Contacts of the strand formed by residues 263 - 271 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C VAL* 3.8 20.6 - - + -
126C ALA* 3.8 21.1 - - + -
129C ALA* 3.6 19.1 - - + -
138C TYR* 3.9 7.0 - - - -
143C LEU* 4.8 3.8 - - + -
253C TYR* 3.3 32.0 - - + +
254C VAL* 3.2 6.3 - - - +
255C GLU* 3.6 45.5 - - + -
261C ALA* 3.6 15.3 - - - +
262C ARG* 1.3 109.8 - - + +
264C PHE* 1.3 64.2 + - - +
299C LEU* 3.7 2.8 - - - +
303C ILE* 3.6 23.3 - - + +
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Residues in contact with PHE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.1 13.5 - - + -
175C GLY* 3.6 26.7 - - - -
252C ALA 3.6 0.9 - - - +
253C TYR* 3.9 6.1 - - - -
254C VAL* 2.9 28.6 + - - +
256C GLY* 6.1 1.6 - - - +
260C TYR* 3.7 41.5 - + + +
261C ALA 4.2 9.6 - - - +
262C ARG 4.2 0.4 - - - +
263C PHE* 1.3 75.8 - - - +
265C SER* 1.3 87.4 + - - +
266C GLN* 3.5 18.2 + - + +
281C ILE* 4.3 12.3 - - + -
292C LEU* 3.6 26.0 - - + -
295C MET* 4.7 1.1 - - - -
296C LEU* 4.4 4.9 - - + -
299C LEU* 4.0 17.0 - - + -
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Residues in contact with SER 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 3.4 21.5 + - - -
173C VAL 3.8 9.1 + - - -
174C ILE* 3.2 13.5 - - - +
175C GLY 2.7 46.1 + - - -
176C GLY* 5.0 1.6 - - - -
251C CYS 4.1 0.2 - - - -
252C ALA 3.1 29.8 + - - -
253C TYR* 3.6 9.3 - - - +
264C PHE* 1.3 76.4 - - - +
266C GLN* 1.3 57.5 + - - +
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Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.2 4.5 - - - -
251C CYS* 3.3 5.8 - - - -
252C ALA 3.3 23.0 + - - -
254C VAL* 4.7 3.6 - - + +
256C GLY* 4.7 9.5 - - - -
257C ASP* 5.3 8.7 + - - +
264C PHE* 3.5 20.1 + - + +
265C SER* 1.3 74.8 + - - +
267C PRO* 1.4 77.3 - - + +
268C LEU* 3.6 14.1 + - + +
278C ARG* 3.7 27.0 + - - +
279C LYS 2.6 27.1 + - - -
280C SER* 4.8 1.4 - - - +
281C ILE* 3.8 15.7 - - + +
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Residues in contact with PRO 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PRO* 5.3 8.1 - - + -
174C ILE* 4.4 7.0 - - + -
185C LEU* 6.4 0.4 - - + -
249C VAL* 4.5 13.2 - - + -
250C GLU 3.9 4.9 - - - +
251C CYS* 4.0 17.9 - - - -
266C GLN* 1.4 89.2 - - + +
268C LEU* 1.3 58.8 + - - +
279C LYS* 2.8 55.6 + - + +
280C SER 4.1 13.7 - - - +
281C ILE* 4.2 11.7 - - + -
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 4.0 13.7 - - + -
249C VAL* 3.1 8.2 - - - +
250C GLU 2.9 35.4 + - - +
252C ALA* 3.7 25.8 - - + +
254C VAL* 3.6 44.9 - - + -
266C GLN* 3.6 12.8 - - + +
267C PRO* 1.3 81.4 - - - +
269C LEU* 1.3 61.8 + - - +
270C LEU* 3.7 13.9 + - + +
275C VAL* 4.2 9.0 - - + -
277C GLU 3.4 4.0 - - - +
278C ARG* 3.9 22.7 - - + -
279C LYS* 4.2 4.5 - - - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLY* 3.9 26.9 - - - +
248C VAL 3.6 15.9 - - - +
249C VAL* 4.1 9.0 - - + -
268C LEU* 1.3 73.0 - - - +
270C LEU* 1.3 62.4 + - - +
275C VAL* 3.7 4.0 - - - +
276C GLU* 2.7 50.4 + - + -
277C GLU* 2.8 38.9 + - + +
279C LYS* 3.8 13.8 - - + +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 4.2 21.5 - - + -
234C PHE* 4.6 3.6 - - + -
237C SER* 4.1 0.7 - - - -
238C LEU* 4.1 37.7 - - + +
241C ALA* 3.6 15.8 - - + +
245C GLU 4.8 4.5 - - - +
246C GLN* 6.0 0.2 - - - -
247C GLY 5.6 0.2 + - - -
248C VAL* 2.8 37.9 + - + +
250C GLU* 4.1 25.1 - - + +
268C LEU* 3.8 30.1 - - + +
269C LEU* 1.3 85.6 - - - +
271C GLY* 1.3 59.4 + - - +
274C GLY 3.4 5.4 - - - +
275C VAL* 4.9 1.3 - - - -
276C GLU* 4.0 3.2 - - - +
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Residues in contact with GLY 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 6.1 0.3 - - - +
241C ALA* 3.4 23.5 - - - +
242C LEU* 3.7 5.7 + - - +
245C GLU 5.5 1.8 - - - -
270C LEU* 1.3 75.1 - - - +
272C LYS* 1.3 65.5 + - - -
273C ASN 3.1 4.0 + - - -
274C GLY* 2.5 22.8 + - - +
276C GLU* 4.0 14.7 - - - +
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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