Contacts of the strand formed by residues 218 - 231 (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 ASN 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ASP* 2.9 28.8 + - - +
217A ARG* 1.3 80.2 - - - +
219A VAL* 1.3 61.1 + - - +
220A THR* 2.8 33.8 + - - +
221A SER* 2.9 28.4 + - - +
274A LEU* 4.6 14.6 - - + +
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Residues in contact with VAL 219 (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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214A LEU* 3.6 38.0 - - + +
215A ASP 3.3 14.6 - - - +
216A PRO* 4.2 15.9 - - + +
218A ASN* 1.3 71.3 + - - +
220A THR* 1.3 65.3 + - + +
221A SER 3.3 1.8 - - - -
250A ARG* 6.4 0.2 - - - +
256A GLU* 5.4 4.3 - - - +
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Residues in contact with THR 220 (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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214A LEU* 4.9 2.8 - - - +
218A ASN* 2.8 28.9 + - - +
219A VAL* 1.3 85.4 - - + +
221A SER* 1.3 60.8 + - - +
222A THR* 3.9 2.9 + - - -
271A GLN* 5.7 0.3 - - - +
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Residues in contact with SER 221 (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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214A LEU* 3.2 8.8 - - - +
215A ASP* 2.9 30.6 + - - -
218A ASN* 2.9 27.8 + - - +
220A THR* 1.3 79.1 + - - +
222A THR* 1.3 60.7 + - - +
223A CYS* 4.0 12.8 - - - -
271A GLN* 3.6 31.8 + - - +
272A PRO 4.6 3.6 + - - -
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Residues in contact with THR 222 (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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212A GLU* 3.8 26.5 - - + +
213A ALA 3.5 11.0 - - - +
214A LEU* 3.6 16.0 - - + +
220A THR 3.9 3.2 + - - -
221A SER* 1.3 70.6 - - - +
223A CYS* 1.3 61.4 + - - +
258A HIS* 6.1 2.2 - - - +
263A CYS* 4.0 22.0 - - + -
269A MET 5.1 1.2 + - - -
270A LEU* 3.5 21.9 - - + -
271A GLN* 2.9 28.6 + - - +
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Residues in contact with CYS 223 (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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212A GLU* 3.3 4.9 - - - -
213A ALA* 2.7 33.6 + - - +
215A ASP* 3.7 22.9 - - - -
221A SER* 4.0 7.0 - - - -
222A THR* 1.3 76.6 - - - +
224A ILE* 1.3 64.3 + - - +
239A LEU* 3.9 21.3 - - + -
270A LEU* 4.3 5.2 - - - -
271A GLN 3.5 21.8 - - - +
272A PRO 3.8 4.3 - - - -
273A PRO* 3.7 26.9 - - + -
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Residues in contact with ILE 224 (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 LYS* 3.9 20.6 - - + -
211A LEU 3.4 5.4 - - - +
212A GLU* 4.2 4.7 - - + -
223A CYS* 1.3 73.7 - - - +
225A ALA* 1.3 62.4 + - - +
239A LEU* 3.5 8.5 - - - +
240A ASP* 3.2 44.3 + - + +
260A ILE* 3.8 27.4 - - + -
270A LEU* 3.8 25.5 - - + +
271A GLN 4.9 1.6 + - - -
273A PRO* 6.0 0.3 - - - +
283A TRP* 5.2 7.6 - - + -
287A LEU* 3.7 25.1 - - + -
290A ILE* 3.9 12.1 - - + -
291A LEU* 4.0 11.2 - - + -
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Residues in contact with ALA 225 (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 LYS* 3.3 5.4 - - - +
211A LEU* 2.9 53.2 + - + +
213A ALA* 4.0 11.7 - - + -
223A CYS 3.6 0.2 + - - -
224A ILE* 1.3 74.5 - - - +
226A THR* 1.3 62.8 + - - +
237A LEU* 4.3 14.6 - - + -
238A ARG 3.3 11.0 - - - +
239A LEU* 3.9 15.9 - - + +
240A ASP* 3.6 1.3 - - - -
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Residues in contact with THR 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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208A GLY* 3.7 26.0 - - - +
209A MET 3.4 3.4 - - - -
210A LYS* 3.2 21.1 + - - +
225A ALA* 1.3 74.4 + - - +
227A VAL* 1.3 77.3 - - - +
228A VAL* 3.2 13.8 + - + +
237A LEU* 3.5 6.6 - - - -
238A ARG* 2.9 32.4 + - - -
240A ASP* 2.8 23.6 + - - -
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Residues in contact with VAL 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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205A PHE* 4.1 21.8 - - + -
206A LYS 3.6 22.7 - - - +
207A ILE* 3.5 5.5 - - - +
208A GLY 2.8 26.3 + - - -
209A MET* 2.9 20.8 + - + +
211A LEU* 3.8 17.0 - - + -
226A THR* 1.3 74.8 - - - +
228A VAL* 1.3 57.5 + - - +
229A GLY 3.4 24.9 - - - +
230A VAL* 3.8 17.5 - - + -
235A LEU* 4.2 9.6 - - + -
236A ARG 3.6 5.8 - - - +
237A LEU* 4.0 8.1 - - + -
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Residues in contact with VAL 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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207A ILE* 4.0 17.1 - - + +
226A THR* 3.2 17.7 + - + +
227A VAL* 1.3 76.6 - - - +
229A GLY* 1.3 57.4 + - - +
236A ARG* 2.9 33.8 + - + +
238A ARG* 3.9 42.2 - - + +
247A ASP* 3.7 24.0 - - - +
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Residues in contact with GLY 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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207A ILE* 3.9 11.1 - - - +
227A VAL* 3.4 14.3 - - - +
228A VAL* 1.3 81.0 - - - +
230A VAL* 1.3 64.0 + - - +
235A LEU* 3.6 0.9 - - - -
236A ARG* 2.9 37.3 + - - -
249A TRP* 5.2 1.8 - - - -
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Residues in contact with VAL 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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203A ASN* 3.2 33.4 - - + +
205A PHE 3.7 22.2 - - - +
207A ILE* 4.6 14.0 - - + +
227A VAL* 3.8 15.9 - - + -
229A GLY* 1.3 78.4 - - - +
231A LEU* 1.3 70.7 + - - +
232A GLY 4.1 4.5 - - - +
234A ARG 3.5 4.3 - - - -
235A LEU* 4.3 6.5 - - + -
236A ARG 4.8 0.2 - - - +
249A TRP* 4.8 1.8 - - - -
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Residues in contact with LEU 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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230A VAL* 1.3 78.8 - - - +
232A GLY* 1.3 62.7 + - - +
233A SER 3.3 0.3 + - - -
234A ARG* 2.9 34.7 + - - +
249A TRP* 3.7 19.0 - - + -
329A GLN* 4.1 28.9 - - + +
376A CYS 4.9 2.9 - - - +
377A HIS* 3.5 35.8 - - + +
378A PRO* 3.9 26.2 - - + -
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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