Contacts of the helix formed by residues 289 - 303 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ALA* 3.8 17.9 - - + -
173E ARG* 2.9 38.9 + - - -
288E GLY* 1.3 69.6 - - - -
290E SER* 1.3 61.6 + - - +
291E ALA 3.0 7.4 + - - -
292E ARG* 3.1 43.3 + - + -
293E VAL* 3.2 18.0 + - + +
324E TYR* 4.5 13.9 - - - +
125G T 3.5 35.8 + - - -
126G A 2.8 9.6 + - - +
115H G 4.3 20.2 - - - +
116H C 4.2 2.7 + - - -
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Residues in contact with SER 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ALA* 3.9 4.3 - - - +
135E LEU 2.7 27.4 + - - +
136E ALA* 3.9 0.2 - - - -
137E PHE* 2.6 41.2 + - - +
265E PHE* 4.5 1.8 - - - -
286E TRP* 3.1 11.6 - - - -
287E SER* 2.6 41.5 + - - -
288E GLY 3.1 1.2 - - - -
289E HIS* 1.3 77.9 - - - +
291E ALA* 1.3 59.3 + - - +
293E VAL* 4.4 0.9 - - - -
294E GLY 3.7 5.5 + - - -
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Residues in contact with ALA 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PHE* 4.1 11.4 - - + +
167E ALA* 3.6 33.2 - - + +
168E TYR* 4.1 8.7 - - + +
171E LEU* 5.5 0.2 - - - -
172E LEU 5.7 2.5 - - - +
265E PHE* 4.1 18.8 - - + -
288E GLY 3.8 5.9 + - - +
289E HIS 3.0 0.6 - - - -
290E SER* 1.3 78.7 - - - +
292E ARG* 1.3 69.5 + - + +
293E VAL 3.2 0.2 + - - -
294E GLY* 3.3 1.2 + - - -
295E ALA* 2.7 27.7 + - - +
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Residues in contact with ARG 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E LEU* 2.6 43.7 + - - +
172E LEU 4.1 9.6 - - - +
173E ARG* 3.0 48.3 - - - +
288E GLY 5.0 1.3 - - - +
289E HIS* 3.4 33.8 - - + +
291E ALA* 1.3 82.0 - - + +
293E VAL* 1.3 51.4 - - - +
295E ALA* 2.7 7.4 - - - +
296E ALA* 2.7 35.0 + - - +
313E GLY 3.8 14.2 + - - -
314E GLY 5.5 1.2 + - - -
315E TRP* 3.3 44.8 - - + +
324E TYR* 4.6 3.9 - - + -
116H C 3.4 8.9 + - - -
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Residues in contact with VAL 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLN* 4.8 9.0 - - - +
134E ALA* 4.1 21.1 - - + +
136E ALA* 4.0 13.7 - - + +
289E HIS* 3.2 15.8 + - + +
290E SER 4.3 3.8 - - - +
292E ARG* 1.3 77.8 - - - +
294E GLY* 1.3 67.1 + - - +
296E ALA* 2.8 5.7 + - - +
297E ARG* 2.8 45.9 + - - +
324E TYR* 3.7 50.2 - - + +
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Residues in contact with GLY 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ALA* 4.2 2.2 - - - +
137E PHE 3.8 11.7 - - - -
138E GLU* 3.4 27.6 - - - -
290E SER 3.7 5.1 + - - -
291E ALA 3.3 3.0 + - - -
293E VAL* 1.3 79.0 - - - +
295E ALA* 1.3 63.8 + - - +
297E ARG* 3.1 5.1 + - - +
298E ASP* 2.8 34.5 + - - +
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Residues in contact with ALA 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TYR* 4.3 20.8 - - + +
171E LEU* 3.0 37.5 - - + -
291E ALA 2.7 18.8 + - - +
292E ARG 2.7 14.8 - - - +
294E GLY* 1.3 73.3 - - - +
296E ALA* 1.3 63.1 + - - +
298E ASP* 3.2 3.0 + - - +
299E MET* 3.2 25.4 + - + +
335F MET* 4.6 4.5 - - - +
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Residues in contact with ALA 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E LEU* 4.9 0.4 - - - +
292E ARG 2.7 13.7 + - - +
293E VAL* 2.8 10.5 + - - +
