Contacts of the helix formed by residues 289 - 302 (chain F) in PDB entry 1NZB
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 HIS 289 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134F ALA* 3.8 15.0 - - + -
173F ARG* 4.0 17.1 - - + +
174F ILE 6.1 0.2 + - - -
283F TYR* 6.1 0.2 - - + -
287F SER* 4.2 0.2 + - - -
288F GLY 1.3 65.5 - - - -
290F SER* 1.3 59.6 + - - +
291F ALA 3.3 1.3 - - - -
292F ARG* 3.2 48.7 + - + +
293F VAL* 2.9 24.6 + - + +
324F TYR* 3.2 26.2 + - - -
115G A 3.9 27.6 - - - +
116G T 3.9 4.8 + - - -
125H T 3.7 34.5 - - - +
126H A 2.3 26.7 + - - +
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Residues in contact with SER 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F ALA* 3.9 2.7 - - - +
135F LEU 2.9 26.2 + - - -
136F ALA* 3.8 1.2 - - - -
137F PHE* 3.2 28.4 + - - -
265F PHE* 4.2 2.2 - - - -
286F TRP* 3.5 6.1 - - - -
287F SER* 2.7 41.0 + - - -
288F GLY 3.0 2.0 + - - -
289F HIS* 1.3 77.9 - - - +
291F ALA* 1.3 57.5 + - - +
293F VAL* 4.1 3.6 - - - -
294F GLY 3.1 19.9 + - - -
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Residues in contact with ALA 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F PHE* 4.1 14.7 - - + +
167F ALA* 3.4 42.4 - - + +
168F TYR* 3.6 13.4 - - + +
171F LEU* 5.1 0.2 - - - -
265F PHE* 4.4 8.6 - - + -
288F GLY 4.0 4.1 + - - +
289F HIS 3.3 0.8 - - - -
290F SER* 1.3 75.7 - - - +
292F ARG* 1.3 66.5 + - - +
295F ALA* 2.8 28.4 + - - +
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Residues in contact with ARG 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F LEU* 2.5 72.7 + - + +
172F LEU* 4.6 3.5 - - - +
173F ARG* 4.2 22.0 - - - +
176F GLU* 5.8 0.2 + - - -
288F GLY 5.2 0.8 + - - +
289F HIS* 3.2 51.9 + - + +
291F ALA* 1.3 78.2 - - - +
293F VAL* 1.3 59.5 + - - +
295F ALA* 3.8 1.4 - - - +
296F ALA* 2.8 31.4 + - - +
313F GLY 3.5 19.6 + - - -
315F TRP* 2.9 44.9 - - + +
324F TYR* 4.5 5.8 + - + -
116G T 3.3 18.6 + - - -
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Residues in contact with VAL 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLN* 4.0 15.0 - - - +
134F ALA* 4.2 21.3 - - + +
136F ALA* 4.0 9.4 - - + +
289F HIS* 2.9 25.1 - - + +
290F SER* 4.0 5.6 - - - +
292F ARG* 1.3 75.1 - - - +
294F GLY* 1.3 64.9 + - - +
296F ALA* 3.2 2.1 - - - +
297F ARG* 3.0 43.3 + - - +
324F TYR* 3.5 42.1 - - + +
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Residues in contact with GLY 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ALA* 3.9 15.3 - - - -
137F PHE 3.7 15.5 - - - -
138F GLU* 4.3 2.5 - - - +
290F SER 3.1 20.7 + - - -
293F VAL* 1.3 78.0 - - - +
295F ALA* 1.3 63.5 + - - +
297F ARG* 2.8 16.4 + - - +
298F ASP* 2.9 17.7 + - - +
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Residues in contact with ALA 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A MET* 3.4 30.5 - - + +
168F TYR* 3.7 19.7 - - + +
171F LEU* 3.7 18.6 - - + -
291F ALA 2.8 19.6 + - - +
294F GLY* 1.3 71.1 - - - -
296F ALA* 1.3 64.0 + - - +
298F ASP* 3.7 4.4 - - - +
299F MET* 2.9 30.6 + - - +
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F LEU* 4.6 0.4 - - - +
