Contacts of the helix formed by residues 295 - 312 (chain E) in PDB entry 2PWZ
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 MET 295 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E GLY* 3.6 20.9 - - - -
180E VAL* 3.3 42.2 - - + +
181E THR* 3.4 32.9 - - + +
183E LEU* 5.0 7.4 - - + -
264E PHE* 4.0 14.1 - - + -
291E ALA 3.3 16.8 + - - +
292E LEU* 3.3 16.6 + - + +
294E GLY* 1.3 79.0 - - - +
296E LEU* 1.3 72.8 + - - +
297E ASP 3.3 3.1 - - - -
298E THR* 3.1 8.9 + - - +
299E LEU* 3.0 31.2 + - + -
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Residues in contact with LEU 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E TYR* 3.5 58.8 - - + +
261E ALA* 4.5 5.6 - - + -
264E PHE* 4.3 14.4 - - + -
292E LEU* 3.4 21.3 - - + +
293E GLU* 3.6 17.5 + - - +
295E MET* 1.3 84.9 - - - +
297E ASP* 1.3 57.9 + - - +
299E LEU* 3.4 3.5 + - + +
300E LYS* 3.0 44.4 + - - +
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Residues in contact with ASP 297 (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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293E GLU 5.0 1.2 + - - -
294E GLY 5.3 2.1 - - - +
295E MET 3.3 0.8 - - - -
296E LEU* 1.3 74.8 - - - +
298E THR* 1.3 67.2 + - - +
300E LYS* 3.2 17.0 + - - +
301E LYS* 3.0 29.9 + - + +
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Residues in contact with THR 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E SER* 5.6 1.1 - - - +
180E VAL* 4.2 17.4 - - + +
181E THR* 3.7 20.0 - - + -
294E GLY 5.2 1.6 + - - -
295E MET* 3.1 13.4 + - - +
297E ASP* 1.3 78.3 - - - +
299E LEU* 1.3 57.3 + - - +
301E LYS* 3.4 9.8 + - - +
302E ASP* 3.0 36.8 + - - +
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Residues in contact with LEU 299 (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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122E ASN* 3.5 35.0 - - + +
175E GLY 4.1 8.3 - - - +
176E GLY* 4.2 1.6 - - - -
181E THR* 4.1 6.0 - - + +
253E TYR* 3.8 16.4 - - + +
261E ALA* 4.2 13.2 - - + -
263E PHE 4.1 9.0 - - - +
264E PHE* 3.9 28.0 - - + -
295E MET* 3.0 33.0 + - + +
296E LEU* 3.6 10.8 - - + +
298E THR* 1.3 73.9 - - - +
300E LYS* 1.3 61.0 + - - +
302E ASP* 3.4 6.1 + - - +
303E ILE* 3.0 33.1 + - + +
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Residues in contact with LYS 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E TYR 3.3 24.8 + - - -
261E ALA* 4.3 15.9 - - + +
262E ARG 5.6 0.4 - - - +
296E LEU* 3.0 31.4 + - - +
297E ASP* 3.2 15.5 + - - +
299E LEU* 1.3 75.7 - - - +
301E LYS* 1.3 57.8 + - - +
303E ILE* 3.5 9.7 + - + +
304E ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 301 (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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297E ASP* 3.0 16.5 + - - +
298E THR* 3.5 11.2 - - - +
300E LYS* 1.3 74.7 - - - +
302E ASP* 1.3 65.9 + - - +
304E ALA* 3.3 7.3 + - + +
305E LEU* 3.0 25.6 + - - +
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Residues in contact with ASP 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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120E PRO* 6.4 0.9 - - - -
122E ASN* 2.9 45.5 + - + -
123E THR* 3.0 26.1 + - - +
178E SER* 4.2 5.7 + - - -
181E THR* 4.2 0.3 - - - +
298E THR* 3.0 32.6 + - - +
299E LEU* 3.4 10.8 - - - +
301E LYS* 1.3 76.4 - - - +
303E ILE* 1.3 62.8 + - - +
305E LEU* 3.4 7.2 + - - +
306E GLY 3.4 12.1 + - - -
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Residues in contact with ILE 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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122E ASN 4.0 5.4 - - - +
126E ALA* 3.6 4.3 - - + +
253E TYR* 3.4 18.6 - - - +
261E ALA* 3.9 15.5 - - + -
262E ARG* 4.0 9.6 - - + +
263E PHE* 3.6 56.8 - - + +
299E LEU* 3.0 19.0 + - + +
300E LYS* 3.7 10.3 - - + +
302E ASP* 1.3 73.4 - - - +
304E ALA* 1.3 64.1 + - - +
306E GLY* 3.2 3.8 + - - -
