Contacts of the strand formed by residues 263 - 271 (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 PHE 263 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E VAL* 3.6 23.1 - - + -
126E ALA* 3.9 18.4 - - + -
129E ALA* 3.5 26.2 - - + -
138E TYR* 3.8 6.7 - - - -
143E LEU* 4.6 2.7 - - + -
253E TYR* 3.3 36.0 - + + +
254E VAL* 3.2 6.1 - - - +
255E GLU* 3.6 40.8 - - + -
261E ALA* 3.4 15.8 - - - +
262E ARG* 1.3 107.6 - - + +
264E PHE* 1.3 64.4 + - - +
299E LEU* 4.1 2.8 - - - +
303E ILE* 3.6 21.9 - - + +
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Residues in contact with PHE 264 (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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174E ILE* 4.0 7.6 - - + -
175E GLY* 3.6 26.2 - - - -
253E TYR* 3.9 2.5 - - - -
254E VAL* 2.8 31.9 + - - +
256E GLY* 6.0 1.6 - - - +
260E TYR* 4.0 33.4 - + + -
261E ALA* 4.2 11.7 - - + +
262E ARG 4.2 0.2 + - - -
263E PHE* 1.3 75.9 - - - +
265E SER* 1.3 87.6 + - - +
266E GLN* 3.7 17.6 + - + +
281E ILE* 4.1 19.1 - - + -
292E LEU* 3.6 33.2 - - + -
295E MET* 4.0 5.8 - - + -
296E LEU* 4.3 2.2 - - + -
299E LEU* 3.9 15.5 - - + -
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Residues in contact with SER 265 (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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147E THR* 3.4 20.4 + - - -
173E VAL 3.9 8.3 + - - -
174E ILE* 3.1 13.6 - - - +
175E GLY 2.8 48.8 + - - -
176E GLY 5.2 0.9 - - - -
251E CYS 4.0 0.3 - - - -
252E ALA 3.3 23.1 + - - -
253E TYR* 3.7 15.8 - - - +
264E PHE* 1.3 76.0 - - - +
266E GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 266 (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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174E ILE* 4.2 4.5 - - - +
251E CYS* 3.3 19.2 - - - -
252E ALA 3.4 6.4 + - - -
254E VAL* 4.7 1.6 - - + +
256E GLY* 4.6 13.0 - - - -
257E ASP* 5.1 9.5 + - - +
264E PHE* 4.3 20.8 - - + +
265E SER* 1.3 74.9 + - - +
267E PRO* 1.4 81.3 - - + +
268E LEU* 3.4 17.0 - - + +
278E ARG* 3.6 26.6 + - - +
279E LYS 2.8 24.7 + - - -
280E SER* 4.9 1.0 - - - +
281E ILE* 3.7 16.2 - - + +
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Residues in contact with PRO 267 (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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172E PRO* 5.2 9.2 - - + -
174E ILE* 4.4 8.5 - - + -
185E LEU* 6.3 0.4 - - + -
249E VAL* 4.3 13.7 - - + -
250E GLU 4.0 1.6 - - - +
251E CYS* 3.9 20.6 - - - +
266E GLN* 1.4 89.9 - - + +
268E LEU* 1.3 63.2 + - - +
279E LYS* 3.0 46.8 + - + +
280E SER 4.0 14.6 - - - +
281E ILE* 4.3 10.5 - - - +
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Residues in contact with LEU 268 (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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144E PHE* 3.9 14.4 - - + -
249E VAL* 3.2 8.6 - - - +
250E GLU 2.9 36.0 + - - +
252E ALA* 3.7 30.5 - - + +
254E VAL* 3.7 30.5 - - + -
266E GLN* 3.4 16.4 - - + +
267E PRO* 1.3 82.1 - - - +
269E LEU* 1.3 62.7 + - - +
270E LEU* 3.5 13.0 + - + +
275E VAL* 4.0 7.9 - - + -
277E GLU 3.5 4.5 - - - +
278E ARG* 3.6 30.1 - - + -
279E LYS* 4.3 0.2 - - - -
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Residues in contact with LEU 269 (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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247E GLY* 3.8 16.2 - - - +
248E VAL 3.5 29.8 - - - +
249E VAL* 4.1 8.5 - - + -
268E LEU* 1.3 71.8 - - - +
270E LEU* 1.3 65.8 + - - +
275E VAL* 3.8 3.5 - - - +
276E GLU* 2.8 46.1 + - + -
277E GLU* 2.8 37.9 + - + +
279E LYS* 3.8 17.1 - - + +
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Residues in contact with LEU 270 (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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144E PHE* 3.9 30.1 - - + -
234E PHE* 4.9 3.4 - - + -
237E SER* 4.2 9.4 - - - +
238E LEU* 4.1 34.5 - - + +
241E ALA* 3.4 21.1 - - + +
245E GLU 4.6 6.4 - - - +
246E GLN* 5.9 0.2 - - - -
247E GLY 5.3 0.3 + - - -
248E VAL* 2.8 23.3 + - + +
250E GLU* 4.0 22.2 - - + -
268E LEU* 4.0 19.1 - - + +
269E LEU* 1.3 88.6 - - - +
271E GLY* 1.3 58.2 + - - +
274E GLY 3.5 10.8 - - - +
275E VAL* 4.5 0.7 - - - -
276E GLU* 4.0 3.4 - - - +
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Residues in contact with GLY 271 (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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238E LEU* 6.1 0.3 - - - +
241E ALA* 3.2 24.8 - - - +
242E LEU* 3.7 5.7 + - - +
245E GLU 5.4 1.3 - - - -
270E LEU* 1.3 75.3 - - - +
272E LYS* 1.3 63.7 + - - -
273E ASN 3.2 4.8 + - - -
274E GLY* 2.7 19.8 + - - +
276E GLU* 3.9 17.5 - - - +
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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