Contacts of the strand formed by residues 300 - 306 (chain D) in PDB entry 2CEA
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 ILE 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D PHE* 5.5 0.3 - - - -
195D LYS* 4.9 0.7 - - - -
246D PHE* 5.4 2.5 - - + -
249D ALA* 4.1 14.8 - - + +
250D LYS* 4.0 39.3 - - + +
253D ALA* 4.2 15.7 - - + -
255D CYS* 3.6 13.7 - - - +
257D VAL* 5.0 3.6 - - + -
294D PHE* 3.6 55.9 - - + -
295D ASP 5.1 0.2 - - - +
296D SER* 3.8 8.2 + - - +
298D GLU* 3.5 9.2 - - + +
299D GLY* 1.3 81.2 - - - +
301D ILE* 1.3 73.5 + - - +
302D VAL* 4.3 8.5 - - + -
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Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D VAL* 4.2 21.8 - - + -
179D PHE* 4.8 9.4 - - + -
180D LEU* 4.5 12.1 - - + +
193D MET* 5.0 8.5 - - + -
194D PRO* 2.7 36.8 - - + +
195D LYS* 3.6 5.2 - - - +
197D ILE* 3.9 17.0 - - + -
255D CYS 3.2 9.1 + - - +
256D ILE* 3.2 16.8 - - + +
257D VAL 3.0 21.0 + - - -
296D SER* 5.3 0.9 - - - +
299D GLY 4.1 0.4 - - - -
300D ILE* 1.3 80.1 - - - +
302D VAL* 1.3 66.1 + - - +
303D MET* 3.8 22.9 - - + -
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Residues in contact with VAL 302 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D LYS 3.0 8.3 + - - +
196D GLY* 3.1 4.7 - - - -
197D ILE 3.0 22.9 + - - -
246D PHE* 4.0 9.0 - - + -
257D VAL* 3.1 33.0 - - + +
259D ILE* 4.1 18.6 - - + -
291D MET* 3.1 37.9 - - + -
294D PHE* 3.8 16.2 - - + -
300D ILE* 4.3 3.6 - - + -
301D ILE* 1.3 74.8 - - - +
303D MET* 1.3 63.1 + - - +
322D PHE* 3.9 10.1 - - + -
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Residues in contact with MET 303 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D LEU* 3.5 33.0 - - + -
176D VAL* 5.8 0.2 - - - -
197D ILE* 3.4 24.9 - - + +
199D LEU* 4.1 23.6 - - + -
211D ALA* 3.8 24.7 - - - -
214D VAL* 4.4 13.7 - - + -
256D ILE* 4.0 13.9 - - + -
257D VAL 2.6 11.5 + - - +
258D PHE* 3.1 19.3 - - + -
259D ILE* 2.7 32.4 + - - +
301D ILE* 3.8 17.5 - - + -
302D VAL* 1.3 80.3 - - - +
304D ALA* 1.3 55.9 + - - +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D ILE 2.9 6.9 + - - -
198D LEU* 3.3 16.9 - - + +
199D LEU* 2.6 36.0 + - - +
258D PHE* 4.3 3.4 - - - -
259D ILE* 3.3 8.7 - - + +
262D ILE* 3.3 35.4 - - + -
303D MET* 1.3 76.1 - - - +
305D ALA* 1.3 55.8 + - - +
322D PHE* 3.8 11.4 - - + -
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Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D LEU* 3.3 7.0 - - + -
207D LYS* 3.8 26.2 - - + +
258D PHE* 3.7 26.6 - - + -
259D ILE 3.1 6.4 + - - +
260D ASP* 3.8 11.7 - - - +
261D GLU 3.4 5.2 + - - -
262D ILE* 3.2 23.0 + - - +
304D ALA* 1.3 73.7 - - - +
306D THR* 1.3 68.5 + - - +
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Residues in contact with THR 306 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.9 30.3 - - + -
199D LEU 3.1 8.0 + - - +
200D VAL* 3.5 6.5 - - + +
201D GLY 3.3 21.7 + - - -
207D LYS* 4.2 5.3 - - - +
261D GLU* 5.3 1.8 - - - +
262D ILE* 4.1 9.2 - - + -
263D ASP* 2.6 28.3 + - - +
305D ALA* 1.3 80.5 - - - +
307D ASN* 1.3 57.7 + - - +
308D ARG 2.8 20.8 + - - +
309D PRO* 4.5 6.5 - - + -
312D LEU* 4.2 8.7 - - + -
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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