Contacts of the helix formed by residues 384 - 396 (chain D) in PDB entry 1SA0
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 ILE 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D CYS* 3.9 25.8 - - + -
267D PHE 3.7 18.4 - - - +
269D MET* 4.1 21.0 - - + -
303D ALA* 4.7 2.7 - - + -
305D CYS* 3.9 10.9 - - - +
381D SER* 2.9 12.6 + - - +
383D ALA* 1.3 78.2 - - - +
385D GLN* 1.3 64.2 + - - +
387D LEU* 2.8 47.3 + - + +
388D PHE* 3.4 14.6 + - + -
432D TYR* 3.4 38.8 - - + +
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Residues in contact with GLN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D HIS 5.4 1.6 - - - +
382D THR 3.0 20.0 + - - +
383D ALA 4.3 0.2 - - - -
384D ILE* 1.3 81.5 - - - +
386D GLU* 1.3 62.2 + - - +
388D PHE* 3.1 9.1 + - - +
389D LYS* 3.0 51.9 + - + +
429D VAL* 3.9 32.2 - - + +
432D TYR* 3.9 15.9 - - + -
433D GLN* 3.7 44.4 - - - +
436D GLN* 4.0 7.1 + - - -
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Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D ALA 4.7 3.4 - - - +
305D CYS* 3.5 26.3 - - - -
306D ASP* 3.5 12.5 + - - +
309D HIS* 3.7 35.5 + - + +
383D ALA* 2.8 16.4 + - - +
385D GLN* 1.3 79.6 - - - +
387D LEU* 1.3 58.8 + - - +
389D LYS* 3.6 12.2 - - + +
390D ARG* 3.2 25.3 + - - +
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D VAL* 3.9 27.6 - - + -
191D VAL* 6.2 0.2 - - + -
203D CYS* 4.6 8.3 - - + -
205D ASP* 3.6 38.1 - - + +
303D ALA* 4.0 17.7 - - + -
304D ALA 4.1 5.4 - - - +
305D CYS* 4.0 7.0 - - - -
383D ALA 4.2 0.2 + - - -
384D ILE* 2.8 30.4 + - + +
386D GLU* 1.3 72.7 - - - +
388D PHE* 1.3 92.0 + - + +
390D ARG* 3.1 26.7 + - - +
391D ILE* 3.4 10.0 + - + +
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Residues in contact with PHE 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 6.3 0.2 - - + -
172D VAL* 5.7 2.5 - - + -
191D VAL* 4.0 24.5 - - + -
203D CYS* 5.0 3.6 - - - -
267D PHE* 3.6 34.8 - + + -
384D ILE* 3.4 35.4 + - + -
385D GLN* 3.1 6.3 + - - +
387D LEU* 1.3 93.5 - - + +
389D LYS* 1.3 62.2 + - - +
391D ILE* 3.3 7.3 + - + +
392D SER* 3.0 26.0 + - - -
425D MET* 3.3 27.2 - - + +
428D LEU* 3.6 24.5 - - + -
429D VAL* 3.9 15.3 - - + -
432D TYR* 3.8 11.9 - + - -
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Residues in contact with LYS 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLN* 3.0 43.7 + - + +
386D GLU* 3.6 12.2 - - + +
388D PHE* 1.3 77.6 - - - +
390D ARG* 1.3 56.2 + - - +
392D SER* 3.4 6.9 + - - -
393D GLU* 3.0 34.3 + - - +
429D VAL* 3.7 25.5 - - + +
433D GLN* 6.0 0.4 - - - +
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Residues in contact with ARG 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PRO 3.5 14.1 + - - -
174D SER* 3.4 32.1 - - - +
175D PRO* 3.9 7.7 - - - +
205D ASP* 2.3 35.6 + - - -
207D GLU* 3.5 10.2 + - - +
304D ALA* 3.3 23.2 + - - +
386D GLU 3.2 12.8 + - - +
387D LEU* 3.1 22.4 - - - +
389D LYS* 1.3 75.6 - - - +
391D ILE* 1.3 68.7 + - - +
393D GLU* 3.3 26.2 + - + +
394D GLN* 3.4 24.8 + - - +
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Residues in contact with ILE 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D VAL* 3.9 28.3 - - + -
173D PRO* 4.3 11.0 - - + +
184D PRO* 4.3 5.5 - - + +
187D ALA* 4.3 13.7 - - + -
188D THR* 3.3 35.0 - - - +
191D VAL* 4.8 2.9 - - + -
387D LEU* 3.4 11.3 + - + +
388D PHE* 3.3 12.9 + - + +
390D ARG* 1.3 82.0 - - - +
392D SER* 1.3 62.1 + - - +
393D GLU 3.0 4.9 - - - -
394D GLN* 3.4 15.1 + - - +
395D PHE* 3.1 26.3 + - - +
425D MET* 3.6 28.7 - - + -
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Residues in contact with SER 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D THR* 5.2 1.1 - - - -
388D PHE 3.0 19.6 + - - -
389D LYS* 3.6 7.9 - - - -
391D ILE* 1.3 79.5 - - - +
393D GLU* 1.3 56.1 + - - +
395D PHE* 3.8 9.6 - - - -
396D THR* 3.3 32.6 + - - -
422D GLU* 5.0 3.6 - - - +
425D MET* 4.2 12.6 - - - -
426D ASN* 2.9 28.8 + - - -
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Residues in contact with GLU 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D LYS* 3.0 21.9 + - - +
390D ARG* 3.3 22.0 - - - +
392D SER* 1.3 78.6 - - - +
394D GLN* 1.3 55.5 + - + +
395D PHE 3.3 0.4 - - - -
396D THR* 4.5 0.7 - - - -
397D ALA* 2.8 31.9 + - - +
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Residues in contact with GLN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PRO 5.4 2.3 + - - +
174D SER* 5.2 1.3 - - - +
175D PRO* 3.4 37.2 - - + +
184D PRO* 3.9 30.6 - - + +
390D ARG* 3.4 29.9 + - - +
391D ILE* 3.4 12.5 + - - +
393D GLU* 1.3 76.7 - - + +
395D PHE* 1.3 66.2 + - - +
397D ALA* 3.8 7.8 - - - +
398D MET* 3.4 29.9 + - + +
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Residues in contact with PHE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D PRO* 3.4 13.5 - - - +
185D TYR* 3.9 23.6 - + - -
188D THR* 3.2 36.6 - - + +
189D LEU* 5.6 1.1 - - + -
391D ILE 3.1 17.4 + - - +
392D SER* 4.0 7.9 - - - +
393D GLU 3.3 0.4 - - - -
394D GLN* 1.3 75.2 - - - +
396D THR* 1.3 54.6 + - - +
397D ALA 2.9 3.8 - - - -
398D MET* 2.7 9.6 + - - +
399D PHE* 2.7 48.5 + + + +
418D PHE* 3.4 44.6 - + + -
421D ALA* 5.7 1.6 - - + -
422D GLU* 3.7 41.1 - - + -
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Residues in contact with THR 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D SER* 3.3 19.2 + - - -
393D GLU* 5.2 0.7 - - - -
395D PHE* 1.3 75.4 - - - +
397D ALA* 1.3 56.8 + - - +
398D MET 3.3 0.4 - - - -
399D PHE* 4.4 5.2 - - + +
400D ARG* 3.1 50.9 + - - +
422D GLU* 2.6 37.5 + - - +
426D ASN* 5.0 2.6 + - - -
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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