307E GLU* 3.0 40.6 + - - +
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Residues in contact with ALA 304 (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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300E LYS 3.0 18.5 + - - +
301E LYS* 3.3 9.2 + - + +
303E ILE* 1.3 74.9 - - - +
305E LEU* 1.3 53.9 + - - +
307E GLU* 3.1 15.3 + - - +
308E GLU* 2.8 52.3 + - - +
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Residues in contact with LEU 305 (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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91E PHE* 3.8 39.5 - - + -
120E PRO* 6.1 1.3 - - + -
123E THR* 4.1 10.5 - - + +
301E LYS 3.0 11.8 + - - +
302E ASP* 3.4 13.0 - - - +
304E ALA* 1.3 74.4 - - - +
306E GLY* 1.3 58.7 + - - +
308E GLU* 3.4 15.5 + - + +
309E PHE* 2.9 29.1 + - - +
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Residues in contact with GLY 306 (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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123E THR* 3.4 24.9 - - - +
126E ALA* 4.1 4.0 - - - -
127E ILE* 3.5 23.0 - - - +
302E ASP 3.4 4.2 + - - -
303E ILE 3.2 7.8 + - - -
305E LEU* 1.3 79.1 - - - +
307E GLU* 1.3 61.0 + - - +
309E PHE* 3.3 13.0 + - - +
310E VAL* 3.4 12.0 + - - +
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Residues in contact with GLU 307 (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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126E ALA* 4.2 5.4 - - + +
130E GLU* 4.1 17.7 - - + -
262E ARG* 2.6 45.6 + - - +
303E ILE* 3.0 25.6 + - - +
304E ALA* 3.5 17.8 + - - +
306E GLY* 1.3 75.5 - - - +
308E GLU* 1.3 57.3 + - + +
310E VAL* 3.5 2.6 + - - +
311E ASN* 3.0 38.3 + - - +
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Residues in contact with GLU 308 (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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304E ALA* 2.8 34.7 + - - +
305E LEU* 3.7 16.5 - - + +
307E GLU* 1.3 70.2 - - + +
309E PHE* 1.3 62.7 + - - +
311E ASN* 5.0 0.9 - - - -
312E LYS* 2.6 49.9 + - - +
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Residues in contact with PHE 309 (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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91E PHE* 4.3 12.3 - + + -
92E ASN* 4.0 24.2 - - - -
95E ALA* 3.4 38.4 - - + -
96E GLY* 3.5 25.8 - - - -
99E LYS* 4.2 17.6 + - + +
127E ILE* 4.2 13.0 - - + -
305E LEU 2.9 14.1 + - - +
306E GLY* 3.3 11.8 + - - +
308E GLU* 1.3 75.9 - - - +
310E VAL* 1.3 68.8 + - + +
312E LYS* 4.5 9.5 + - - +
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Residues in contact with VAL 310 (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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99E LYS* 4.5 17.7 + - + +
127E ILE* 3.7 41.3 - - + +
130E GLU* 3.8 26.5 - - + +
131E VAL* 4.1 20.2 - - + +
134E LYS* 4.7 12.1 - - + -
306E GLY 3.4 9.7 + - - +
307E GLU 4.1 2.5 - - - +
308E GLU 3.2 0.6 - - - -
309E PHE* 1.3 81.6 - - + +
311E ASN* 1.3 67.9 + - - +
312E LYS* 3.3 23.1 + - - -
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Residues in contact with ASN 311 (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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130E GLU* 2.7 29.8 + - - +
134E LYS* 4.6 13.7 - - - +
307E GLU* 3.0 21.2 + - - +
308E GLU* 5.0 0.9 - - - -
310E VAL* 1.3 87.7 + - - +
312E LYS* 1.3 78.9 - - - +
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Residues in contact with LYS 312 (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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99E LYS* 4.6 13.0 - - - +
134E LYS* 5.6 7.5 - - - +
308E GLU* 2.6 44.5 + - - +
309E PHE 4.7 7.9 - - - +
310E VAL 3.3 21.6 + - - -
311E ASN* 1.3 86.0 - - - +
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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