Contacts of the strand formed by residues 300 - 306 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B PHE* 5.0 1.0 - - - -
194B PRO 5.0 0.2 - - - +
195B LYS* 4.5 1.7 - - - +
246B PHE* 5.4 2.5 - - + -
249B ALA* 3.9 8.1 - - + +
250B LYS* 3.9 42.6 - - + +
253B ALA* 3.7 20.4 - - + -
255B CYS* 3.7 10.5 - - - +
257B VAL* 4.5 12.3 - - + -
294B PHE* 3.4 54.6 - - + -
295B ASP 4.7 3.1 + - - +
296B SER* 4.0 7.9 + - - +
298B GLU* 4.7 5.4 - - + +
299B GLY* 1.3 78.9 - - - +
301B ILE* 1.3 76.2 + - - +
302B VAL* 4.5 6.1 - - + -
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Residues in contact with ILE 301 (chain B).
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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176B VAL* 4.2 18.4 - - + -
179B PHE* 4.4 10.8 - - + -
180B LEU* 4.2 12.3 - - + -
193B MET* 4.5 17.3 - - + -
194B PRO* 3.1 28.9 - - + +
195B LYS 3.9 3.6 - - - +
197B ILE* 4.2 15.9 - - + -
255B CYS 3.2 7.7 + - - +
256B ILE* 3.4 15.1 - - + +
257B VAL* 3.0 23.4 + - - +
296B SER* 5.8 0.2 - - - +
299B GLY 3.9 0.2 + - - -
300B ILE* 1.3 80.3 - - - +
302B VAL* 1.3 70.4 + - - +
303B MET* 3.8 25.4 + - + -
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Residues in contact with VAL 302 (chain B).
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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195B LYS 2.9 6.3 + - - -
196B GLY* 3.0 8.0 - - - -
197B ILE 2.9 22.7 + - - -
246B PHE* 3.9 21.3 - - + -
257B VAL* 3.2 20.4 - - + +
259B ILE* 3.6 28.5 - - + -
291B MET* 3.2 32.8 - - + -
294B PHE* 4.0 7.2 - - + -
300B ILE* 4.5 3.6 - - + -
301B ILE* 1.3 78.0 - - - +
303B MET* 1.3 62.6 + - - +
322B PHE* 3.7 18.2 - - + -
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Residues in contact with MET 303 (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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173B LEU* 3.9 25.1 - - + -
176B VAL* 5.4 1.6 - - - -
197B ILE* 3.2 20.0 - - + -
199B LEU* 3.5 40.8 - - + -
211B ALA* 4.3 19.5 - - + -
214B VAL* 4.8 9.2 - - - -
256B ILE* 4.3 17.9 - - + -
257B VAL 2.8 8.5 + - - +
258B PHE* 3.1 18.3 - - + -
259B ILE 2.8 30.1 + - - -
301B ILE* 3.8 16.6 + - + -
302B VAL* 1.3 80.0 - - - +
304B ALA* 1.3 55.3 + - - +
322B PHE* 4.3 0.7 - - - -
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Residues in contact with ALA 304 (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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197B ILE 3.0 6.3 + - - -
198B LEU* 3.1 15.9 - - + +
199B LEU* 2.7 34.2 + - - +
258B PHE* 4.2 3.8 - - - -
259B ILE* 3.3 11.9 - - + +
262B ILE* 3.5 33.7 - - + -
303B MET* 1.3 75.8 - - - +
305B ALA* 1.3 56.0 + - - +
322B PHE* 3.6 13.9 - - + -
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Residues in contact with ALA 305 (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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199B LEU* 3.3 5.2 - - + -
207B LYS* 3.9 26.9 - - + +
258B PHE* 3.8 17.9 - - + -
259B ILE 3.1 6.3 + - - -
260B ASP* 3.6 20.4 - - - +
261B GLU 3.2 5.7 + - - -
262B ILE* 3.2 23.6 + - - +
304B ALA* 1.3 75.5 - - - +
306B THR* 1.3 66.6 + - - +
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Residues in contact with THR 306 (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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198B LEU* 4.0 18.4 - - + -
199B LEU 3.1 4.5 + - - +
200B VAL* 3.3 11.9 - - + +
201B GLY 3.2 21.2 + - - +
207B LYS* 4.0 4.3 - - - +
261B GLU* 5.1 1.6 - - - +
262B ILE* 4.0 7.9 - - - -
263B ASP* 2.9 32.8 + - - +
305B ALA* 1.3 79.1 - - - +
307B ASN* 1.3 56.5 + - - +
308B ARG* 3.1 13.7 + - - +
309B PRO* 4.0 23.3 - - + -
312B LEU* 4.4 6.5 - - + -
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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