Contacts of the helix formed by residues 438 - 459 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B GLU 5.0 0.3 - - - +
347B LEU* 4.1 4.9 - - + +
348B CYS* 3.6 37.7 + - - +
351B ASP* 2.8 14.9 + - - +
437B GLN* 1.3 87.3 - - + +
439B LYS* 1.3 62.5 + - - +
440B VAL* 3.2 3.6 - - - -
441B LYS* 3.3 43.0 + - + +
442B ILE* 3.2 25.9 + - + +
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ALA* 2.8 33.9 + - + +
432B ASP* 3.8 7.7 + - - +
433B ARG 2.7 28.7 + - - -
434B SER* 5.7 0.2 - - - +
435B TRP 5.4 2.0 - - - +
436B LEU* 3.8 26.9 - - + +
437B GLN 3.6 2.8 + - - -
438B GLU* 1.3 75.4 - - - +
440B VAL* 1.3 60.6 + - + +
442B ILE* 3.3 8.0 + - - -
443B GLU* 2.8 33.1 + - - +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLU* 3.2 1.5 - - - -
439B LYS* 1.3 78.9 - - + +
441B LYS* 1.3 63.7 + - - +
443B GLU* 3.2 7.2 + - - +
444B LYS* 3.1 45.7 + - + +
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Residues in contact with LYS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 4.9 17.9 + - + +
347B LEU* 3.9 20.0 - - + -
438B GLU* 3.3 41.7 + - + +
440B VAL* 1.3 79.0 - - - +
442B ILE* 1.3 62.4 + - - +
444B LYS* 3.4 13.3 + - + +
445B LEU* 3.2 31.0 + - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.8 23.6 - - + -
351B ASP* 3.9 12.1 - - - +
355B LEU* 4.1 13.7 - - + -
429B MET* 3.7 31.1 - - + +
430B SER 3.8 3.4 - - - +
431B ALA* 3.8 17.9 - - + +
436B LEU* 3.9 33.7 - - + -
438B GLU 3.2 18.2 + - - +
439B LYS 3.7 4.0 - - - +
441B LYS* 1.3 73.2 - - - +
443B GLU* 1.3 60.2 + - - +
445B LEU* 3.2 9.6 + - - +
446B GLN* 2.9 27.0 + - - +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ALA* 3.6 20.1 - - + +
439B LYS 2.8 19.2 + - - +
440B VAL* 3.2 8.0 + - - +
442B ILE* 1.3 76.7 - - - +
444B LYS* 1.3 58.2 + - + +
446B GLN* 3.3 17.2 + - - +
447B GLN* 3.0 62.0 + - - +
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Residues in contact with LYS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B VAL* 3.1 37.3 + - + +
441B LYS* 3.6 12.1 - - - +
443B GLU* 1.3 75.7 - - + +
445B LEU* 1.3 68.0 + - + +
447B GLN* 3.5 9.6 + - - +
448B LYS* 3.3 34.1 + - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ASP 4.7 11.2 - - - +
343B GLY* 4.2 24.0 - - - +
346B GLU* 5.4 4.0 - - - +
347B LEU* 4.5 7.0 - - + -
429B MET* 3.8 29.6 - - + -
441B LYS* 3.2 24.6 + - + +
442B ILE* 3.2 11.2 + - - +
444B LYS* 1.3 82.9 - - + +
446B GLN* 1.3 61.4 + - - +
448B LYS* 3.3 15.3 + - + +
449B ILE* 3.0 31.2 + - + +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 3.0 59.2 + - + +
427B VAL* 5.0 0.4 - - - +
429B MET* 3.1 24.1 + - + +
430B SER* 3.6 15.1 + - - +
431B ALA 4.0 8.8 + - - -
442B ILE 2.9 11.4 + - - +
443B GLU* 3.3 21.9 + - - +
445B LEU* 1.3 76.5 - - - +
447B GLN* 1.3 58.2 + - - +
449B ILE* 3.2 10.2 + - - +
450B GLN* 2.8 28.6 + - - +
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLU* 3.0 46.3 + - - +
444B LYS* 3.8 9.4 - - - +
445B LEU 3.3 0.2 - - - -
446B GLN* 1.3 77.7 - - - +
448B LYS* 1.3 55.9 + - + +
450B GLN* 3.3 12.2 + - - +
451B LEU* 3.0 36.2 + - + +
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU* 5.6 4.2 + - - -
273B LEU* 3.6 13.1 - - + +
276B LEU* 3.6 15.2 - - + +
444B LYS* 3.3 22.6 + - - +
445B LEU* 3.3 16.2 + - + +
447B GLN* 1.3 74.0 - - + +
449B ILE* 1.3 66.0 + - - +
451B LEU* 3.3 10.5 + - + -
452B ALA* 3.0 22.7 + - - +
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.0 13.2 - - + -
280B ILE* 4.0 14.6 - - + -
341B ILE* 4.9 5.6 - - + -
422B LEU* 3.6 31.8 - - + +
425B ALA* 4.0 17.3 - - + +
