Contacts of the strand formed by residues 260 - 269 (chain A) in PDB entry 2D7I
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 THR 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ARG* 4.7 3.1 - - + -
254A ILE* 3.5 22.9 - - - +
257A ASN* 3.0 34.3 + - - +
258A ARG 3.3 2.6 - - - +
259A LYS* 1.3 77.9 - - - +
261A ILE* 1.3 78.0 + - - +
262A VAL* 4.0 8.1 - - + -
324A VAL* 4.9 1.9 - - - -
328A TRP* 5.0 0.7 - - - -
359A ARG* 3.4 27.5 + - + +
361A GLU* 3.6 32.4 + - + +
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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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260A THR* 1.3 75.0 - - - +
262A VAL* 1.3 63.8 + - - +
263A CYS* 4.7 0.2 - - - -
317A MET* 3.6 27.8 - - + -
322A PHE* 3.6 13.0 - - + -
323A ALA 3.5 12.8 - - - +
324A VAL* 3.7 28.3 - - + -
328A TRP* 4.6 1.8 - - + -
329A PHE* 5.8 0.4 - - + -
332A LEU* 4.8 4.5 - - + -
349A ILE* 4.2 20.2 - - + -
353A VAL* 3.5 38.1 - - + -
359A ARG 2.8 11.8 + - - +
360A MET* 3.3 9.3 - - + +
361A GLU 2.9 24.4 + - - -
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Residues in contact with VAL 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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250A LEU* 3.6 37.5 - - + +
253A ARG* 3.7 31.2 - - + -
254A ILE* 4.1 9.2 - - + -
260A THR* 3.8 9.4 + - + -
261A ILE* 1.3 78.1 - - - +
263A CYS* 1.3 62.5 + - - +
264A PRO* 4.3 1.4 - - - +
322A PHE* 3.2 5.0 - - - +
323A ALA* 2.9 46.7 + - + +
361A GLU* 3.2 4.3 - - - +
363A ILE* 3.1 21.8 - - + -
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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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261A ILE* 4.7 0.4 - - - -
262A VAL* 1.3 80.7 - - - +
264A PRO* 1.3 72.0 - - - +
266A ILE* 5.9 2.9 - - + -
317A MET* 3.7 34.3 - - + -
318A ALA 6.2 0.4 - - - +
321A LEU 3.7 9.0 - - - +
322A PHE* 3.8 13.7 - - - -
360A MET* 4.3 11.4 - - - -
361A GLU 2.7 11.2 + - - -
362A ASP* 3.2 22.7 - - - +
363A ILE* 2.8 30.0 + - - -
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Residues in contact with PRO 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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236A LEU* 5.9 0.7 - - + -
246A TRP* 5.4 0.9 - - + -
250A LEU* 3.9 15.2 - - + -
262A VAL 4.3 1.6 - - - +
263A CYS* 1.3 92.4 - - - +
265A MET* 1.3 69.9 + - - +
266A ILE* 3.4 10.1 + - + +
321A LEU* 3.7 31.6 - - + +
322A PHE* 4.5 1.6 - - - +
362A ASP* 4.6 4.7 - - - +
363A ILE 4.1 3.1 - - - +
366A SER* 3.2 37.9 - - - +
368A VAL* 3.8 24.2 - - + -
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Residues in contact with MET 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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264A PRO* 1.3 73.6 - - - +
266A ILE* 1.3 60.5 + - - +
267A ASP* 3.7 1.2 + - - +
282A ASP* 5.1 2.2 - - - +
283A ALA* 4.4 18.2 - - - -
312A PHE* 3.6 15.3 - - + -
362A ASP* 3.4 35.9 - - + +
363A ILE 3.3 8.5 + - - +
364A PRO* 3.2 52.7 - - + +
366A SER 2.7 10.7 + - - +
367A ARG* 3.4 32.5 - - + +
368A VAL 3.1 25.3 + - - +
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Residues in contact with ILE 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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263A CYS* 5.9 2.5 - - + -
264A PRO* 3.4 14.3 + - + +
265A MET* 1.3 73.1 - - - +
267A ASP* 1.3 60.2 + - - +
279A GLN* 2.7 37.9 + - - +
318A ALA* 3.5 32.5 - - + +
321A LEU* 4.3 32.3 - - + +
368A VAL 3.5 4.9 - - - +
370A HIS* 3.6 26.7 - - + -
372A TYR* 3.3 19.5 - - - +
702A NGA 4.1 11.4 - - + +
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Residues in contact with ASP 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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130A ILE* 4.0 0.7 - - - -
265A MET* 4.6 1.1 - - - +
266A ILE* 1.3 78.4 - - - +
268A VAL* 1.3 58.4 + - - +
276A TYR* 2.6 45.6 + - + +
277A GLU 3.7 6.5 - - - +
278A THR* 3.2 13.6 + - - +
279A GLN 4.6 0.2 - - - +
367A ARG* 2.6 54.6 + - - +
368A VAL 2.8 8.6 + - - +
369A GLY* 4.0 0.4 - - - -
370A HIS* 2.6 35.7 + - - +
372A TYR* 4.2 1.2 - - - -
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Residues in contact with VAL 268 (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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267A ASP* 1.3 74.1 - - - +
269A ILE* 1.3 75.2 + - - +
270A ASP* 4.0 8.1 - - + +
275A ARG 3.3 3.5 - - - +
276A TYR* 3.4 3.1 - - - +
277A GLU* 2.6 50.9 + - + +
278A THR 4.7 0.7 - - - +
279A GLN* 3.5 33.2 - - + -
370A HIS 3.5 2.7 - - - -
372A TYR* 3.6 23.3 - - + +
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Residues in contact with ILE 269 (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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125A ARG* 3.5 22.7 - - - +
240A CYS 4.4 2.2 - - - -
241A GLU* 3.6 30.3 - - + +
268A VAL* 1.3 80.2 - - - +
270A ASP* 1.3 65.7 + - - +
271A HIS 3.3 1.9 + - - -
274A PHE* 3.7 24.5 - - + +
275A ARG 3.2 3.1 - - - -
276A TYR* 4.2 10.3 - - + -
369A GLY* 3.4 32.3 - - - +
370A HIS* 2.9 16.9 + - - +
371A ILE* 3.5 34.7 - - + +
372A TYR 4.1 2.1 + - - -
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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