Contacts of the strand formed by residues 245 - 251 (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 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 3.5 0.9 - - - +
194A TYR* 3.5 3.6 - - - -
195A LEU* 2.7 45.0 + - - +
196A PRO 3.4 17.7 - - - -
198A ILE* 3.5 39.9 - - + -
201A VAL* 3.6 27.6 - - + -
218A VAL* 4.7 6.7 - - + -
219A LEU 3.5 7.6 - - - +
220A GLU* 3.5 38.1 - - + -
242A HIS* 3.5 13.7 - + - -
244A ALA* 1.3 74.1 - - - +
246A LEU* 1.3 65.0 + - - +
247A VAL* 5.0 0.4 - - - +
226B TRP* 4.0 14.4 - + - -
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Residues in contact with LEU 246 (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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81A ASP* 4.0 11.2 - - + +
84A ALA* 3.8 23.1 - - + -
85A MET* 3.8 24.9 - - + -
88A LEU* 3.7 29.6 - - + -
192A VAL* 4.4 3.4 - - + -
193A ALA 3.3 2.7 - - - +
194A TYR* 3.7 33.0 - - + -
217A ARG* 3.8 1.7 - - - +
218A VAL* 3.3 5.7 + - - +
219A LEU* 2.8 44.3 + - + +
221A VAL* 3.9 14.6 - - + +
244A ALA 5.0 2.0 - - - +
245A PHE* 1.3 76.7 - - - +
247A VAL* 1.3 60.5 + - - +
248A ALA 4.2 0.4 - - - -
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Residues in contact with VAL 247 (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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191A LEU* 3.6 3.1 - - - +
192A VAL* 3.2 6.1 - - - +
193A ALA* 2.8 41.0 + - - +
195A LEU* 4.4 3.8 - - + -
201A VAL* 3.9 38.1 - - + -
204A LEU* 3.9 32.1 - - + -
205A VAL* 4.7 5.8 - - + -
215A LEU* 3.9 23.8 - - + -
217A ARG 3.4 3.6 - - - +
218A VAL* 4.4 5.6 - - + -
245A PHE 5.0 0.9 - - - +
246A LEU* 1.3 77.8 - - - +
248A ALA* 1.3 60.8 + - - +
249A LEU* 4.1 10.0 + - + -
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Residues in contact with ALA 248 (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* 5.1 9.6 - - + +
190A PHE* 4.8 9.2 - - + -
191A LEU 3.3 4.7 - - - +
192A VAL* 4.1 17.9 - - + -
215A LEU* 3.8 4.3 - - - +
216A GLU* 2.9 28.6 + - + -
217A ARG* 2.8 39.8 + - + +
246A LEU 4.2 0.8 - - - -
247A VAL* 1.3 72.1 - - - +
249A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 249 (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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178A LEU* 4.2 9.4 - - + -
190A PHE* 3.3 9.8 - - - -
191A LEU* 2.8 56.6 + - + +
204A LEU* 4.7 8.5 - - + -
205A VAL* 5.8 1.8 - - - -
208A ALA* 3.9 30.7 - - + -
213A PHE* 3.7 29.3 - - + -
214A ARG 3.3 5.6 - - - +
215A LEU* 3.8 30.1 - - + +
216A GLU* 4.3 0.2 - - - -
247A VAL* 4.2 10.3 - - + -
248A ALA* 1.3 81.5 - - - +
250A ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 250 (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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188A ASP* 3.1 54.4 + - - +
189A ARG 3.5 4.0 - - - +
190A PHE* 3.4 28.3 - - + -
213A PHE* 3.4 3.6 - - - -
214A ARG* 2.8 46.8 + - + +
216A GLU* 3.3 32.4 + - + +
249A LEU* 1.3 73.0 - - - +
251A ARG* 1.3 68.8 + - - +
252A TRP* 3.5 0.5 + - - -
10B LYS* 3.3 19.6 - - - +
59B HIS* 3.3 33.1 + - - +
60B ARG 5.1 4.0 + - - -
62B THR* 5.4 0.6 - - - +
65B GLU* 3.2 28.5 + - - -
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Residues in contact with ARG 251 (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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161A GLU* 5.6 5.5 + - - +
182A ALA* 2.8 40.5 + - - +
183A LEU* 5.1 2.2 + - - +
185A LEU* 3.5 27.2 + - + +
186A LYS 3.4 18.8 - - - +
187A PRO* 3.6 6.9 - - + +
188A ASP* 2.8 27.8 + - - +
189A ARG 2.9 13.4 + - - +
212A PRO* 3.4 41.4 - - - +
213A PHE* 3.9 10.9 - - - -
214A ARG* 5.5 0.4 + - - -
250A ARG* 1.3 74.8 - - - +
252A TRP* 1.3 86.9 + - - +
253A LYS 3.7 5.9 + - - -
254A GLY* 4.9 4.4 - - - -
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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