Contacts of the helix formed by residues 416 - 429 (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 THR 416 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B HIS 4.6 1.3 - - - +
415B LEU* 1.3 75.2 - - - +
417B GLU* 1.3 66.6 + - - +
418B ASP* 3.6 12.0 + - - +
419B GLU* 2.8 39.6 + - - +
420B ILE* 2.9 22.4 + - - +
460B ASN* 3.7 19.5 + - - +
462B ARG* 3.9 12.6 - - - +
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Residues in contact with GLU 417 (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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281B SER* 6.0 0.2 - - - -
284B HIS* 3.1 22.2 + - + +
285B LEU* 5.7 9.7 - - + +
288B CYS* 4.5 0.3 - - - -
292B ARG* 3.4 32.2 + - + +
293B GLU* 5.6 1.6 - - - +
370B ARG* 2.8 46.2 + - - -
416B THR* 1.3 73.4 - - - +
418B ASP* 1.3 63.3 + - - +
420B ILE* 3.4 11.6 + - - +
421B ALA* 2.8 28.8 + - - +
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Residues in contact with ASP 418 (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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281B SER* 3.0 33.8 + - - +
416B THR* 3.2 11.6 + - - +
417B GLU* 1.3 79.3 + - - +
419B GLU* 1.3 60.9 + - - +
421B ALA* 3.3 3.9 + - - +
422B LEU* 2.9 35.1 + - + +
456B VAL* 4.3 17.0 - - + -
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 3.3 15.5 - - + +
416B THR* 2.8 37.6 + - - +
418B ASP* 1.3 74.0 - - - +
420B ILE* 1.3 61.1 + - - +
422B LEU 3.9 0.3 - - - -
423B PHE* 2.9 32.8 + - - +
453B LEU* 3.9 11.4 - - + +
456B VAL* 3.6 17.3 - - + -
457B LEU* 3.4 31.8 - - + +
460B ASN* 2.8 28.1 + - - +
462B ARG* 3.1 22.3 + - - -
470B LEU* 5.6 0.4 - - + +
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Residues in contact with ILE 420 (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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284B HIS* 3.7 20.4 - - - +
292B ARG* 4.1 4.9 - - - +
366B ILE* 4.0 19.9 - - + +
367B ARG* 5.0 3.1 - - + -
369B CYS* 3.8 19.7 - - - -
370B ARG* 3.6 30.3 - - + -
415B LEU* 3.7 29.4 - - + +
416B THR 2.9 18.1 + - - +
417B GLU* 3.6 15.5 - - - +
419B GLU* 1.3 74.5 - - - +
421B ALA* 1.3 55.8 + - - +
423B PHE* 3.9 5.1 - - - +
424B SER* 2.7 41.2 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.5 13.8 - - + +
281B SER* 3.9 21.1 - - - +
284B HIS* 3.5 34.3 - - + +
337B PHE* 3.7 2.4 - - - -
417B GLU 2.8 16.0 + - - +
418B ASP 3.3 9.9 - - - +
420B ILE* 1.3 78.0 - - - +
422B LEU* 1.3 62.9 + - - +
424B SER* 3.3 4.8 + - - -
425B ALA 3.1 17.8 + - - -
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Residues in contact with LEU 422 (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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277B ALA* 4.2 17.3 - - + +
280B ILE* 3.7 36.6 - - + -
281B SER* 5.3 1.3 - - - +
418B ASP* 2.9 19.4 + - + +
421B ALA* 1.3 75.7 - - + +
423B PHE* 1.3 61.3 + - - +
425B ALA* 3.3 0.9 + - - -
426B PHE* 2.9 29.0 + - - +
449B ILE* 3.6 12.8 - - + +
452B ALA* 3.8 28.9 - - + +
453B LEU* 3.8 23.3 - - + -
456B VAL* 3.5 33.2 - - + -
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Residues in contact with PHE 423 (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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366B ILE* 3.6 38.8 - - + -
406B PHE* 5.5 0.2 - + - -
410B LEU* 4.6 10.5 - - + -
415B LEU* 4.9 6.1 - - + -
419B GLU 2.9 20.1 + - - +
420B ILE* 3.9 3.8 - - - +
422B LEU* 1.3 76.5 - - - +
424B SER* 1.3 62.7 + - - +
426B PHE* 3.3 12.5 + + - +
427B VAL* 3.1 40.2 + - + +
