Contacts of the strand formed by residues 300 - 306 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PHE* 4.8 0.3 - - - -
195A LYS* 4.6 0.9 - - - +
246A PHE* 5.6 1.8 - - + -
249A ALA* 4.1 21.8 - - + +
250A LYS* 4.0 27.1 - - + -
253A ALA* 3.7 21.1 - - + -
255A CYS* 3.5 9.4 - - - +
257A VAL* 4.7 3.8 - - + -
294A PHE* 3.2 52.6 - - + -
295A ASP 4.4 0.9 - - - +
296A SER* 3.6 10.1 + - - +
298A GLU* 3.8 24.5 - - + -
299A GLY* 1.3 76.8 - - - +
301A ILE* 1.3 75.8 + - - +
302A VAL* 4.6 6.3 - - + -
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Residues in contact with ILE 301 (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 VAL* 3.3 36.8 - - + -
179A PHE* 3.4 33.2 - - + -
180A LEU* 4.3 7.2 - - + -
193A MET* 4.7 2.5 - - + -
194A PRO 3.8 19.7 - - - +
195A LYS 3.9 3.8 - - - +
197A ILE* 4.6 9.4 - - + -
255A CYS 3.1 9.4 + - - +
256A ILE* 3.3 14.9 - - + -
257A VAL 2.9 22.7 + - - -
299A GLY 4.0 0.2 + - - -
300A ILE* 1.3 77.6 - - - +
302A VAL* 1.3 64.8 + - - +
303A MET* 3.8 26.3 + - + -
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Residues in contact with VAL 302 (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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195A LYS 2.9 15.2 + - - +
196A GLY* 3.1 5.4 - - - -
197A ILE 3.0 22.2 + - - -
246A PHE* 3.9 28.0 - - + -
257A VAL* 3.1 26.7 - - + +
259A ILE* 3.8 20.6 - - + -
291A MET* 4.1 13.0 - - + -
294A PHE* 4.1 9.2 - - + -
300A ILE* 4.6 2.9 - - + -
301A ILE* 1.3 74.2 - - - +
303A MET* 1.3 62.4 + - - +
322A PHE* 3.7 23.7 - - + -
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Residues in contact with MET 303 (chain A).
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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173A LEU* 4.2 23.1 - - + -
176A VAL* 5.7 0.7 - - - -
197A ILE* 3.4 18.2 - - + +
199A LEU* 3.3 34.1 - - + -
211A ALA* 3.7 27.1 - - + +
214A VAL* 4.3 17.9 - - + -
256A ILE* 4.4 14.4 - - + -
257A VAL 2.8 7.8 + - - +
258A PHE* 3.2 17.4 - - + -
259A ILE 2.9 24.1 + - - -
301A ILE* 3.8 21.2 + - + -
302A VAL* 1.3 75.0 - - - +
304A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 304 (chain A).
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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197A ILE 2.9 5.7 + - - -
198A LEU* 3.2 16.8 - - + +
199A LEU* 2.5 35.5 + - - +
258A PHE* 4.2 3.4 - - - -
259A ILE* 3.4 10.8 - - + +
262A ILE* 3.8 20.2 - - + -
303A MET* 1.3 76.8 - - - +
305A ALA* 1.3 54.3 + - - +
322A PHE* 3.4 25.8 - - + -
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Residues in contact with ALA 305 (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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199A LEU* 3.3 10.3 - - + +
207A LYS* 3.9 24.0 - - + +
258A PHE* 3.7 26.0 - - + -
259A ILE 3.2 6.7 + - - -
260A ASP* 4.1 10.3 - - - +
261A GLU 3.3 6.0 + - - -
262A ILE* 3.1 26.4 + - - +
304A ALA* 1.3 74.6 - - - +
306A THR* 1.3 63.1 + - - +
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Residues in contact with THR 306 (chain A).
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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198A LEU* 4.3 19.3 - - + -
199A LEU 3.0 12.7 + - - +
200A VAL* 3.3 4.1 - - + +
201A GLY 3.2 23.0 + - - +
207A LYS* 4.0 5.9 - - - +
261A GLU* 5.1 2.5 - - - +
262A ILE* 4.0 8.3 - - - -
263A ASP* 3.1 22.3 + - - +
305A ALA* 1.3 78.1 - - - +
307A ASN* 1.3 58.1 + - - +
308A ARG 2.8 29.7 + - - +
309A PRO* 4.0 22.0 - - + -
312A LEU* 4.5 3.6 - - + -
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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