 23.0 - - - +
425A GLU* 2.8 39.8 + - - +
426A ASP* 2.8 12.6 + - - +
428A SER* 1.3 67.2 - - - +
430A ILE* 1.3 56.2 + - - +
431A MET 3.0 1.3 - - - -
432A ARG* 2.8 46.5 + - - +
433A VAL* 3.1 13.3 + - - +
447A ILE* 3.7 19.0 - - + +
448A GLN 4.1 6.4 + - - +
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Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP 2.6 27.9 + - - +
427A ILE* 3.6 10.5 - - + +
429A ASN* 1.3 72.2 - - - +
431A MET* 1.3 66.1 + - + +
433A VAL* 3.4 6.7 + - - +
434A LEU* 3.3 24.7 + - + +
447A ILE* 4.3 5.2 - - + -
449A ILE* 4.3 14.1 - - + -
454A ASN* 3.6 27.4 - - + +
457A TYR* 3.7 31.2 - - + -
458A LEU* 4.4 13.0 - - + -
461A ILE* 4.6 15.0 - - + +
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Residues in contact with MET 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.7 17.5 - - + +
427A ILE* 2.9 34.3 + - + +
428A SER* 3.0 17.9 - - - +
429A ASN 3.0 0.2 - - - -
430A ILE* 1.3 81.6 - - + +
432A ARG* 1.3 62.3 + - - +
434A LEU* 3.4 25.9 + - + +
435A SER* 3.1 19.8 + - - -
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Residues in contact with ARG 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A CYS* 4.4 9.2 - - - -
338A GLY* 4.1 22.3 + - - -
393A SER* 5.7 2.0 + - - -
394A ALA* 3.7 30.7 - - + +
395A MET* 3.3 29.1 - - + +
413A ILE* 4.3 12.6 - - + -
425A GLU* 5.4 1.8 + - - -
428A SER* 3.1 28.6 + - - -
429A ASN* 2.8 36.9 + - - +
431A MET* 1.3 74.8 - - - +
433A VAL* 1.3 56.4 + - - +
435A SER* 2.8 4.2 + - - -
436A ILE* 2.7 40.5 + - + +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 3.3 26.6 - - + +
429A ASN 3.1 7.7 + - - +
430A ILE* 3.7 7.0 - - - +
431A MET 3.4 0.4 - - - -
432A ARG* 1.3 76.5 - - - +
434A LEU* 1.3 56.1 + - - +
436A ILE* 3.9 0.8 - - - +
437A LYS* 2.9 35.1 + - + +
445A ILE* 3.6 28.7 - - + -
447A ILE* 3.7 15.9 - - + -
458A LEU* 3.8 17.0 - - + -
461A ILE* 3.7 19.5 - - + -
464A TRP* 4.1 11.7 - - + -
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Residues in contact with LEU 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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430A ILE* 3.3 11.7 + - + +
431A MET* 3.5 31.6 - - + +
432A ARG 3.1 0.8 - - - -
433A VAL* 1.3 79.7 - - - +
435A SER* 1.3 63.0 + - - +
437A LYS* 3.8 3.8 - - + +
438A ASN* 2.9 26.4 + - - +
461A ILE* 4.0 34.3 - - + -
462A PRO* 5.6 2.9 - - + -
463A SER* 5.7 1.3 - - - +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ALA 2.9 13.5 + - - -
395A MET* 2.8 43.2 + - - -
400A LEU* 3.6 7.8 - - - +
431A MET 3.1 9.8 + - - -
432A ARG 2.8 12.7 + - - -
434A LEU* 1.3 76.9 - - - +
436A ILE* 1.3 60.9 + - - -
438A ASN* 3.4 8.8 + - - +
439A TYR* 3.4 14.0 + - - +
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Residues in contact with ILE 436 (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 CYS* 4.4 14.8 - - - -
394A ALA* 4.6 4.9 - - + +
400A LEU* 4.2 21.1 - - + -
405A VAL* 5.2 15.2 - - + +
411A CYS* 4.0 29.4 - - + -
413A ILE* 4.3 21.8 - - + -
432A ARG* 2.7 26.4 + - + +
433A VAL 3.9 2.9 - - - +
435A SER* 1.3 69.8 - - - +
437A LYS* 1.3 65.9 + - - +
439A TYR* 3.0 18.4 + - - +
440A ASP 3.3 6.6 + - - +
443A THR* 4.0 17.2 + - - +
445A ILE* 4.1 16.2 - - + -
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Residues in contact with LYS 437 (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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433A VAL* 2.9 27.1 + - + +
434A LEU* 3.9 3.8 - - + +
436A ILE* 1.3 77.3 - - - +
438A ASN* 1.3 62.9 + - - +
439A TYR 3.2 0.2 + - - -
440A ASP 4.4 1.3 - - - -
441A SER* 2.9 53.7 + - - +
442A THR 5.0 0.2 - - - -
443A THR* 3.4 21.3 + - - -
445A ILE* 3.9 16.2 - - + -
461A ILE* 5.1 4.7 - - + -
463A SER* 2.9 48.4 + - - +
464A TRP* 3.6 6.2 - - - +
465A ASN* 4.1 1.8 - - - +
468A THR* 4.6 4.0 + - - -
470A ASP* 2.6 35.1 + - - -
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Residues in contact with ASN 438 (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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397A TRP* 5.7 7.2 - - - -
434A LEU 2.9 18.8 + - - +
435A SER* 3.4 10.1 + - - +
437A LYS* 1.3 78.4 - - - +
439A TYR* 1.3 61.1 + - - +
441A SER 5.1 0.2 + - - -
463A SER* 5.4 1.1 + - - -
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Residues in contact with TYR 439 (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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397A TRP* 3.5 43.0 + + + +
400A LEU* 3.9 19.5 - - + -
401A ARG* 3.2 47.3 - - + +
405A VAL* 3.4 20.0 - - + -
406A GLU* 3.3 34.9 + - + -
435A SER 3.4 7.2 + - - +
436A ILE 3.0 11.5 + - - +
438A ASN* 1.3 82.5 - - - +
440A ASP* 1.3 66.6 + - + +
441A SER 4.0 0.6 + - - -
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Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 5.3 0.2 - - - +
406A GLU* 3.5 26.5 - - + +
436A ILE 3.3 3.5 + - - +
437A LYS* 3.3 2.8 - - - -
439A TYR* 1.3 92.5 - - + +
441A SER* 1.3 55.5 + - - +
442A THR* 3.0 26.1 + - - +
443A THR* 2.6 61.3 + - + +
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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