Contacts of the strand formed by residues 262 - 267 (chain B) in PDB entry 2Z1Z
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 ALA 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ILE* 3.5 16.8 - - + +
252B ILE* 3.9 35.2 - - + -
253B PHE* 3.5 5.2 - - + -
258B ALA* 2.7 21.9 + - + +
260B GLU 4.6 0.2 - - - +
261B VAL* 1.3 77.9 - - + +
263B MET* 1.3 60.8 + - - +
285B PRO* 2.9 29.8 - - - +
288B LEU* 3.7 7.6 - - - +
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.4 39.9 - - + -
138B MET* 4.2 0.2 - - + -
139B PHE* 4.1 14.4 - - + -
233B ILE* 4.3 4.0 - - + -
234B ILE 3.1 12.7 + - - +
235B VAL* 4.1 15.7 - - + -
236B TYR* 2.9 26.9 + - - +
252B ILE* 4.3 0.2 - - - +
253B PHE* 4.0 3.4 - - - -
262B ALA* 1.3 77.6 - - - +
264B GLU* 1.3 62.1 + - - +
265B THR* 6.5 0.2 - - - -
282B THR* 4.7 2.5 - - - +
283B VAL 3.1 15.9 - - - +
284B ILE* 3.9 20.0 - - + -
288B LEU* 3.8 12.3 - - + +
296B VAL* 3.5 31.9 - - + -
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR* 2.6 33.6 + - - +
236B TYR* 3.2 16.4 - - + +
238B SER* 2.7 30.5 + - - +
250B ARG 4.2 0.9 - - - +
251B SER* 2.7 29.3 + - - -
252B ILE* 3.2 17.7 + - + +
253B PHE* 3.7 14.8 - - + -
263B MET* 1.3 77.7 - - - +
265B THR* 1.3 67.2 + - - +
281B TRP* 4.2 0.7 - - - +
282B THR* 3.1 5.2 + - - -
283B VAL* 2.6 40.0 + - + +
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 4.6 8.1 + - + +
131B ASP* 3.6 27.2 + - - +
132B ILE* 5.0 11.2 - - + -
135B LEU* 4.9 4.5 - - + -
155B TYR* 5.8 0.4 - - + -
235B VAL* 4.1 21.1 - - + -
236B TYR 2.7 17.2 + - - +
237B ASP* 3.5 25.8 - - + +
238B SER* 3.0 25.3 + - - -
264B GLU* 1.3 78.1 - - - +
266B ALA* 1.3 61.9 + - - +
281B TRP 3.7 5.0 + - - -
282B THR* 4.4 7.6 - - - -
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 4.4 1.3 - - - +
128B ALA* 4.3 6.6 - - - +
131B ASP* 4.0 4.7 - - - +
237B ASP* 5.2 0.7 - - - -
238B SER* 3.6 17.5 - - - +
239B ALA* 4.6 5.8 - - - +
264B GLU 4.2 0.4 + - - -
265B THR* 1.3 75.6 + - - +
267B SER* 1.3 62.9 + - - +
271B TYR* 4.4 6.1 - - - +
280B GLY* 3.5 2.4 - - - -
281B TRP* 2.9 69.3 + - + +
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 4.1 3.6 - - - -
239B ALA* 4.5 12.2 - - - +
266B ALA* 1.3 79.3 - - - +
268B PHE* 1.3 60.3 + - - +
269B SER* 3.1 18.5 + - - -
270B LYS* 4.3 3.8 + - - -
271B TYR* 3.5 24.1 - - - -
279B LEU 3.9 7.2 + - - -
280B GLY* 4.1 1.6 - - - -
281B TRP* 4.3 5.6 - - - -
501B PLP 2.5 45.6 + - - -
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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