Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 2R5A
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 LYS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLY 3.9 5.3 + - - +
209A MET* 1.3 74.1 - - - +
211A LEU* 1.3 63.6 + - - +
224A ILE* 3.9 16.2 - - + -
225A ALA 3.3 5.4 - - - +
226A THR* 3.2 18.6 + - - +
240A ASP* 3.0 28.2 + - - +
260A ILE* 3.6 20.1 + - + +
290A ILE* 3.4 26.7 - - - +
291A LEU* 4.6 4.0 - - + -
294A ALA* 3.9 13.9 - - + +
295A MET 2.7 23.2 + - - +
296A VAL* 3.6 5.2 - - + +
297A ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 211 (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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205A PHE* 4.8 6.5 - - + -
209A MET 3.7 11.7 - - - +
210A LYS* 1.3 79.3 - - - +
212A GLU* 1.3 79.7 + - - +
213A ALA* 4.3 0.2 - - + -
224A ILE* 3.4 8.7 - - - +
225A ALA* 2.9 51.1 + - + +
227A VAL* 3.8 9.9 - - + -
235A LEU* 5.3 1.1 - - + -
237A LEU* 3.7 26.9 - - + -
257A ILE* 4.1 19.5 - - + -
258A HIS 3.4 11.9 - - - +
260A ILE* 3.9 9.8 - - - +
297A ALA* 4.7 1.3 - - + -
302A PHE* 3.8 20.0 - - + -
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Residues in contact with GLU 212 (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 LEU* 1.3 77.7 - - - +
213A ALA* 1.3 59.6 + - - +
222A THR* 3.8 13.5 - - + +
223A CYS 3.3 4.0 - - - -
224A ILE* 4.2 2.2 - - + -
256A GLU 3.9 0.2 - - - +
257A ILE* 3.3 4.7 - - - -
258A HIS* 2.8 47.2 + - + +
259A ALA 3.6 4.6 - - - +
260A ILE* 3.4 13.4 - - + +
261A GLY* 2.8 31.1 + - - -
262A HIS* 3.5 6.9 + - - +
263A CYS* 2.8 31.5 + - - +
264A GLU* 5.1 0.3 + - - +
270A LEU* 3.8 34.7 - - + +
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Residues in contact with ALA 213 (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 LEU* 4.2 1.3 + - + -
212A GLU* 1.3 74.6 - - - +
214A LEU* 1.3 62.0 + - - +
215A ASP 3.5 0.5 + - - -
222A THR* 4.3 4.9 - - - -
223A CYS* 2.7 40.1 + - - +
225A ALA* 4.0 14.8 - - + -
237A LEU* 4.6 0.2 - - + -
239A LEU* 4.7 1.5 - - + +
248A PHE* 4.0 27.8 - - + -
256A GLU 3.4 10.1 - - - +
257A ILE* 4.2 13.0 - - + -
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Residues in contact with LEU 214 (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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213A ALA* 1.3 77.7 - - - +
215A ASP* 1.3 63.4 + - - +
216A PRO* 3.3 11.1 - - - +
219A VAL* 3.6 38.4 - - + +
220A THR 4.9 2.5 - - - +
221A SER 3.2 7.2 - - - +
222A THR* 3.6 21.8 - - + +
239A LEU* 5.4 0.2 - - - -
248A PHE* 4.3 4.4 - - - -
250A ARG* 5.0 3.6 + - - -
256A GLU* 3.3 51.4 + - + +
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Residues in contact with ASP 215 (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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213A ALA 3.5 2.2 + - - -
214A LEU* 1.3 69.6 - - - +
216A PRO* 1.4 67.4 - - - +
217A ARG* 3.0 20.2 + - - +
218A ASN* 2.9 50.0 + - - +
219A VAL* 3.1 5.9 + - - -
221A SER* 2.9 11.1 + - - +
223A CYS* 3.7 17.1 - - - -
239A LEU* 3.4 20.1 - - + +
272A PRO 4.6 0.3 - - - +
273A PRO* 3.7 3.6 - - - +
274A LEU* 2.8 34.2 + - - +
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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