Contacts of the strand formed by residues 213 - 229 (chain B) in PDB entry 2PWY
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 PHE 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B LEU* 4.0 27.4 - - + -
181B ALA* 4.3 2.0 - - + -
182B ALA* 3.8 39.9 - - + -
185B LEU* 3.8 24.9 - - + -
191B LEU* 4.0 20.9 - - + -
208B ALA* 4.2 12.3 - - + +
211B HIS* 2.8 28.0 + - + +
212B PRO* 1.3 73.2 - - - +
214B ARG* 1.3 58.5 + - - +
215B LEU 4.1 0.9 + - - -
249B LEU* 3.8 34.7 - - + +
250B ARG 3.3 2.9 - - - -
251B ARG* 3.8 22.0 - - + -
252B TRP* 3.4 15.5 - - - -
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 3.9 13.8 - - - +
59A HIS* 6.4 1.6 - - - -
213B PHE* 1.3 72.4 - - - +
215B LEU* 1.3 80.9 + - - +
216B GLU* 3.3 33.5 + - + +
249B LEU* 3.4 3.3 - - - -
250B ARG* 2.9 37.5 + - + +
252B TRP* 3.9 13.4 - - + -
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A VAL* 3.6 34.1 - - + +
205B VAL* 3.8 36.1 - - + -
208B ALA* 6.4 0.2 - - + -
213B PHE 4.1 1.4 + - - -
214B ARG* 1.3 92.4 + - - +
216B GLU* 1.3 58.7 + - - +
217B ARG 3.8 15.7 - - - +
218B VAL* 4.1 4.7 - - + -
247B VAL* 3.7 23.8 - - + -
248B ALA 3.8 1.6 - - - +
249B LEU* 3.7 26.3 - - + +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 2.9 29.5 + - - -
59A HIS* 4.6 1.7 - - - -
65A GLU* 4.3 2.9 - - - +
236A ARG* 5.0 9.5 + - - -
190B PHE* 3.6 14.6 - - + -
214B ARG* 3.7 31.6 + - + +
215B LEU* 1.3 75.6 - - - +
217B ARG* 1.3 81.1 + - + +
248B ALA 2.8 12.3 + - - +
250B ARG* 3.3 47.7 + - + +
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 2.8 42.3 + - - -
223A TRP* 3.7 11.1 - - - -
225A GLU* 2.8 39.7 + - - +
226A TRP 5.6 0.9 - - - -
236A ARG* 6.3 0.4 - - - +
88B LEU* 3.4 15.6 - - + +
190B PHE* 5.9 1.3 - - + -
215B LEU* 3.8 5.4 - - - +
216B GLU* 1.3 96.9 - - + +
218B VAL* 1.3 69.0 + - - +
219B LEU* 3.6 19.4 - - + +
246B LEU 4.2 1.3 - - - +
247B VAL* 3.3 1.0 - - - -
248B ALA* 2.8 47.2 + - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 3.8 2.0 + - - +
226A TRP* 2.8 60.5 + - + +
228A VAL* 4.0 20.4 - - + -
198B ILE* 4.8 1.1 - - + -
201B VAL* 3.9 29.6 - - + -
205B VAL* 4.7 0.7 - - + -
215B LEU* 4.1 20.2 - - + -
217B ARG* 1.3 78.8 - - - +
219B LEU* 1.3 63.7 + - - +
245B PHE* 4.7 11.9 - - + -
246B LEU 3.2 8.1 - - - +
247B VAL* 4.3 7.0 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TRP* 4.3 15.3 - - + -
224A ARG 3.2 15.0 - - - +
225A GLU* 3.5 29.6 - - - +
226A TRP* 4.5 1.3 - - - -
88B LEU* 4.2 14.8 - - + -
217B ARG* 3.6 25.4 - - + +
218B VAL* 1.3 75.8 - - - +
220B GLU* 1.3 66.2 + - - +
221B VAL* 3.6 29.7 + - + -
245B PHE* 3.5 6.8 - - - -
246B LEU* 2.9 52.6 + - + +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY 3.5 1.7 - - - +
223A TRP* 3.5 0.7 - - - -
224A ARG* 2.8 61.8 + - + +
226A TRP* 2.8 33.1 + - - +
219B LEU* 1.3 74.5 - - - +
221B VAL* 1.3 66.7 + - - +
222B GLY 3.9 0.3 + - - -
241B GLY 5.4 2.9 - - - +
242B HIS* 4.2 16.1 + - + +
244B ALA 4.5 6.3 - - - +
245B PHE* 3.6 31.4 - - + -
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY 3.4 3.1 - - - -
223A TRP* 3.9 19.5 - - + +
