Contacts of the strand formed by residues 263 - 270 (chain B) in PDB entry 2W77
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 GLY 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B ALA* 3.5 32.5 - - - +
210B ARG* 4.0 3.6 - - - -
212B PHE* 3.9 8.1 - - - -
214B ILE* 5.4 0.9 - - - -
250B LYS* 3.6 3.8 - - - +
251B GLY* 2.9 33.9 + - - -
262B LEU* 1.3 75.7 - - - +
264B ALA* 1.3 60.8 + - - +
638B ILE* 4.6 5.2 - - - +
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Residues in contact with ALA 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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209B ALA* 4.0 5.4 - - + -
214B ILE* 3.4 43.0 - - + +
216B ASN* 3.0 23.2 + - - -
248B VAL* 4.3 13.0 - - + -
249B LEU 3.0 13.9 - - - +
250B LYS* 4.4 1.8 - - + -
251B GLY 3.9 2.1 + - - +
253B THR* 4.3 5.6 - - - -
261B SER* 4.6 0.4 + - - -
262B LEU 3.3 4.4 + - - +
263B GLY* 1.3 77.9 - - - +
265B THR* 1.3 61.4 + - - +
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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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154B THR* 5.9 0.9 - - + -
216B ASN* 3.1 23.2 + - + +
218B GLN* 3.4 36.6 - - + +
247B GLU 3.8 0.7 - - - +
248B VAL* 3.6 4.5 - - - +
249B LEU* 2.9 39.2 + - + +
253B THR* 2.9 28.3 + - - +
257B THR* 3.0 10.2 + - - +
264B ALA* 1.3 73.1 - - - +
266B ILE* 1.3 74.4 + - - +
267B ASN* 4.2 2.0 - - + +
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Residues in contact with ILE 266 (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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185B ILE* 4.2 10.1 - - + -
189B MET* 3.8 21.8 - - + -
207B TYR* 3.8 9.6 - - + -
214B ILE* 3.5 31.0 - - + -
216B ASN 3.0 8.1 + - - +
217B PHE* 3.4 29.9 - - + -
218B GLN 2.6 33.8 + - - +
246B VAL* 3.8 25.1 - - + -
247B GLU 3.7 2.9 - - - -
248B VAL* 4.1 14.1 - - + -
265B THR* 1.3 76.6 - - - +
267B ASN* 1.3 54.4 + - - +
268B LEU* 4.0 15.0 - - + +
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Residues in contact with ASN 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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154B THR* 4.5 11.2 - - + +
218B GLN* 3.3 30.2 + - - +
220B ASP 3.7 1.9 + - - -
221B GLY* 3.1 29.3 + - - +
246B VAL* 3.5 2.1 - - - -
247B GLU* 2.6 73.7 + - + +
265B THR* 4.6 2.5 - - + -
266B ILE* 1.3 72.1 - - - +
268B LEU* 1.3 64.4 + - - +
269B ILE* 3.3 19.0 + - - +
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Residues in contact with LEU 268 (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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185B ILE* 4.9 5.6 - - + -
217B PHE* 4.8 5.2 - - + -
218B GLN 2.9 20.1 + - - +
219B TYR* 3.6 22.5 - - + +
220B ASP* 2.8 26.5 + - - -
238B SER* 4.2 11.9 - - - -
240B MET* 4.2 9.0 - - + -
243B TYR* 3.4 52.9 - - + +
245B ARG 3.9 4.5 - - - -
246B VAL* 4.3 13.0 - - + +
266B ILE* 4.0 20.9 - - + +
267B ASN* 1.3 76.2 - - - +
269B ILE* 1.3 62.1 + - - +
270B ARG 4.0 0.7 + - - -
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Residues in contact with ILE 269 (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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137B LEU* 4.1 30.1 - - + +
220B ASP* 3.5 9.4 - - - +
243B TYR* 3.2 9.0 - - - +
244B ASP* 2.8 29.0 + - + +
245B ARG* 3.1 64.5 + - + +
247B GLU* 3.8 9.4 - - + +
267B ASN* 3.3 31.0 - - - +
268B LEU* 1.3 73.0 - - - +
270B ARG* 1.3 68.4 + - - +
272B LYS* 6.0 3.4 - - + -
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Residues in contact with ARG 270 (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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219B TYR* 4.0 31.3 + - - +
220B ASP* 2.7 38.5 + - - +
222B ILE* 5.8 0.4 - - - +
242B ILE* 3.4 10.8 - - + +
243B TYR* 3.8 22.8 + - + -
244B ASP* 4.2 4.2 - - - +
268B LEU 4.0 0.6 + - - +
269B ILE* 1.3 83.2 - - - +
271B LYS* 1.3 64.0 + - - +
272B LYS* 3.6 10.1 + - + +
333B TYR* 3.6 35.4 - - + +
335B ILE* 6.0 0.7 - - + -
351B ASP* 2.6 33.4 + - - -
397B THR* 3.9 12.5 + - - +
399B PHE* 3.5 31.0 - - - -
417B ASP* 4.4 12.5 + - - -
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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