453B LEU* 4.3 20.7 - - + +
470B LEU* 3.5 57.9 - - + -
471B ILE* 5.5 0.7 - - + -
473B LYS* 4.3 4.9 - - + -
474B VAL* 4.0 10.1 - - + -
477B LEU* 4.2 9.2 - - + -
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Residues in contact with SER 424 (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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284B HIS* 5.1 3.1 - - - -
337B PHE* 3.8 19.1 - - - -
363B VAL* 3.7 20.2 - - - +
366B ILE* 3.6 25.5 - - - +
367B ARG* 4.8 3.5 + - - +
420B ILE* 2.7 28.7 + - - +
421B ALA* 3.4 6.1 - - - -
422B LEU 3.2 0.2 - - - -
423B PHE* 1.3 77.1 - - - +
425B ALA* 1.3 62.5 + - - +
427B VAL* 3.2 5.8 - - - +
428B LEU* 3.0 24.4 + - - +
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Residues in contact with ALA 425 (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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280B ILE* 3.9 31.6 - - + -
337B PHE* 4.0 1.7 - - + -
341B ILE* 4.0 24.0 - - + -
421B ALA 3.1 12.5 + - - +
422B LEU 3.7 7.6 - - - +
424B SER* 1.3 75.9 - - - +
426B PHE* 1.3 58.0 + - - +
428B LEU* 3.3 1.2 + - - +
429B MET* 2.9 35.7 + - - +
449B ILE* 4.0 11.9 - - + -
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Residues in contact with PHE 426 (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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422B LEU 2.9 14.7 + - - +
423B PHE* 3.4 19.3 - + + +
425B ALA* 1.3 79.4 - - - +
427B VAL* 1.3 72.8 + - + +
429B MET 3.5 6.6 + - - +
446B GLN* 3.0 63.4 + - + -
449B ILE* 3.7 8.7 - - + +
450B GLN* 3.4 42.4 - - + -
453B LEU* 4.8 8.5 - - + -
471B ILE* 3.7 31.6 - - + -
474B VAL* 4.0 17.9 - - + -
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Residues in contact with VAL 427 (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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359B GLY* 5.1 0.4 - - - +
362B GLU* 3.9 22.2 - - + +
363B VAL* 4.0 12.8 - - + -
366B ILE* 3.6 22.9 - - + -
423B PHE* 3.1 36.4 + - + +
424B SER 3.2 11.7 - - - +
426B PHE* 1.3 78.7 - - + +
428B LEU* 1.3 64.2 + - - +
430B SER* 3.6 10.9 - - - -
433B ARG* 3.1 23.0 + - - -
446B GLN* 5.0 0.4 - - - +
474B VAL* 4.1 20.4 - - + -
477B LEU* 4.1 6.5 - - + -
478B ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 428 (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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334B VAL* 5.0 3.1 - - + -
337B PHE* 4.3 11.9 - - + -
338B ALA* 3.6 34.8 - - + -
341B ILE* 4.0 14.1 - - + -
344B PHE* 5.1 8.1 - - + -
355B LEU* 3.4 43.2 - - - +
356B LEU* 4.3 12.1 - - + -
359B GLY* 3.9 21.5 - - - +
360B SER* 4.3 3.1 - - - +
363B VAL* 4.3 8.5 - - + -
424B SER 3.0 17.2 + - - +
425B ALA* 3.7 4.7 - - - +
427B VAL* 1.3 79.8 - - - +
429B MET* 1.3 61.3 + - + +
430B SER* 3.1 6.0 + - - -
433B ARG* 5.0 2.6 + - - +
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Residues in contact with MET 429 (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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341B ILE* 4.6 16.2 - - + -
342B ASP 5.8 0.2 - - - +
344B PHE* 4.0 32.1 - - + +
347B LEU* 3.9 20.6 - - + -
355B LEU* 4.4 5.4 - - + -
425B ALA* 2.9 20.5 + - - +
426B PHE 3.7 5.2 - - - +
427B VAL 3.4 0.2 - - - -
428B LEU* 1.3 78.9 - - + +
430B SER* 1.3 60.1 + - - +
431B ALA 3.7 0.7 + - - -
442B ILE* 3.7 14.9 - - + +
445B LEU* 3.8 33.2 - - + -
446B GLN* 3.1 29.6 - - + +
449B ILE* 3.7 23.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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