295E ALA* 1.3 70.8 - - - +
297E ARG* 1.3 65.2 + - - +
299E MET* 3.1 18.8 + - - +
300E ALA* 2.9 21.0 + - - +
309E ILE* 4.3 12.1 - - + +
315E TRP* 4.0 19.3 - - + -
321E VAL* 5.0 4.0 - - + -
324E TYR* 4.3 16.6 - - + -
325E ILE* 4.3 7.4 - - + -
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Residues in contact with ARG 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 5.2 5.5 + - - -
133E GLN* 5.4 5.1 - - - +
136E ALA* 3.9 13.0 - - - +
138E GLU* 3.3 25.0 + - - +
293E VAL* 2.8 37.8 + - - +
294E GLY 3.5 4.9 - - - +
296E ALA* 1.3 71.2 - - - +
298E ASP* 1.3 63.9 + - - +
300E ALA* 3.1 4.9 + - - +
301E ARG* 2.9 37.3 + - - +
324E TYR 2.8 32.4 + - - +
325E ILE* 4.0 9.9 - - + -
327E ASN* 2.9 42.6 + - - +
328E LEU* 3.6 25.1 - - + +
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Residues in contact with ASP 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLU* 3.6 3.9 - - - +
139E ARG* 3.1 29.4 + - + +
140E THR* 6.2 0.2 - - - +
168E TYR* 2.9 27.9 + - - +
294E GLY 2.8 27.8 + - - +
295E ALA 3.7 3.6 - - - +
297E ARG* 1.3 71.4 - - - +
299E MET* 1.3 64.0 + - + +
301E ARG* 2.9 35.5 + - - +
302E ALA* 3.0 13.0 + - - +
335F MET* 5.7 1.8 - - + -
338F LEU* 5.0 13.3 - - + +
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Residues in contact with MET 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E LEU* 3.5 31.9 - - + -
295E ALA 3.2 17.7 + - - +
296E ALA* 3.1 18.3 + - - +
298E ASP* 1.3 74.9 - - - +
300E ALA* 1.3 58.4 - - - +
302E ALA* 2.8 22.2 + - - +
303E GLY 3.0 10.2 + - - -
304E VAL* 3.2 32.1 + - + -
309E ILE* 3.6 28.0 - - + +
312E ALA* 3.7 19.3 - - + -
334F ALA* 4.9 7.9 - - - -
335F MET* 3.7 26.0 - - + +
338F LEU* 5.0 7.6 - - + +
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Residues in contact with ALA 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E ALA 2.9 12.9 + - - +
297E ARG 3.2 10.1 - - - +
299E MET* 1.3 78.3 - - - +
301E ARG* 1.3 61.2 + - - +
302E ALA 3.3 0.3 + - - -
303E GLY* 3.4 10.3 + - - +
304E VAL 4.9 1.8 - - - +
306E ILE* 6.2 0.4 - - + -
309E ILE* 3.7 13.8 - - + +
325E ILE* 3.9 23.6 - - + -
328E LEU* 3.5 20.0 - - + -
330E SER* 4.3 11.4 + - - -
331E GLU* 4.8 5.1 - - - +
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Residues in contact with ARG 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 4.7 11.5 + - - +
138E GLU* 2.6 29.9 + - - +
297E ARG* 2.9 21.5 + - - +
298E ASP* 2.9 41.6 + - - +
300E ALA* 1.3 76.2 - - - +
302E ALA* 1.3 59.8 + - - +
328E LEU* 3.4 35.0 - - + +
330E SER* 5.3 4.7 - - - -
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Residues in contact with ALA 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E ASP 3.0 10.2 + - - +
299E MET* 2.8 11.2 + - - +
301E ARG* 1.3 78.9 - - - +
303E GLY* 1.3 57.3 + - - +
304E VAL* 3.6 5.6 - - + -
338F LEU* 3.7 30.7 - - + -
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Residues in contact with GLY 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E MET 3.0 2.4 + - - -
300E ALA 3.4 7.0 + - - -
301E ARG 3.4 3.2 - - - -
302E ALA* 1.3 80.7 - - - +
304E VAL* 1.3 66.1 + - - +
305E SER* 3.4 3.3 + - - -
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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