Contacts of the helix formed by residues 438 - 460 (chain A) in PDB entry 4S15
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 GLU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A GLU 5.0 2.3 - - - +
347A LEU* 3.7 8.1 - - - +
348A CYS* 2.8 46.5 + - - +
351A ASP* 2.7 17.7 + - - +
437A GLN* 1.3 74.0 - - + +
439A LYS* 1.3 63.9 + - - +
440A VAL* 3.3 3.1 - - - -
441A LYS* 3.3 27.3 + - + +
442A ILE* 3.1 26.0 + - + +
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA* 3.6 25.1 + - + +
432A ASP* 4.7 4.0 + - - +
433A ARG 3.2 24.5 + - - -
434A SER* 4.8 1.6 - - - +
435A TRP 4.8 3.0 - - - +
436A LEU* 3.5 34.3 - - + +
437A GLN 3.3 6.0 + - - +
438A GLU* 1.3 74.7 - - - +
440A VAL* 1.3 61.4 + - + +
442A ILE* 3.3 7.5 + - - +
443A GLU* 2.9 30.9 + - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLU 3.3 1.0 - - - -
439A LYS* 1.3 78.1 - - + +
441A LYS* 1.3 64.6 + - - +
443A GLU* 3.4 6.9 + - - +
444A LYS* 3.1 23.9 + - + +
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Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY 5.2 0.7 - - - -
346A GLU* 3.8 45.5 + - - +
347A LEU* 3.9 18.3 - - + +
438A GLU* 3.3 30.9 + - + +
440A VAL* 1.3 81.4 - - - +
442A ILE* 1.3 61.4 + - - +
444A LYS* 3.4 12.6 + - + +
445A LEU* 3.2 22.3 + - + +
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.8 22.7 - - + -
351A ASP* 3.8 17.3 - - + +
355A LEU* 4.1 9.9 - - + -
429A MET* 3.7 32.9 - - + +
430A SER 4.2 1.8 - - - +
431A ALA* 3.7 17.0 - - + +
436A LEU* 3.7 36.1 - - + -
438A GLU 3.1 18.9 + - - +
439A LYS* 3.8 3.6 - - - +
441A LYS* 1.3 75.4 - - - +
443A GLU* 1.3 60.7 + - - +
445A LEU* 3.3 6.4 + - - +
446A GLN* 2.9 27.7 + - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA* 3.5 19.9 - - + +
439A LYS 2.9 17.7 + - - +
440A VAL* 3.7 7.2 - - - +
442A ILE* 1.3 77.4 - - - +
444A LYS* 1.3 56.9 + - - +
446A GLN* 3.3 14.0 + - - +
447A GLN* 2.9 43.0 + - + +
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Residues in contact with LYS 444 (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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440A VAL* 3.1 15.2 + - + +
441A LYS* 3.6 15.0 - - + +
443A GLU* 1.3 78.2 - - - +
445A LEU* 1.3 62.3 + - - +
447A GLN* 3.4 5.4 + - - +
448A LYS* 3.1 59.3 + - + +
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Residues in contact with LEU 445 (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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276A LEU* 4.5 20.0 - - + -
341A ILE* 5.2 3.8 - - + -
343A GLY* 3.6 39.9 - - - +
344A PHE 4.0 0.9 - - - +
347A LEU* 5.3 2.0 - - + -
429A MET* 3.5 33.7 - - + -
441A LYS* 3.2 12.1 + - + +
442A ILE* 3.7 6.5 - - - +
444A LYS* 1.3 79.8 - - - +
446A GLN* 1.3 58.4 + - - +
448A LYS* 3.3 7.0 + - + +
449A ILE* 3.0 49.2 + - + +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 3.1 53.1 + - + +
429A MET* 3.1 32.5 + - + +
430A SER* 3.4 15.5 + - - +
431A ALA* 3.9 8.8 + - - +
442A ILE 2.9 13.5 + - - +
443A GLU* 3.3 17.7 + - - +
445A LEU* 1.3 77.7 - - - +
447A GLN* 1.3 56.6 + - - +
449A ILE* 3.3 5.1 + - - +
450A GLN* 3.0 27.5 + - - +
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Residues in contact with GLN 447 (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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443A GLU* 2.9 30.0 + - + +
444A LYS* 3.8 6.3 - - - +
446A GLN* 1.3 76.5 - - - +
448A LYS* 1.3 64.4 + - + +
450A GLN* 3.3 19.5 + - - +
451A LEU* 3.0 48.0 + - + +
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Residues in contact with LYS 448 (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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272A GLU* 4.5 14.1 + - - -
273A LEU* 3.4 18.1 - - + +
276A LEU* 3.7 17.7 - - + +
444A LYS* 3.1 52.9 + - + +
445A LEU* 3.7 8.3 - - + +
447A GLN* 1.3 75.4 - - + +
449A ILE* 1.3 60.4 + - - +
451A LEU* 3.3 11.5 + - + -
452A ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 449 (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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276A LEU* 4.1 11.2 - - + -
280A ILE* 3.8 17.5 - - + -
341A ILE* 5.6 2.2 - - + -
422A LEU* 3.5 32.8 - - + +
425A ALA* 3.9 17.9 - - + +
426A PHE* 3.7 15.5 - - + +
429A MET* 3.6 32.5 - - + -
445A LEU* 3.0 31.8 + - + +
446A GLN* 3.6 5.6 - - - +
448A LYS* 1.3 77.7 - - - +
450A GLN* 1.3 57.1 + - - +
452A ALA* 3.2 5.9 + - - +
453A LEU* 2.9 26.9 + - - +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 3.4 40.4 - - + -
446A GLN 3.0 16.0 + - - +
447A GLN* 3.6 20.2 + - - +
