Contacts of the strand formed by residues 213 - 229 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.8 24.5 - - + -
181A ALA 4.1 3.4 - - - -
182A ALA* 3.7 37.5 - - + -
185A LEU* 3.7 25.4 - - + -
191A LEU* 4.0 22.2 - - + -
208A ALA* 4.0 18.6 - - + +
209A GLU* 5.5 0.5 - - - -
211A HIS* 2.8 27.1 + - + +
212A PRO* 1.3 75.4 - - - +
214A ARG* 1.3 59.4 + - - +
215A LEU 4.3 0.2 + - - -
249A LEU* 3.7 35.0 - - + -
250A ARG 3.4 9.6 - - - -
251A ARG* 3.9 9.2 - - - -
252A TRP* 3.4 12.9 + - - +
503A SO4 3.4 10.0 + - - -
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 1.3 73.6 - - - +
215A LEU* 1.3 71.7 + - - +
216A GLU* 3.4 19.7 + - - +
249A LEU* 3.3 3.5 - - - -
250A ARG* 2.8 47.5 + - + +
251A ARG 5.5 0.6 + - - -
252A TRP* 3.6 42.4 - - - +
253A LYS* 5.0 3.6 - - - +
503A SO4 3.7 24.0 + - - +
45B GLY* 5.1 8.1 + - - -
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Residues in contact with LEU 215 (chain A).
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* 3.9 31.2 - - + -
208A ALA* 6.2 0.4 - - - +
213A PHE 4.2 0.8 - - - -
214A ARG* 1.3 75.3 - - - +
216A GLU* 1.3 70.9 + - - +
217A ARG 3.9 16.8 - - - +
218A VAL* 4.1 7.2 - - + -
247A VAL* 3.9 11.2 - - + -
248A ALA 3.8 9.9 - - - +
249A LEU* 3.8 21.1 - - + +
503A SO4 2.7 22.4 + - - +
228B VAL* 3.4 33.4 - - + +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 4.1 11.0 - - + -
214A ARG* 3.5 27.9 + - - +
215A LEU* 1.3 81.5 - - - +
217A ARG* 1.3 79.9 + - + +
248A ALA* 2.9 16.4 + - + +
250A ARG* 3.3 46.1 + - + +
10B LYS* 3.4 18.8 + - - -
236B ARG* 5.3 7.1 + - - -
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.5 23.1 - - + +
190A PHE* 6.4 0.2 - - + -
215A LEU* 3.9 3.9 - - - +
216A GLU* 1.3 90.9 - - + +
218A VAL* 1.3 69.3 + - - +
219A LEU* 3.8 11.6 - - + +
246A LEU 4.2 0.9 - - - +
247A VAL* 3.4 1.6 - - - -
248A ALA* 2.8 45.3 + - + +
64B GLU* 2.9 41.1 + - - -
223B TRP* 3.8 11.1 - - - -
225B GLU* 2.8 41.7 + - - +
226B TRP 5.6 0.7 - - - -
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Residues in contact with VAL 218 (chain A).
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* 4.9 1.1 - - + -
201A VAL* 4.0 29.2 - - + -
205A VAL* 4.6 0.7 - - + -
215A LEU* 4.1 18.2 - - + -
217A ARG* 1.3 79.0 - - - +
219A LEU* 1.3 63.3 + - - +
245A PHE* 4.7 11.7 - - + -
246A LEU 3.3 6.7 - - - +
247A VAL* 4.4 7.2 - - + -
225B GLU* 3.6 2.5 + - - +
226B TRP* 2.7 64.2 + - + +
228B VAL* 4.0 21.8 - - + -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 4.1 17.9 - - + -
217A ARG* 3.8 22.4 - - + +
218A VAL* 1.3 77.3 - - - +
220A GLU* 1.3 66.8 + - - +
221A VAL* 3.6 30.6 + - + -
245A PHE* 3.5 7.0 - - - -
246A LEU* 2.8 53.0 + - + +
223B TRP* 4.5 14.4 - - + -
224B ARG 3.2 15.5 - - - +
225B GLU* 3.7 28.9 - - - +
226B TRP* 4.5 1.1 - - - -
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Residues in contact with GLU 220 (chain A).
