Contacts of the strand formed by residues 259 - 267 (chain A) in PDB entry 2ADU
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 ARG 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ILE* 3.9 35.4 - - - +
168A ASP* 3.7 25.5 + - + +
169A PHE* 3.7 43.7 - - + +
172A ALA* 4.1 7.8 - - - +
254A THR 4.0 0.3 - - - +
255A HIS* 3.5 15.8 - - - -
256A ILE 2.9 19.8 + - - +
257A SER* 3.8 4.0 + - - +
258A GLY* 1.3 73.8 - - - +
260A ILE* 1.3 61.7 + - - +
261A ILE 3.8 0.9 + - - -
335A GLN* 3.2 52.3 + - - +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.4 19.5 - - - -
218A ALA* 3.5 29.2 - - + +
219A PHE* 4.6 1.6 - - + -
254A THR 3.7 3.8 - - - -
255A HIS* 4.0 4.9 - - + -
258A GLY 3.0 11.1 + - - +
259A ARG* 1.3 71.6 - - - +
261A ILE* 1.3 72.4 + - - +
262A ASP* 4.2 1.3 - - + +
333A ILE* 3.8 23.4 - - + +
334A GLY 4.2 2.7 - - - +
336A TYR* 4.0 0.9 - - - -
337A ARG 3.6 17.7 - - - +
338A ILE* 3.6 50.9 - - + +
413A LEU* 3.8 18.8 - - + -
461A THR* 4.1 2.1 - - - +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.4 31.0 - - + +
172A ALA* 3.3 26.5 - - + -
173A ALA* 3.5 10.5 - - + +
176A HIS* 4.0 29.8 - - + -
252A PHE 4.0 0.2 - - - +
253A GLY* 3.1 26.2 - - - -
254A THR* 2.9 18.6 + - - +
260A ILE* 1.3 76.2 - - - +
262A ASP* 1.3 57.6 + - - +
263A CYS* 3.9 2.3 + - + -
461A THR* 3.9 5.4 - - + +
472A VAL* 3.8 27.1 - - + -
473A SER* 4.2 15.3 - - - -
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.2 13.4 - - + -
251A ASP* 3.0 5.7 - - - +
260A ILE 3.9 1.2 - - - -
261A ILE* 1.3 70.0 - - - +
263A CYS* 1.3 61.7 + - - +
331A HIS* 3.0 7.8 + - - -
333A ILE* 4.1 8.1 - - + -
338A ILE* 3.7 16.2 - - + +
362A ALA* 4.3 1.5 - - + +
459A GLU* 2.4 15.9 - - - +
460A HIS 3.5 4.3 - - - +
461A THR* 2.7 35.9 + - - +
501A CO 1.9 26.3 + - - -
502A CO 2.0 29.6 + - - -
906A R20 2.6 8.6 + - - -
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Residues in contact with CYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A HIS* 2.9 34.1 + - + +
180A ARG* 3.1 20.9 - - - -
251A ASP* 4.1 1.6 - - - -
252A PHE* 3.1 17.3 + - - +
261A ILE* 3.9 1.5 + - + -
262A ASP* 1.3 78.4 + - - +
264A ALA* 1.3 62.9 + - - +
459A GLU* 3.2 20.0 - - - +
460A HIS* 3.6 16.6 - - - -
473A SER* 3.8 12.8 - - - +
478A TYR* 3.0 28.9 - - - -
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE 3.1 18.4 - - - +
251A ASP* 3.4 26.2 - - + +
263A CYS* 1.3 75.8 - - - +
265A PHE* 1.3 60.6 + - - +
457A GLN* 3.8 18.4 - - - +
458A PHE* 3.5 3.5 - - - -
459A GLU* 3.0 31.9 + - + +
478A TYR* 3.3 17.2 - - - -
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 3.8 23.3 - - + -
183A VAL* 4.5 8.3 - - + -
184A MET* 3.8 33.9 - - + -
249A LYS* 3.7 3.3 - - - +
250A ILE* 2.9 63.0 + - + +
252A PHE* 4.3 4.9 - + - -
264A ALA* 1.3 77.7 - - - +
266A THR* 1.3 67.6 + - - +
267A VAL* 3.5 27.4 - - + -
457A GLN 3.6 8.0 - - - +
458A PHE* 3.8 13.2 - - + -
478A TYR* 3.5 33.4 - + + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 3.6 31.6 - - + -
248A CYS 3.4 7.9 - - - +
249A LYS* 3.8 8.8 - - + +
265A PHE* 1.3 81.2 - - - +
267A VAL* 1.3 68.7 + - - +
268A THR 4.2 0.3 + - - -
277A LEU* 3.7 36.7 - - + +
456A ALA* 3.8 2.0 - - + +
457A GLN* 2.7 39.6 + - - -
458A PHE* 3.8 10.3 - - - -
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A MET* 5.6 0.9 - - + -
187A ILE* 3.8 35.9 - - + -
242A LEU* 5.2 0.2 - - + -
246A ASP 3.8 1.4 - - - +
247A ILE* 3.6 0.9 - - - -
248A CYS* 2.6 45.2 + - + +
250A ILE* 4.1 7.6 - - + -
265A PHE* 3.5 31.6 - - + -
266A THR* 1.3 73.5 - - - +
268A THR* 1.3 73.3 + - - +
269A PHE* 3.8 30.7 - - + -
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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