448A LYS 3.3 0.2 - - - -
449A ILE* 1.3 77.8 - - - +
451A LEU* 1.3 57.2 + - - +
453A LEU* 3.3 7.4 + - + +
454A GLN* 2.9 28.6 + - - +
467A LEU* 4.4 17.7 - - + +
471A ILE* 3.5 31.7 - - - +
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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
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273A LEU* 4.0 24.1 - - + +
447A GLN* 3.0 42.3 + - + +
448A LYS* 3.6 15.0 - - + +
449A ILE 3.3 0.2 - - - -
450A GLN* 1.3 76.5 - - - +
452A ALA* 1.3 62.6 + - - +
454A GLN* 3.4 21.6 + - - +
455A HIS* 3.0 22.7 + - - +
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Residues in contact with ALA 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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273A LEU* 4.0 29.3 - - + +
276A LEU* 4.6 5.6 - - + -
277A ALA* 4.5 4.0 - - + -
422A LEU* 3.9 20.4 - - + -
448A LYS 3.0 13.2 + - - +
449A ILE* 3.2 9.6 + - - +
451A LEU* 1.3 74.9 - - - +
453A LEU* 1.3 64.3 + - - +
455A HIS* 3.2 8.1 + - - +
456A VAL* 3.0 28.8 + - - +
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Residues in contact with LEU 453 (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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419A GLU* 3.7 31.0 - - + +
422A LEU* 3.8 21.5 - - + +
423A PHE* 4.0 33.4 - - + -
426A PHE* 5.0 8.7 - - + -
449A ILE 2.9 16.3 + - - +
450A GLN* 3.6 9.0 - - + +
452A ALA* 1.3 77.6 - - - +
454A GLN* 1.3 61.9 + - - +
456A VAL* 3.3 1.6 + - + +
457A LEU* 2.9 48.6 + - + +
467A LEU* 3.8 21.3 - - + -
470A LEU* 4.2 5.2 - - + -
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Residues in contact with GLN 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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450A GLN 2.9 16.9 + - - +
451A LEU* 3.6 23.2 - - - +
452A ALA 3.3 0.2 - - - -
453A LEU* 1.3 77.5 - - - +
455A HIS* 1.3 61.8 + - - +
457A LEU* 3.4 6.6 + - - +
458A GLN* 3.0 48.3 + - + +
467A LEU* 4.1 24.0 - - + +
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Residues in contact with HIS 455 (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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270A MET* 3.5 39.3 - - + +
273A LEU* 5.3 9.4 - - + -
274A GLU* 4.1 22.0 + - + +
451A LEU 3.0 14.5 + - - +
452A ALA* 3.5 11.2 - - - +
454A GLN* 1.3 76.7 - - - +
456A VAL* 1.3 64.1 + - + +
458A GLN* 3.3 17.3 + - - +
459A LYS* 3.0 35.7 + - + +
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Residues in contact with VAL 456 (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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277A ALA* 4.5 12.8 - - + -
418A ASP* 4.5 16.6 - - + -
419A GLU* 3.8 17.7 - - + +
422A LEU* 3.6 18.8 - - + -
452A ALA 3.0 16.8 + - - +
453A LEU 3.8 3.8 - - - +
455A HIS* 1.3 83.3 - - + +
457A LEU* 1.3 63.7 + - - +
459A LYS* 3.2 10.2 + - + +
460A ASN* 3.0 40.2 + - - +
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Residues in contact with LEU 457 (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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415A LEU* 4.6 4.9 - - + -
419A GLU* 3.5 34.5 - - + +
453A LEU* 2.9 41.9 + - + +
454A GLN* 3.7 5.4 - - - +
456A VAL* 1.3 76.8 - - - +
458A GLN* 1.3 62.8 + - + +
460A ASN 3.4 4.5 + - - -
462A ARG* 3.0 34.4 + - + +
466A ILE* 3.8 42.8 - - + -
467A LEU* 3.9 23.3 - - + -
470A LEU* 4.2 6.7 - - + -
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Residues in contact with GLN 458 (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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454A GLN* 3.0 47.0 + - + +
455A HIS* 3.6 17.5 + - - +
457A LEU* 1.3 77.3 - - + +
459A LYS* 1.3 54.1 + - - +
461A HIS* 2.8 29.3 + - - -
462A ARG 4.6 8.3 - - - +
464A ASP* 4.6 17.1 - - - +
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Residues in contact with LYS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A HIS* 3.0 26.3 + - + +
456A VAL* 3.5 9.4 - - + +
458A GLN* 1.3 75.9 - - - +
460A ASN* 1.3 68.5 + - - +
461A HIS* 3.0 23.9 + - + -
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Residues in contact with ASN 460 (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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416A THR* 3.8 16.3 + - + +
419A GLU* 2.6 36.0 + - - +
456A VAL* 3.0 26.1 + - - +
457A LEU 3.9 2.5 - - - +
458A GLN 3.2 0.6 - - - -
459A LYS* 1.3 85.1 - - - +
461A HIS* 1.3 72.2 + - - +
462A ARG* 3.1 20.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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