Contacts of the helix formed by residues 359 - 374 (chain B) in PDB entry 1SA4
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 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.3 11.0 + - - -
93B TYR* 4.3 7.9 - - - +
350B LEU 3.7 2.8 + - - +
357B SER 4.0 9.4 - - - +
358B ARG* 1.3 76.7 - - - +
360B PHE* 1.3 61.7 + - - +
361B TYR* 2.9 11.4 + - - +
362B HIS* 2.6 54.2 + - - +
363B THR* 2.9 22.2 + - - -
441B JAN 3.5 39.4 - - - +
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Residues in contact with PHE 360 (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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81B TYR* 3.5 51.8 - + - -
82B LEU* 4.1 11.1 - - + +
85B GLY* 3.6 20.6 - - - -
89B LEU* 3.8 15.3 - - + -
93B TYR* 3.3 38.5 + + - -
103B LEU* 3.9 24.5 - - + -
106B TRP* 3.5 12.5 - - + +
107B ILE* 3.7 31.4 - - + -
110B SER* 4.8 0.2 + - - -
359B ASP* 1.3 71.6 - - - +
361B TYR* 1.3 60.6 + - - +
363B THR* 3.6 5.0 - - - -
364B CYS* 3.0 28.6 + - - +
441B JAN 5.0 1.4 + - - -
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Residues in contact with TYR 361 (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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106B TRP* 3.6 22.7 - + + -
299B CYS* 3.3 26.7 - - + -
303B TRP* 2.9 27.9 + + - -
359B ASP* 2.9 6.4 + - - +
360B PHE* 1.3 77.8 - - - +
362B HIS* 1.3 77.7 + + - +
364B CYS* 3.1 3.6 + - - +
365B TYR* 3.1 54.3 + + - -
440B FPP 3.5 12.5 - - - +
441B JAN 3.4 87.3 + + + -
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Residues in contact with HIS 362 (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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297B ASP* 3.2 11.4 + - - -
299B CYS* 3.5 16.6 - - + -
350B LEU 3.7 4.7 - - - +
351B LEU* 3.6 20.4 - - - +
352B ASP* 3.7 27.2 + - + +
357B SER 5.5 0.4 + - - -
359B ASP* 2.6 38.3 + - - +
361B TYR* 1.3 77.1 - + - +
363B THR* 1.3 60.9 + - - +
365B TYR 4.5 0.7 - - - +
366B CYS* 2.9 35.3 + - - +
439B ZN 2.1 37.3 - - - -
441B JAN 3.6 23.8 - + - -
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Residues in contact with THR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 5.5 1.1 - - + -
81B TYR* 3.5 5.5 - - + -
82B LEU* 3.9 22.0 - - + -
110B SER* 3.8 13.0 - - - +
349B GLY* 3.5 10.8 - - - -
350B LEU* 2.9 41.0 + - + +
359B ASP 2.9 20.6 + - - -
360B PHE* 3.6 9.4 - - - -
361B TYR 3.2 0.4 - - - -
362B HIS* 1.3 78.8 - - - +
364B CYS* 1.3 62.9 + - - +
366B CYS* 4.3 0.3 - - - +
367B LEU* 3.2 34.7 + - + +
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Residues in contact with CYS 364 (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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105B TYR* 4.2 4.9 - - - -
106B TRP* 3.7 42.6 - - + +
109B HIS* 3.8 25.4 - - - -
110B SER* 3.3 11.4 + - - +
113B LEU* 4.2 1.4 - - - +
360B PHE 3.0 14.7 + - - +
361B TYR 3.4 8.1 - - - +
363B THR* 1.3 77.4 - - - +
365B TYR* 1.3 73.3 + - - +
367B LEU* 3.4 2.8 + - - +
368B SER* 2.8 32.0 + - - -
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Residues in contact with TYR 365 (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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102B TRP* 3.9 8.8 - - - -
105B TYR* 3.6 19.1 + - - -
106B TRP* 3.4 27.6 + + - -
154B TYR* 4.9 3.2 + - - -
298B GLY 4.4 2.0 - - - -
299B CYS* 3.7 25.4 - - + +
301B SER* 4.2 0.7 - - - -
302B PHE* 3.6 32.6 + + + +
303B TRP* 3.3 35.9 - + - -
361B TYR* 3.1 48.7 + + - +
362B HIS 4.7 0.2 - - - +
364B CYS* 1.3 78.9 - - - +
366B CYS* 1.3 61.9 + - - +
368B SER* 4.1 1.6 - - - -
369B GLY* 3.0 23.6 + - - -
402B ASN* 3.5 22.4 - - + -
441B JAN 5.7 0.4 - - + +
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Residues in contact with CYS 366 (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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298B GLY* 3.7 28.3 - - - -
299B CYS 4.3 0.2 - - - -
301B SER* 4.7 2.0 - - - -
339B ILE* 3.5 13.5 - - + +
343B CYS* 3.9 13.2 - - - -
350B LEU* 3.6 25.1 - - + -
351B LEU 3.3 26.9 - - - -
362B HIS* 2.9 24.1 + - - +
365B TYR* 1.3 77.1 - - - +
367B LEU* 1.3 58.1 - - - +
369B GLY 3.4 0.2 + - - -
