Contacts of the strand formed by residues 263 - 271 (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 PHE 263 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125G VAL* 3.8 24.7 - - + -
126G ALA* 3.6 20.2 - - + -
129G ALA* 3.6 16.8 - - + -
138G TYR* 4.0 7.2 - - - -
143G LEU* 5.0 0.7 - - + -
253G TYR* 3.3 33.0 - + + +
254G VAL 3.3 3.4 - - - +
255G GLU* 3.5 34.1 - - + -
261G ALA* 3.4 17.5 - - - +
262G ARG* 1.3 118.1 - - + +
264G PHE* 1.3 64.3 + - - +
299G LEU* 3.9 2.6 - - - +
303G ILE* 3.5 27.5 - - + +
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Residues in contact with PHE 264 (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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174G ILE* 3.8 16.2 - - + -
175G GLY* 3.5 28.0 - - - -
252G ALA 3.7 1.7 - - - +
253G TYR* 3.8 5.2 - - - -
254G VAL* 3.0 28.8 + - - +
256G GLY* 6.1 1.8 - - - +
257G ASP 5.7 2.0 - - - +
260G TYR* 3.8 35.0 - + + +
261G ALA 4.2 11.0 - - - +
262G ARG 4.2 0.6 + - - +
263G PHE* 1.3 74.3 - - - +
265G SER* 1.3 82.7 + - - +
266G GLN* 3.8 20.7 + - + +
281G ILE* 4.1 10.1 - - + -
292G LEU* 3.5 21.5 - - + -
295G MET* 3.7 20.0 - - + -
299G LEU* 3.9 15.7 - - + -
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Residues in contact with SER 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G THR* 3.5 20.0 + - - +
173G VAL 3.8 9.9 + - - -
174G ILE* 3.1 12.5 - - - +
175G GLY 2.9 45.9 + - - -
176G GLY 4.7 1.1 - - - -
251G CYS 4.2 0.2 - - - -
252G ALA 3.2 22.8 + - - -
253G TYR* 3.7 15.0 - - - -
264G PHE* 1.3 73.6 - - - +
266G GLN* 1.3 64.0 + - - +
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Residues in contact with GLN 266 (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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174G ILE* 4.1 4.7 - - - -
251G CYS* 3.3 14.3 - - - -
252G ALA 3.3 2.5 + - - -
254G VAL* 5.0 1.8 - - + +
256G GLY* 4.9 6.9 - - - -
257G ASP* 5.0 8.5 + - - +
264G PHE* 4.2 21.9 - - + +
265G SER* 1.3 78.3 + - - +
267G PRO* 1.4 75.9 - - + +
268G LEU* 3.3 28.3 + - + +
278G ARG* 4.0 22.0 + - - +
279G LYS 2.6 35.6 + - - +
280G SER* 4.9 0.6 - - - +
281G ILE* 3.9 17.2 - - + +
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Residues in contact with PRO 267 (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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172G PRO* 5.1 9.9 - - + -
174G ILE* 4.3 12.8 - - + -
188G GLN* 6.1 0.2 - - - +
249G VAL* 4.2 15.3 - - + -
250G GLU 4.0 2.0 - - - +
251G CYS* 4.0 19.9 - - - +
266G GLN* 1.4 88.8 - - + +
268G LEU* 1.3 61.4 + - - +
279G LYS* 2.9 42.4 + - + +
280G SER 4.0 21.1 - - - +
281G ILE* 4.4 6.1 - - - +
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Residues in contact with LEU 268 (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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144G PHE* 4.1 7.0 - - + -
248G VAL 3.4 1.2 - - - +
249G VAL* 3.3 9.0 - - - +
250G GLU 2.8 36.7 + - - +
252G ALA* 3.6 31.4 - - + +
254G VAL* 3.6 39.5 - - + -
266G GLN* 3.3 20.6 - - + +
267G PRO* 1.3 77.4 - - - +
269G LEU* 1.3 62.2 + - - +
270G LEU* 3.5 13.3 + - + +
275G VAL* 4.0 14.1 - - + -
277G GLU 3.6 3.4 - - - +
278G ARG* 3.9 21.1 - - + -
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Residues in contact with LEU 269 (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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165C GLN* 3.6 32.3 - - + +
168C GLU* 3.9 24.7 - - + +
247G GLY* 3.8 20.2 - - - -
248G VAL 3.6 15.9 - - - +
249G VAL* 4.2 5.2 - - + +
268G LEU* 1.3 70.2 - - - +
270G LEU* 1.3 54.9 + - - +
275G VAL* 3.7 3.3 - - - -
276G GLU* 2.6 55.6 + - + -
277G GLU* 2.8 44.0 + - + +
279G LYS* 3.9 12.3 - - + +
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Residues in contact with LEU 270 (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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165C GLN* 3.6 14.4 + - - -
144G PHE* 4.1 21.5 - - + -
234G PHE* 4.6 9.0 - - + -
237G SER* 4.4 13.5 - - - +
238G LEU* 4.5 16.2 - - + +
241G ALA* 3.6 21.3 - - + +
245G GLU 4.4 2.1 - - - +
248G VAL* 2.9 32.7 + - + +
250G GLU* 3.8 27.4 - - + +
268G LEU* 3.8 23.3 - - + +
269G LEU* 1.3 82.0 - - - +
271G GLY* 1.3 58.7 + - - +
274G GLY 3.6 2.5 - - - +
275G VAL* 4.5 4.9 - - - -
276G GLU* 3.7 2.5 - - - -
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Residues in contact with GLY 271 (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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165C GLN* 4.4 2.9 - - - -
238G LEU* 5.5 1.0 - - - +
241G ALA* 3.4 24.0 - - - +
242G LEU* 3.8 5.9 + - - +
245G GLU 5.3 1.1 - - - -
270G LEU* 1.3 73.0 - - - +
272G LYS* 1.3 62.0 + - - -
273G ASN 3.2 6.6 + - - -
274G GLY* 2.8 18.9 + - - +
276G GLU* 3.6 22.0 - - - +
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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