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* 1.3 76.4 - - - +
221A VAL* 1.3 64.1 + - - +
222A GLY 3.8 0.2 + - - -
241A GLY 5.3 3.3 - - - +
242A HIS* 4.3 14.8 + - + +
244A ALA 4.6 6.3 - - - +
245A PHE* 3.5 32.2 - - + -
222B GLY 3.5 2.8 - - - +
223B TRP* 3.6 0.3 - - - -
224B ARG* 2.9 57.2 + - + +
226B TRP* 2.7 33.0 + - - +
235B PRO* 4.7 0.2 - - - +
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 2.7 60.4 + - + +
81A ASP* 3.6 13.8 + - - +
84A ALA* 3.5 26.2 - - + -
219A LEU* 3.6 20.2 + - + -
220A GLU* 1.3 75.0 - - - +
222A GLY* 1.3 59.9 + - - +
223A TRP* 3.9 11.2 - - + +
244A ALA 4.9 1.8 + - - -
246A LEU* 3.9 9.4 - - + +
222B GLY 3.4 3.6 - - - -
223B TRP* 3.9 19.7 - - + +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 4.5 2.0 - - - -
220A GLU 3.8 0.8 + - - -
221A VAL* 1.3 73.8 - - - +
223A TRP* 1.3 70.9 + - - -
224A ARG* 3.8 2.5 - - - -
220B GLU 3.5 0.6 - - - +
221B VAL* 3.4 1.0 - - - -
222B GLY* 2.8 41.8 + - - +
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Residues in contact with TRP 223 (chain A).
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* 3.7 22.7 - - - -
79A PRO 4.5 0.7 - - - -
80A LYS* 3.5 54.6 + - + +
83A SER* 4.1 9.2 - - - -
221A VAL* 3.9 8.7 - - + +
222A GLY* 1.3 82.5 - - - -
224A ARG* 1.3 60.4 + - - +
225A GLU* 3.3 23.1 + - - +
239A GLN* 3.8 4.7 - - - +
240A VAL 5.5 2.3 - - - +
84B ALA* 3.6 30.3 - - + +
87B THR* 4.0 26.0 - - + -
88B LEU* 4.3 9.4 - - + -
217B ARG* 3.7 18.6 - - - -
219B LEU* 4.3 14.8 - - + -
220B GLU 3.5 4.0 - - - -
221B VAL* 3.9 25.7 - - + +
223B TRP* 5.1 1.2 - - - +
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Residues in contact with ARG 224 (chain A).
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 3.8 1.7 - - - -
223A TRP* 1.3 69.6 - - - +
225A GLU* 1.3 62.6 + - - +
226A TRP* 3.7 3.6 - - - +
235A PRO* 3.4 37.5 - - + +
236A ARG 5.4 0.6 + - - -
239A GLN* 3.6 26.8 - - - +
219B LEU* 3.2 4.5 - - - -
220B GLU* 2.8 62.6 + - + +
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Residues in contact with GLU 225 (chain A).
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* 3.8 15.6 - - - +
224A ARG* 1.3 72.8 - - - +
226A TRP* 1.3 55.9 + - - +
235A PRO* 3.5 2.8 - - - +
236A ARG* 2.8 38.4 + - - +
239A GLN* 2.8 36.7 + - - +
217B ARG* 2.8 50.9 + - - +
218B VAL 3.8 4.5 + - - +
219B LEU* 3.5 17.2 - - - +
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Residues in contact with TRP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 3.7 11.6 - - - +
225A GLU* 1.3 82.7 - - - +
227A GLU* 1.3 60.1 + - - +
228A VAL* 3.9 11.7 + - + -
233A ALA* 4.0 11.7 - - + -
234A HIS* 3.4 34.8 - - - -
235A PRO* 3.6 27.6 - - + +
236A ARG* 3.6 19.0 + - - -
198B ILE* 4.0 27.4 - - + -
217B ARG* 5.6 0.3 - - - -
218B VAL* 2.8 48.4 + - + +
220B GLU* 2.8 34.7 + - + +
245B PHE* 3.9 16.3 - + - -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 1.3 71.4 - - - +
228A VAL* 1.3 64.5 + - - +
229A ARG* 4.9 6.8 - - + +
232A VAL* 3.9 13.4 - - + +
233A ALA* 3.2 4.5 + - - -
234A HIS* 2.8 65.1 + - + +
236A ARG* 3.4 33.6 + - + +
237A PHE* 4.9 5.4 + - - -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 3.9 19.4 + - + -
227A GLU* 1.3 80.9 - - - +
229A ARG* 1.3 64.0 + - - +
230A LEU* 4.0 20.9 - - + -
232A VAL 3.4 8.7 - - - +
233A ALA* 4.3 13.2 - - + -
236A ARG* 5.4 0.6 - - - +
198B ILE* 6.1 0.7 - - + -
201B VAL* 5.4 2.5 - - + -
202B LEU* 4.5 6.3 - - + -
205B VAL* 4.2 14.5 - - + +
215B LEU* 3.6 32.8 - - + +
218B VAL* 4.0 23.3 - - + -
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 4.1 9.1 - - + +
228A VAL* 1.3 74.7 - - - +
230A LEU* 1.3 68.4 + - - +
231A PRO* 4.1 0.7 - - - +
232A VAL* 2.9 32.7 + - + +
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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