Contacts of the helix formed by residues 245 - 256 (chain H) in PDB entry 1ZWS
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 SER 245 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113H GLU* 2.5 33.8 + - - -
243H HIS 3.7 1.9 + - - -
244H THR* 1.3 88.7 - - - +
246H GLU* 1.3 62.5 - - - +
247H LEU* 3.3 11.9 + - - +
248H ALA 2.8 20.8 + - - -
249H LYS* 3.3 5.4 + - - +
274H TRP* 3.7 0.9 + - - -
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Residues in contact with GLU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245H SER* 1.3 71.1 - - - +
247H LEU* 1.3 57.5 + - - +
249H LYS* 3.1 38.3 + - - +
250H ASP* 2.7 37.1 + - - +
253H ARG* 4.5 11.3 + - - +
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Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245H SER* 3.5 10.7 - - - +
246H GLU* 1.3 79.7 - - - +
248H ALA* 1.3 65.7 + - - +
250H ASP* 3.4 6.4 - - + +
251H PHE 3.1 12.5 + - - -
272H HIS* 3.3 27.8 - - + +
273H PRO* 3.7 18.4 - - + +
274H TRP* 3.3 32.7 - - + +
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Residues in contact with ALA 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H GLU* 3.6 3.1 - - - +
207H THR* 6.3 0.2 - - - -
211H LEU* 3.6 13.5 - - + -
244H THR* 3.4 21.5 - - + -
245H SER* 2.8 16.8 + - - +
247H LEU* 1.3 73.8 - - - +
249H LYS* 1.3 55.9 + - - +
251H PHE* 2.6 35.4 + - - +
252H ILE* 3.2 7.8 + - - +
274H TRP* 3.4 30.0 - - + +
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Residues in contact with LYS 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H LEU* 5.2 0.2 - - - +
236H PHE* 3.5 24.9 - - + -
238H GLU* 4.9 4.5 + - - -
241H PHE* 3.9 26.8 + - + -
244H THR* 3.1 38.6 + - + +
245H SER 3.3 7.2 - - - +
246H GLU* 3.1 41.8 + - - +
248H ALA* 1.3 78.9 - - - +
250H ASP* 1.3 57.0 + - - +
252H ILE* 3.1 13.3 - - - +
253H ARG* 2.9 53.5 + - - +
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Residues in contact with ASP 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H GLU 2.7 21.2 + - - +
247H LEU* 3.4 11.2 - - + +
248H ALA 2.7 3.0 + - - -
249H LYS* 1.3 68.0 - - - +
251H PHE* 1.3 68.1 + - - +
253H ARG* 2.8 26.7 + - - +
254H LYS* 2.7 45.2 + - - +
272H HIS* 2.9 24.9 + - + +
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Residues in contact with PHE 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H ILE* 4.1 15.0 - - + -
124H LEU* 4.4 11.2 - - + -
203H ILE* 4.9 1.8 - - + -
207H THR* 4.1 16.2 - - + -
247H LEU 3.1 3.1 + - - +
248H ALA 2.6 16.1 + - - +
250H ASP* 1.3 75.8 + - - +
252H ILE* 1.3 66.1 + - - +
254H LYS* 3.1 11.2 + - - +
255H LEU* 3.3 33.6 + - + +
264H LEU* 4.6 3.1 - - + -
269H ALA* 3.3 40.4 - - + -
272H HIS* 3.5 36.5 + + + -
274H TRP* 3.6 32.5 - + + -
275H ILE* 3.9 14.8 - - + -
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Residues in contact with ILE 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H GLY* 4.0 5.2 - - - +
207H THR* 3.4 40.4 - - + -
208H TYR* 3.7 20.9 - - + +
211H LEU* 4.9 6.3 - - + -
234H TYR* 4.3 0.2 - - + -
236H PHE* 3.6 24.7 - - + -
241H PHE* 5.7 1.6 - - + -
248H ALA 3.6 13.2 - - - +
249H LYS* 3.1 15.7 - - - +
251H PHE* 1.3 74.9 - - + +
253H ARG* 1.3 55.3 + - - +
255H LEU* 2.7 31.2 + - - +
256H LEU* 3.0 39.8 + - + +
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Residues in contact with ARG 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234H TYR* 3.5 16.1 + - - +
236H PHE* 3.4 34.5 - - + -
246H GLU* 4.5 13.7 + - - +
249H LYS* 2.9 45.5 + - - +
250H ASP* 2.8 19.8 + - - +
252H ILE* 1.3 77.1 - - - +
254H LYS* 1.3 63.8 + - + +
255H LEU 3.2 0.5 + - - -
256H LEU 3.5 7.4 - - - +
257H VAL* 3.1 18.7 - - - +
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Residues in contact with LYS 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H ASP* 2.7 50.2 + - - +
251H PHE 3.6 3.8 - - - +
252H ILE 3.0 0.2 + - - -
253H ARG* 1.3 77.6 - - + +
255H LEU* 1.3 56.8 + - - +
257H VAL* 3.6 13.7 - - - +
262H LYS 4.6 0.9 - - - +
263H ARG* 3.6 1.6 - - - +
264H LEU* 3.3 61.1 + - + +
272H HIS* 4.2 9.4 - - + -
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Residues in contact with LEU 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H MET* 3.8 44.2 - - + +
201H TRP* 3.9 6.9 - - - -
203H ILE* 4.0 10.3 - - + -
204H GLY* 3.5 34.8 - - - +
251H PHE* 3.6 38.6 - - + +
252H ILE 2.7 13.4 + - - +
254H LYS* 1.3 72.8 - - - +
256H LEU* 1.3 57.7 + - - +
257H VAL 2.8 11.5 + - - -
263H ARG* 2.9 24.1 + - + -
264H LEU* 3.9 23.3 - - + +
269H ALA* 4.5 1.8 - - + -
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Residues in contact with LEU 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H TRP* 3.6 38.1 - - + +
204H GLY* 4.0 5.2 - - - -
205H VAL* 3.7 22.4 - - + +
208H TYR* 4.5 2.5 - - + -
216H PRO* 4.5 10.1 - - + -
217H PHE* 4.4 15.7 - - + -
232H VAL* 4.2 10.6 - - - +
234H TYR* 3.5 42.3 + - + +
252H ILE* 3.0 36.6 + - + +
253H ARG 3.5 8.1 - - - +
255H LEU* 1.3 72.3 - - - +
257H VAL* 1.3 60.2 + - - +
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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