370B LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 367 (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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73B LEU* 4.0 30.3 - - + -
78B HIS* 5.0 2.0 - - + -
82B LEU* 5.1 0.2 - - + -
110B SER* 3.9 26.9 - - - +
113B LEU* 3.7 15.2 - - + +
114B LEU* 4.3 24.5 - - + -
350B LEU* 4.0 19.1 - - + -
363B THR* 3.2 28.1 + - + +
364B CYS 3.8 0.7 - - - +
365B TYR 3.3 0.2 - - - -
366B CYS* 1.3 76.7 - - - +
368B SER* 1.3 64.1 + - - +
370B LEU* 3.2 5.0 + - + -
371B SER* 3.0 20.8 + - - -
394B LEU* 3.3 23.3 - - + +
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Residues in contact with SER 368 (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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109B HIS* 3.1 27.3 + - - -
113B LEU* 3.5 7.8 - - - +
302B PHE* 3.8 14.8 - - - -
364B CYS 2.8 21.9 + - - -
365B TYR* 3.8 6.7 - - - -
366B CYS 3.4 0.2 - - - -
367B LEU* 1.3 76.0 - - - +
369B GLY* 1.3 62.2 + - - +
371B SER* 3.4 5.4 + - - -
372B ILE* 3.1 26.7 + - - +
397B THR* 4.0 2.1 - - - +
402B ASN* 3.3 22.2 + - - -
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Residues in contact with GLY 369 (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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301B SER* 3.3 34.7 - - - +
302B PHE* 4.0 2.8 - - - +
335B LEU* 4.1 4.2 - - - +
339B ILE* 4.1 5.6 - - - -
365B TYR 3.0 13.1 + - - -
368B SER* 1.3 75.6 - - - +
370B LEU* 1.3 64.1 + - - +
372B ILE* 3.2 6.3 + - - +
373B ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 370 (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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73B LEU* 4.1 18.4 - - + -
336B GLN* 3.8 36.3 - - + +
339B ILE* 3.7 18.0 - - + +
340B LEU* 4.1 30.5 - - + -
366B CYS 3.0 18.3 + - - +
367B LEU* 3.2 8.5 + - + +
369B GLY* 1.3 75.2 - - - +
371B SER* 1.3 58.0 + - - +
373B ALA* 3.2 4.5 + - - +
374B GLN* 3.0 52.5 + - - +
392B ASN* 5.8 0.2 - - + -
394B LEU* 3.7 15.7 - - + -
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Residues in contact with SER 371 (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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113B LEU* 4.1 11.0 - - - -
367B LEU 3.0 13.2 + - - -
368B SER 3.6 8.5 - - - -
369B GLY 3.2 0.2 - - - -
370B LEU* 1.3 74.0 - - - +
372B ILE* 1.3 65.0 + - - +
374B GLN* 3.2 11.6 + - - -
375B HIS* 3.1 31.7 + - - +
394B LEU* 3.9 7.1 - - - +
395B GLN 2.7 27.9 + - - -
396B PRO* 3.5 12.1 - - - +
397B THR* 3.7 6.9 + - - -
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Residues in contact with ILE 372 (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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301B SER 5.3 0.7 - - - +
302B PHE* 3.6 35.4 - - + -
305B ALA* 4.2 12.6 - - + +
306B GLY* 3.6 19.3 - - - +
309B PRO* 3.8 27.1 - - + -
328B TRP* 3.0 32.4 + - + +
330B PHE* 4.4 6.5 - - + -
368B SER 3.1 9.2 + - - +
369B GLY* 3.2 8.9 + - - +
371B SER* 1.3 76.6 - - - +
373B ALA* 1.3 61.3 + - - +
375B HIS* 3.3 8.2 - - - +
397B THR* 3.8 18.4 - - + +
399B PRO* 4.9 8.3 - - + -
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Residues in contact with ALA 373 (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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330B PHE* 4.0 13.5 - - + -
332B GLN* 2.9 33.4 + - - +
335B LEU* 4.1 17.5 - - + -
336B GLN* 3.1 33.3 + - + -
369B GLY 2.9 16.6 + - - +
370B LEU* 3.5 6.7 - - - +
372B ILE* 1.3 79.1 - - - +
374B GLN* 1.3 56.5 + - - +
385B VAL* 4.1 0.9 - - - +
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Residues in contact with GLN 374 (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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332B GLN* 4.7 1.3 + - - -
336B GLN* 3.7 17.0 + - - +
340B LEU* 6.1 0.4 - - - +
370B LEU* 3.0 44.7 + - + +
371B SER* 3.2 4.5 + - - +
373B ALA* 1.3 77.9 - - - +
375B HIS* 1.3 71.6 + - + +
376B PHE 4.3 0.2 - - - -
383B HIS 4.0 0.5 - - - +
384B ASP* 3.3 9.0 - - - +
385B VAL* 2.9 37.0 + - - +
386B VAL* 4.0 14.7 - - + +
387B LEU 5.3 0.6 + - - +
392B ASN* 3.0 30.9 + - - +
393B ALA* 3.7 4.4 - - - +
394B LEU* 2.9 31.5 + - - +
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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