Contacts of the helix formed by residues 416 - 429 (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 THR 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ARG* 3.9 1.8 - - - +
414A HIS 4.8 0.4 - - - +
415A LEU* 1.3 76.7 - - - +
417A GLU* 1.3 64.5 + - - +
418A ASP* 3.5 8.4 + - - +
419A GLU* 2.9 40.4 + - - +
420A ILE* 3.0 21.5 + - - +
460A ASN* 3.8 20.8 + - - +
462A ARG* 3.8 12.1 - - - +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 3.0 20.3 + - + -
285A LEU* 3.9 26.8 - - + +
292A ARG* 2.9 41.5 + - + +
370A ARG* 2.7 47.0 + - - +
416A THR* 1.3 73.2 - - - +
418A ASP* 1.3 61.6 + - - +
420A ILE* 3.3 5.3 + - - +
421A ALA* 2.9 29.0 + - - +
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Residues in contact with ASP 418 (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* 6.5 0.7 - - + -
281A SER* 2.7 35.7 + - - +
285A LEU* 5.1 5.0 - - - +
416A THR* 3.3 7.6 + - - +
417A GLU* 1.3 80.4 - - - +
419A GLU* 1.3 58.0 + - - +
421A ALA* 3.3 7.6 + - - +
422A LEU* 3.0 35.5 + - + +
456A VAL* 4.5 15.8 - - + +
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Residues in contact with GLU 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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415A LEU* 3.3 12.6 - - + +
416A THR* 2.9 36.2 + - - +
418A ASP* 1.3 72.7 - - - +
420A ILE* 1.3 60.3 + - - +
422A LEU 3.5 0.2 + - - -
423A PHE* 2.9 31.0 + - - +
453A LEU* 3.7 13.0 - - + +
456A VAL* 3.8 16.8 - - + -
457A LEU* 3.5 27.4 - - + +
460A ASN* 2.6 29.6 + - - +
462A ARG* 2.8 34.2 + - - -
470A LEU* 5.6 0.6 - - + +
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Residues in contact with ILE 420 (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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284A HIS* 3.9 18.8 - - - +
292A ARG* 3.3 31.6 - - - +
366A ILE* 4.1 14.5 - - + +
367A ARG* 5.1 3.1 - - + -
369A CYS* 3.7 19.1 - - - -
370A ARG* 3.6 25.1 - - + -
415A LEU* 3.8 19.5 - - + +
416A THR 3.0 13.3 + - - +
417A GLU* 3.5 10.1 - - - +
419A GLU* 1.3 75.7 - - - +
421A ALA* 1.3 55.1 + - - +
423A PHE* 3.4 5.3 + - - +
424A SER* 2.8 45.7 + - - +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.4 24.8 - - + +
281A SER* 4.0 9.9 - - - +
284A HIS* 3.4 34.8 - - + -
337A PHE* 3.7 2.6 - - - -
417A GLU 2.9 17.0 + - - +
418A ASP 3.5 6.3 - - - +
420A ILE* 1.3 77.7 - - - +
422A LEU* 1.3 57.4 + - + +
424A SER* 3.3 5.1 + - - -
425A ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 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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277A ALA* 4.2 18.2 - - + +
280A ILE* 3.7 35.2 - - + -
418A ASP* 3.0 21.5 + - + +
421A ALA* 1.3 74.3 - - + +
423A PHE* 1.3 60.8 + - - +
425A ALA* 3.3 0.6 + - - -
426A PHE* 2.8 29.9 + - - +
449A ILE* 3.5 13.7 - - + +
452A ALA* 3.8 19.3 - - + +
453A LEU* 3.8 33.4 - - + +
456A VAL* 3.6 32.1 - - + -
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Residues in contact with PHE 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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366A ILE* 3.6 39.7 - - + -
406A PHE* 5.3 0.2 - + - -
410A LEU* 4.5 11.4 - - + -
415A LEU* 5.0 4.7 - - + -
419A GLU 2.9 19.0 + - - +
