Contacts of the strand formed by residues 225 - 231 (chain A) in PDB entry 2C11
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 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR* 3.7 0.4 - - - +
213A THR* 3.6 26.0 - - - +
215A PRO 5.5 1.1 - - - +
216A ARG* 2.8 42.7 + - + +
224A ALA* 1.3 72.8 - - - +
226A TRP* 1.3 71.8 + - - +
227A PHE* 3.2 31.7 - - + -
247A LEU 3.5 0.5 - - - +
248A LEU* 3.0 5.6 - - - +
249A VAL 2.9 33.0 + - - +
251A HIS* 2.7 21.4 + - - -
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Residues in contact with TRP 226 (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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211A MET 3.8 1.4 - - - +
213A THR* 3.0 34.0 + - - +
224A ALA 4.9 2.2 - - - -
225A THR* 1.3 80.5 - - - +
227A PHE* 1.3 60.6 + - - +
228A GLY 4.1 0.2 + - - -
246A GLU* 3.7 22.7 - - + -
247A LEU* 3.1 26.2 - - - -
248A LEU* 3.4 34.4 - - + +
263A LYS* 4.2 19.1 - - + -
264A VAL 4.5 1.1 - - - -
265A PHE* 3.7 27.1 - - + -
270A TYR* 4.7 3.4 - + - -
377A PRO* 3.4 32.5 - - + -
378A ALA* 3.8 16.7 - - - +
381A THR* 4.7 7.2 - - - -
553B TRP* 3.3 42.6 - + - +
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Residues in contact with PHE 227 (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 TYR* 4.7 10.8 - + - -
179A ILE* 3.7 37.7 - - + -
180A ASP* 5.6 0.2 - - - -
183A ILE* 4.9 7.0 - - + -
210A THR* 3.9 31.4 - - + -
211A MET 3.7 4.5 - - - -
212A THR* 3.5 35.9 - - - -
216A ARG* 4.8 1.6 - - - -
225A THR* 3.2 39.3 - - + -
226A TRP* 1.3 77.5 - - - +
228A GLY* 1.3 61.8 + - - +
229A LEU* 4.1 2.5 - - + +
245A LEU 4.0 0.5 - - - +
246A GLU* 3.1 3.4 - - - -
247A LEU* 2.6 44.9 + - + +
249A VAL* 4.3 17.0 - - + -
251A HIS* 5.1 0.2 - - - -
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Residues in contact with GLY 228 (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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210A THR* 3.3 4.5 - - - -
211A MET 3.2 21.6 + - - -
226A TRP 4.1 1.2 + - - -
227A PHE* 1.3 75.2 - - - +
229A LEU* 1.3 59.3 + - - +
230A TYR* 3.1 31.5 + - - -
242A HIS* 3.9 9.6 - - - -
245A LEU 3.6 6.5 - - - -
246A GLU* 3.9 10.1 - - - -
378A ALA* 5.0 4.4 - - - +
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Residues in contact with LEU 229 (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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183A ILE* 4.6 2.0 - - + -
184A PHE* 4.6 3.1 - - + -
188A LEU* 4.3 24.5 - - + -
208A LEU* 4.6 14.6 - - + -
209A VAL 3.4 7.6 - - - +
210A THR* 3.4 26.7 - - + -
227A PHE 4.1 2.9 - - - +
228A GLY* 1.3 75.8 - - - +
230A TYR* 1.3 64.1 + - - +
242A HIS* 3.7 4.4 + - - -
243A VAL* 2.9 42.0 + - + +
245A LEU* 2.8 42.2 + - + +
247A LEU* 3.5 31.2 - - + -
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Residues in contact with TYR 230 (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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208A LEU* 3.2 5.6 - - - +
209A VAL* 2.7 43.1 + - - +
211A MET* 3.4 38.9 + - + +
213A THR* 6.0 1.7 - - - +
228A GLY* 3.1 33.7 + - - -
229A LEU* 1.3 73.5 - - - +
231A TYR* 1.3 60.7 + - - +
238A PHE* 3.1 41.7 - + + +
239A PHE* 4.1 10.1 - - - -
241A HIS 2.9 13.2 - - - +
242A HIS* 3.4 45.7 + + + -
243A VAL* 4.1 2.5 - - - -
497A SER 4.0 11.7 + - - -
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Residues in contact with TYR 231 (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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198A CYS 3.9 5.2 + - - -
199A CYS* 3.9 13.8 - - + -
200A PHE* 3.5 10.5 - + - -
207A ASN* 3.8 9.0 - - - +
208A LEU* 3.5 17.3 - - + -
209A VAL* 3.7 0.2 - - - +
230A TYR* 1.3 73.6 - - - +
232A ASN* 1.3 59.8 - - - +
233A ILE* 3.0 23.3 + - + +
238A PHE* 3.1 22.0 - - - +
241A HIS* 3.2 20.3 + - + -
243A VAL* 3.3 23.6 - - + -
291A ILE* 2.4 43.8 + - + +
292A PRO 3.1 23.8 - - - -
293A ASP* 3.2 30.7 - - + -
300A TRP* 4.9 0.4 - + - -
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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