426B PHE* 3.7 14.8 - - + +
429B MET* 3.7 34.3 - - + -
445B LEU* 3.0 19.2 + - + +
446B GLN* 3.5 7.4 - - - +
448B LYS* 1.3 74.4 - - - +
450B GLN* 1.3 56.6 + - - +
452B ALA* 3.2 4.6 + - - +
453B LEU* 2.9 26.7 + - + +
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 3.4 33.7 - - + -
446B GLN* 2.8 20.1 + - - +
447B GLN* 3.5 11.8 - - - +
448B LYS 3.2 0.2 - - - -
449B ILE* 1.3 74.5 - - - +
451B LEU* 1.3 60.1 + - + +
453B LEU* 3.3 6.9 + - + +
454B GLN* 2.9 29.4 + - + +
467B LEU* 4.3 25.7 - - + +
471B ILE* 4.7 10.5 - - - +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 3.8 25.2 - - + +
447B GLN* 3.0 23.4 + - + +
448B LYS* 3.3 13.9 + - + +
450B GLN* 1.3 75.7 - - + +
452B ALA* 1.3 64.7 + - - +
454B GLN* 3.4 19.5 + - - +
455B HIS* 3.0 23.9 + - - +
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 3.8 28.0 - - + +
276B LEU* 4.3 8.5 - - + -
277B ALA* 4.3 3.8 - - + -
422B LEU* 3.9 21.5 - - + -
448B LYS 3.0 13.6 + - - +
449B ILE 3.5 9.0 - - - +
451B LEU* 1.3 74.7 - - - +
453B LEU* 1.3 64.2 + - - +
455B HIS* 3.2 7.1 + - - +
456B VAL* 3.0 27.7 + - - +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU* 3.9 22.0 - - + +
422B LEU* 3.8 29.8 - - + +
423B PHE* 4.3 29.6 - - + -
426B PHE* 4.8 11.7 - - + -
449B ILE 2.9 14.1 + - - +
450B GLN* 3.5 10.8 - - + +
452B ALA* 1.3 77.6 - - - +
454B GLN* 1.3 56.9 + - - +
456B VAL* 3.3 1.3 + - + +
457B LEU* 3.0 54.6 + - + +
467B LEU* 4.1 18.8 - - + -
470B LEU* 4.3 8.7 - - + -
471B ILE* 5.8 1.1 - - + -
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B GLN* 2.9 18.7 + - - +
451B LEU* 3.7 21.9 - - - +
452B ALA 3.3 0.2 - - - -
453B LEU* 1.3 76.2 - - - +
455B HIS* 1.3 58.3 + - - +
457B LEU* 3.6 10.8 + - + +
458B GLN* 3.0 31.9 + - + +
467B LEU* 3.8 30.4 - - + +
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B MET* 3.7 35.7 - - + +
273B LEU* 5.1 7.2 - - + -
274B GLU* 4.5 22.4 + - + +
277B ALA* 6.0 2.2 - - + -
451B LEU 3.0 17.5 + - - +
452B ALA* 3.5 7.6 - - - +
453B LEU 3.2 0.2 - - - -
454B GLN* 1.3 74.7 - - - +
456B VAL* 1.3 65.3 + - + +
458B GLN* 3.2 19.3 + - + +
459B LYS* 3.0 56.6 + - + +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 4.3 14.1 - - + -
418B ASP* 4.3 18.2 - - + -
419B GLU* 3.6 19.7 - - + +
422B LEU* 3.5 19.1 - - + -
452B ALA 3.0 16.1 + - - +
453B LEU* 3.8 3.8 - - + +
455B HIS* 1.3 77.7 - - + +
457B LEU* 1.3 64.1 + - - +
459B LYS* 3.3 24.6 + - - +
460B ASN* 3.1 45.8 + - - +
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 4.6 1.3 - - + -
419B GLU* 3.4 36.1 - - + +
453B LEU* 3.0 41.2 + - + +
454B GLN* 3.8 5.4 - - + +
456B VAL* 1.3 76.3 - - - +
458B GLN* 1.3 61.2 + - - +
460B ASN 3.5 2.8 + - - -
462B ARG* 3.2 40.5 + - + +
466B ILE* 3.7 19.5 - - + -
467B LEU* 3.9 38.1 - - + +
470B LEU* 4.2 10.3 - - + -
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Residues in contact with GLN 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLN* 3.0 22.8 + - + +
455B HIS* 3.3 18.4 + - + +
456B VAL 3.1 0.2 - - - -
457B LEU* 1.3 74.0 - - - +
459B LYS* 1.3 58.1 + - + +
460B ASN 3.0 4.3 - - - -
461B HIS* 3.0 22.9 + - - -
462B ARG 4.9 4.7 - - - +
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Residues in contact with LYS 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLU* 5.7 4.6 - - - +
277B ALA* 6.2 1.6 - - - +
455B HIS* 3.0 39.5 + - + +
456B VAL* 3.5 33.6 - - - +
458B GLN* 1.3 75.3 - - + +
460B ASN* 1.3 64.7 + - - +
461B HIS* 3.3 18.8 + - - -
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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