420A ILE* 3.8 4.0 - - - +
422A LEU* 1.3 75.6 - - - +
424A SER* 1.3 62.6 + - - +
426A PHE* 3.3 11.6 + + - +
427A VAL* 3.2 32.6 + - + +
453A LEU* 4.0 22.6 - - + +
470A LEU* 3.5 59.2 - - + -
471A ILE* 6.3 0.2 - - + -
473A LYS* 4.3 8.5 - - + -
474A VAL* 4.0 19.3 - - + -
477A LEU* 4.5 4.7 - - + -
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 5.3 1.9 - - - -
337A PHE* 3.9 18.6 - - - -
363A VAL* 3.7 21.2 + - - +
366A ILE* 3.6 19.8 - - - +
367A ARG* 4.8 4.5 + - - +
420A ILE* 2.8 28.7 + - - +
421A ALA* 3.5 6.1 - - - -
422A LEU 3.2 0.2 - - - -
423A PHE* 1.3 74.1 - - - +
425A ALA* 1.3 64.6 + - - +
427A VAL* 3.2 12.4 - - - +
428A LEU* 3.1 23.4 + - - +
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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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280A ILE* 3.8 31.6 - - + -
337A PHE* 4.1 5.3 - - + -
341A ILE* 4.1 14.4 - - + -
421A ALA 3.0 17.6 + - - +
422A LEU 3.3 4.7 + - - +
424A SER* 1.3 77.5 - - - +
426A PHE* 1.3 57.1 + - - +
428A LEU* 3.3 6.1 + - - +
429A MET* 2.9 36.7 + - + +
449A ILE* 4.0 9.6 - - + -
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU 2.8 18.3 + - - +
423A PHE* 3.5 19.3 - + + +
424A SER 3.2 0.4 - - - -
425A ALA* 1.3 78.8 - - - +
427A VAL* 1.3 71.8 + - + +
429A MET 3.4 5.0 + - - -
446A GLN* 3.1 68.0 + - + +
449A ILE* 3.7 11.4 - - + +
450A GLN* 3.4 48.5 - - + -
453A LEU* 5.0 6.7 - - + -
471A ILE* 5.1 8.3 - - + -
474A VAL* 4.1 21.3 - - + -
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Residues in contact with VAL 427 (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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359A GLY* 5.0 0.4 - - - +
362A GLU* 3.6 22.2 - - + +
363A VAL* 4.0 11.7 - - + -
366A ILE* 3.7 28.9 - - + -
423A PHE* 3.2 21.7 + - + +
424A SER 3.2 12.1 - - - +
426A PHE* 1.3 87.1 - - + +
428A LEU* 1.3 64.7 + - - +
430A SER* 2.7 24.5 + - - -
433A ARG* 3.1 14.2 + - - -
474A VAL* 4.3 14.4 - - + -
477A LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 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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334A VAL* 5.5 1.6 - - + +
337A PHE* 4.8 10.1 - - + -
338A ALA* 3.7 31.0 - - + -
341A ILE* 4.8 12.6 - - + -
344A PHE* 4.4 10.8 - - + -
355A LEU* 3.5 44.6 - - + +
356A LEU* 3.9 20.9 - - + +
359A GLY* 4.4 12.3 - - - -
363A VAL* 4.3 9.9 - - + -
424A SER 3.1 17.1 + - - +
425A ALA* 3.7 4.5 - - - +
427A VAL* 1.3 81.4 - - - +
429A MET* 1.3 64.4 + - - +
430A SER* 3.0 5.9 + - - -
433A ARG* 4.9 3.4 + - - +
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Residues in contact with MET 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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341A ILE* 6.0 3.4 - - + -
344A PHE* 4.0 27.1 - - - -
347A LEU* 3.5 25.4 - - + -
355A LEU* 3.7 9.9 - - + -
425A ALA* 2.9 22.8 + - + +
426A PHE 3.4 5.6 + - - +
427A VAL 3.3 0.4 - - - -
428A LEU* 1.3 81.7 - - + +
430A SER* 1.3 60.0 + - - +
431A ALA 3.4 1.2 + - - -
442A ILE* 3.7 19.4 - - + +
445A LEU* 3.5 28.7 - - + -
446A GLN* 3.1 35.1 - - + +
449A ILE* 3.6 21.1 - - + -
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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