80B LYS* 2.8 55.8 + - + +
81B ASP* 3.6 16.1 + - - +
84B ALA* 3.7 22.4 - - + -
219B LEU* 3.6 22.4 - - + -
220B GLU* 1.3 74.6 - - - +
222B GLY* 1.3 61.5 + - - +
223B TRP* 3.9 11.0 - - + +
244B ALA 4.8 3.4 + - - -
246B LEU* 3.8 10.1 - - + +
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Residues in contact with GLY 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU 3.5 0.7 - - - +
221A VAL* 3.4 1.4 - - - -
222A GLY* 2.8 42.0 + - - +
80B LYS* 4.5 2.2 - - - -
220B GLU 3.9 0.6 + - - -
221B VAL* 1.3 74.6 - - - +
223B TRP* 1.3 69.2 + - - -
224B ARG* 3.8 2.5 - - - -
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Residues in contact with TRP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 3.7 29.3 - - + +
87A THR* 4.0 26.0 - - + -
88A LEU* 4.1 9.4 - - + -
217A ARG* 3.8 19.7 - - - -
219A LEU* 4.5 14.4 - - + -
220A GLU 3.6 4.3 - - - -
221A VAL* 3.9 24.3 - - + +
223A TRP* 5.1 1.2 - - - +
64B GLU* 3.8 21.8 - - - -
79B PRO 4.6 0.4 - - - -
80B LYS* 3.5 52.3 + - + +
83B SER* 4.1 9.4 - - - -
221B VAL* 3.9 9.8 - - + +
222B GLY* 1.3 82.2 - - - -
224B ARG* 1.3 63.0 + - - +
225B GLU* 3.4 17.8 + - - +
239B GLN* 3.8 6.4 - - - +
240B VAL 5.8 0.2 - - - +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.2 5.1 - - - -
220A GLU* 2.9 62.3 + - + +
222B GLY 3.8 1.8 - - - -
223B TRP* 1.3 70.3 - - - +
225B GLU* 1.3 61.2 + - - +
226B TRP* 3.7 3.9 - - - +
235B PRO* 3.4 38.7 - - + +
236B ARG 5.5 0.6 + - - -
239B GLN* 3.7 25.6 - - - +
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 2.8 50.0 + - - +
218A VAL 3.6 6.0 + - - +
219A LEU* 3.7 17.1 - - - +
223B TRP* 3.9 15.5 - - - +
224B ARG* 1.3 72.7 - - - +
226B TRP* 1.3 55.0 + - - +
235B PRO* 3.5 2.8 - - - +
236B ARG* 2.8 37.0 + - - +
239B GLN* 2.7 37.3 + - - +
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 4.0 27.8 - - + -
217A ARG* 5.6 0.5 - - - -
218A VAL* 2.7 48.9 + - + +
220A GLU* 2.7 35.4 + - + +
245A PHE* 4.0 16.4 - + - -
224B ARG* 3.7 15.0 - - - +
225B GLU* 1.3 78.0 - - - +
227B GLU* 1.3 61.1 + - - +
228B VAL* 3.9 11.5 + - + -
233B ALA* 3.9 12.8 - - + -
234B HIS* 3.5 31.9 - - - -
235B PRO* 3.6 27.4 - - + +
236B ARG* 3.7 16.3 + - - -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TRP* 1.3 72.0 - - - +
228B VAL* 1.3 64.1 + - - +
229B ARG* 4.5 12.1 - - + +
232B VAL* 4.0 19.3 - - + +
233B ALA* 3.2 4.5 + - - -
234B HIS* 2.8 54.1 + - + +
236B ARG* 3.5 36.1 + - + +
237B PHE* 5.6 2.1 - - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 5.8 1.1 - - + -
201A VAL* 5.1 4.7 - - + -
202A LEU* 4.0 24.9 - - + -
205A VAL* 4.1 25.9 - - + +
215A LEU* 3.4 27.1 - - + +
218A VAL* 4.0 28.5 - - + +
226B TRP* 3.9 17.3 + - + -
227B GLU* 1.3 80.6 - - - +
229B ARG* 1.3 64.1 + - - +
230B LEU* 4.8 4.7 - - + +
232B VAL 3.5 7.2 - - - +
233B ALA* 4.5 4.9 - - + -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 6.2 0.4 - - - -
227B GLU* 4.1 14.4 - - + +
228B VAL* 1.3 74.1 - - - +
230B LEU* 1.3 66.4 + - - +
232B VAL* 2.8 31.0 + - + +
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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