292F ARG 2.8 19.7 + - - +
293F VAL* 3.2 12.8 - - - +
295F ALA* 1.3 78.0 - - - +
297F ARG* 1.3 61.6 + - - +
299F MET* 3.8 11.4 - - - +
300F ALA* 3.2 21.7 + - - +
309F ILE* 4.8 6.2 - - - +
315F TRP* 4.2 15.9 - - + -
321F VAL* 5.3 8.7 - - + +
324F TYR* 3.8 21.1 - - + -
325F ILE* 4.5 3.2 - - + +
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Residues in contact with ARG 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLN* 5.2 2.6 + - - -
136F ALA* 3.7 21.7 - - - +
138F GLU* 2.7 40.1 + - - +
293F VAL* 3.0 26.2 + - - +
294F GLY 2.8 4.8 + - - +
296F ALA* 1.3 74.7 - - - +
298F ASP* 1.3 67.6 + - - +
299F MET 2.9 1.0 + - - -
300F ALA* 2.9 3.7 + - - +
301F ARG* 2.8 44.9 + - - +
324F TYR 3.2 28.8 + - - +
325F ILE* 4.1 12.8 - - + -
326F ARG* 4.7 17.6 - - - +
327F ASN* 4.4 19.8 + - - +
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Residues in contact with ASP 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A MET* 5.8 0.4 - - - -
338A LEU* 4.2 9.6 - - + +
138F GLU* 3.4 8.2 - - - +
139F ARG* 2.5 42.3 + - + +
140F THR 5.1 0.2 + - - -
168F TYR* 2.7 25.0 + - - +
294F GLY 2.9 12.9 + - - +
295F ALA* 3.7 7.2 - - - +
297F ARG* 1.3 72.4 - - - +
299F MET* 1.3 62.8 + - - +
301F ARG* 3.3 28.4 + - - +
302F ALA* 3.1 23.2 + - - +
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Residues in contact with MET 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ALA* 4.3 13.7 - - + -
335A MET* 3.3 42.6 - - + +
338A LEU* 3.9 8.7 - - + -
171F LEU* 3.9 18.4 - - + -
295F ALA 2.9 21.0 + - - +
296F ALA* 3.8 6.5 - - - +
298F ASP* 1.3 73.6 - - - +
300F ALA* 1.3 60.1 + - - +
302F ALA* 2.7 24.6 + - - -
303F GLY 3.2 7.8 + - - -
304F VAL* 3.4 29.1 + - + +
309F ILE* 4.2 23.6 - - + -
312F ALA* 3.7 27.1 - - + -
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Residues in contact with ALA 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E SER* 4.0 2.8 + - - -
307E PRO* 4.9 11.6 - - + +
308E GLU* 3.8 19.5 - - + +
296F ALA 3.2 11.9 + - - +
297F ARG 2.9 7.8 + - - +
299F MET* 1.3 79.0 - - - +
301F ARG* 1.3 61.1 + - - +
303F GLY* 3.2 13.5 + - - -
304F VAL 4.9 1.3 - - - +
309F ILE* 3.8 17.4 - - + +
321F VAL* 5.6 2.7 - - + -
325F ILE* 3.9 22.4 - - + -
327F ASN* 4.9 7.2 - - - +
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Residues in contact with ARG 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E GLU* 3.6 18.1 - - - +
138F GLU* 3.1 38.1 + - - -
297F ARG* 2.8 32.0 + - - +
298F ASP* 3.3 27.0 + - - +
300F ALA* 1.3 78.4 - - - +
302F ALA* 1.3 57.3 + - - +
303F GLY 3.2 1.6 + - - -
327F ASN* 4.1 31.7 + - - +
328F LEU* 4.3 28.8 - - + +
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Residues in contact with ALA 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 4.4 24.7 - - + -
298F ASP 3.1 11.8 + - - +
299F MET 2.7 13.0 + - - +
301F ARG* 1.3 72.9 - - - +
303F GLY* 1.3 61.6 + - - +
304F VAL* 3.5 3.1 - - + +
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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
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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