Contacts of the helix formed by residues 195 - 208 (chain G) 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 THR 195 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194G PHE* 1.3 77.7 - - - +
196G GLU* 1.3 59.3 + - - +
197G GLN* 3.6 8.0 + - - +
198G GLU* 3.1 39.3 + - - +
199G VAL* 3.0 28.2 + - - +
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Residues in contact with GLU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G THR* 1.3 75.5 - - - +
197G GLN* 1.3 57.8 + - - +
199G VAL* 3.8 6.6 - - - +
200G ALA* 3.1 27.9 + - - +
287G PHE* 5.6 9.1 - - + -
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Residues in contact with GLN 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G THR* 3.2 8.0 + - - +
196G GLU* 1.3 77.3 - - - +
198G GLU* 1.3 56.6 + - + +
200G ALA* 3.2 8.8 + - - +
201G ASP* 2.8 71.1 + - - +
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Residues in contact with GLU 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G LEU* 3.7 37.4 - - + +
162G LYS* 3.4 18.0 + - - -
194G PHE* 3.4 14.3 - - + +
195G THR* 3.1 44.7 + - - +
197G GLN* 1.3 77.0 - - + +
199G VAL* 1.3 54.8 + - - +
201G ASP* 3.2 8.8 + - - +
202G LEU* 2.7 42.4 + - - +
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Residues in contact with VAL 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G LEU* 4.0 22.2 - - + -
194G PHE* 3.6 22.4 - - + +
195G THR 3.0 20.6 + - - +
196G GLU* 3.8 6.5 - - - +
198G GLU* 1.3 76.8 - - - +
200G ALA* 1.3 54.8 + - - +
202G LEU* 4.0 0.5 - - - +
203G THR* 2.7 40.2 + - - +
287G PHE* 3.7 42.0 - - + -
288G GLU* 6.0 1.8 - - - +
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Residues in contact with ALA 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G GLU 3.1 18.7 + - - +
197G GLN* 3.2 9.8 + - - +
199G VAL* 1.3 77.2 - - - +
201G ASP* 1.3 64.4 + - - +
203G THR* 4.1 1.5 - - - -
204G LYS* 3.1 25.6 + - - +
287G PHE* 4.6 17.0 - - + -
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Residues in contact with ASP 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G GLN* 2.8 58.8 + - - +
198G GLU* 3.4 7.6 + - - +
200G ALA* 1.3 71.8 - - - +
202G LEU* 1.3 67.1 + - + +
204G LYS* 3.3 5.0 + - - +
205G ARG* 3.0 24.6 + - - +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G PHE* 3.8 41.7 - - + +
158G VAL* 4.3 8.3 - - + +
161G LEU* 3.7 29.8 - - + -
186G LEU* 3.8 20.4 - - + -
194G PHE* 3.8 24.7 - - + -
198G GLU 2.7 22.4 + - - +
201G ASP* 1.3 73.2 - - + +
203G THR* 1.3 57.5 + - - +
205G ARG* 3.1 7.3 + - + +
206G ILE* 2.8 41.8 + - + +
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Residues in contact with THR 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G LEU* 5.3 3.8 - - + -
184G PRO* 4.1 30.7 + - + +
186G LEU* 4.1 5.0 - - - +
199G VAL* 2.7 26.6 + - - +
200G ALA 4.1 2.5 - - - -
202G LEU* 1.3 76.6 - - - +
204G LYS* 1.3 61.3 + - - +
206G ILE* 3.6 0.7 + - - +
207G GLN* 2.9 57.7 + - - +
287G PHE* 3.9 27.2 - - + -
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Residues in contact with LYS 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G VAL* 5.0 9.5 - - - +
200G ALA 3.1 19.7 + - - +
201G ASP* 3.7 5.2 - - - +
203G THR* 1.3 78.0 - - - +
205G ARG* 1.3 63.5 + - - +
207G GLN* 3.3 14.2 + - - +
208G ASN* 3.0 51.0 + - - +
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Residues in contact with ARG 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E SER* 5.7 1.2 + - - -
48E HIS* 4.7 1.2 + - - -
157G PHE* 3.6 41.2 - - + +
160G GLU* 3.1 29.7 + - - -
201G ASP 3.0 17.5 + - - +
202G LEU* 3.1 9.4 + - - +
204G LYS* 1.3 77.8 - - - +
206G ILE* 1.3 56.3 + - - +
208G ASN* 3.6 2.2 - - - -
209G ALA* 2.9 32.4 + - - +
212G GLU* 2.9 39.1 + - - +
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Residues in contact with ILE 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G ASP* 4.5 11.2 - - + +
153G ARG* 4.8 8.0 + - + -
154G SER* 3.5 38.1 - - - +
157G PHE* 3.8 24.0 - - + -
158G VAL* 5.6 0.2 - - + -
173G VAL* 5.5 0.2 - - + -
182G ILE* 3.7 30.6 - - + +
184G PRO* 3.7 27.6 - - + -
186G LEU* 4.9 5.4 - - + -
202G LEU* 2.8 37.9 + - + +
203G THR 3.8 3.4 - - - +
205G ARG* 1.3 72.2 - - - +
207G GLN* 1.3 61.0 + - - +
208G ASN 3.4 0.5 + - - -
209G ALA* 3.5 14.0 + - - +
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Residues in contact with GLN 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G GLY* 3.2 40.2 + - - +
180G VAL* 3.9 27.9 + - - +
182G ILE* 2.9 40.4 + - + +
183G LEU* 5.1 3.8 - - - +
203G THR* 2.9 47.9 + - + +
204G LYS* 3.3 16.9 + - - +
206G ILE* 1.3 76.5 - - + +
208G ASN* 1.3 66.9 + - - +
209G ALA 3.6 0.4 + - - -
210G GLY 5.3 0.2 + - - -
291G ALA* 5.6 4.0 - - - +
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Residues in contact with ASN 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G GLY* 5.6 2.3 - - - -
204G LYS* 3.0 55.5 + - - +
205G ARG* 3.6 2.9 - - - +
207G GLN* 1.3 84.7 - - - +
209G ALA* 1.3 62.7 + - - +
210G GLY 3.1 3.4 - - - -
211G THR* 3.1 28.0 + - + -
212G GLU* 3.2 10.0 + - - +
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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
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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