Contacts of the strand formed by residues 213 - 222 (chain A) in PDB entry 5ODS
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 SER 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ALA 3.5 0.7 - - - +
203A GLN* 3.5 4.0 - - - -
204A PHE 2.9 40.9 + - - +
206A MET* 4.3 9.2 - - - +
209A ASN* 3.9 19.9 + - - -
211A GLU 3.6 1.2 + - - -
212A GLU* 1.3 73.9 - - - +
214A THR* 1.3 62.9 + - - +
215A LEU* 3.5 15.8 + - - +
232A GLU* 3.6 22.9 + - - -
237A PRO* 5.3 5.0 - - - +
240A ASN* 4.5 2.6 + - - +
243A PHE* 5.0 3.8 - - - -
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Residues in contact with THR 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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159A ASP* 4.0 24.8 + - + +
161A LYS* 4.6 6.4 - - - +
164A TRP* 5.1 5.2 - - + -
201A PHE* 4.8 2.0 - - + -
202A ALA 3.6 4.7 - - - +
203A GLN* 3.0 32.6 + - - +
212A GLU 4.0 2.2 + - - -
213A SER* 1.3 70.2 - - - +
215A LEU* 1.3 65.3 + - - +
232A GLU* 3.6 7.8 - - - +
233A VAL* 3.0 49.6 + - + +
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Residues in contact with LEU 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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201A PHE* 3.3 10.3 - - - +
202A ALA* 2.6 48.7 + - + +
204A PHE* 3.6 33.2 - - + -
213A SER* 4.1 13.5 - - - +
214A THR* 1.3 77.6 - - - +
216A PHE* 1.3 60.1 + - - +
217A CYS* 4.0 1.7 + - + +
230A ILE* 4.0 18.4 - - + -
231A ILE 3.4 4.0 - - - +
232A GLU* 3.9 13.5 - - + -
233A VAL* 4.7 0.7 - - - -
243A PHE* 3.7 43.5 - - + -
287A LEU* 4.2 14.1 - - + -
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Residues in contact with PHE 216 (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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166A LEU* 3.6 33.4 - - + -
181A MET* 3.8 24.5 - - + -
183A LEU* 4.1 10.5 - - + -
194A ILE* 3.7 20.4 - - + -
199A ALA* 3.8 11.0 - - + -
200A SER 3.9 4.3 - - - -
201A PHE* 3.6 24.9 - + + -
214A THR 4.1 0.6 + - - -
215A LEU* 1.3 72.9 - - - +
217A CYS* 1.3 62.0 + - - +
218A PHE* 3.5 23.2 + + + -
229A HIS 3.7 2.4 - - - +
230A ILE* 4.8 0.2 - - - -
231A ILE* 2.7 53.2 + - + +
233A VAL* 3.6 21.8 - - + -
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Residues in contact with CYS 217 (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 ALA* 3.2 3.2 - - - +
200A SER 2.8 44.5 + - - +
215A LEU* 4.0 1.7 - - + +
216A PHE* 1.3 74.5 - - - +
218A PHE* 1.3 63.5 + - - +
228A LEU* 3.8 13.9 - - - -
229A HIS 3.2 12.3 - - - +
230A ILE* 3.9 18.2 - - + -
264A MET* 3.4 24.4 - - - +
266A ILE* 3.9 14.4 - - + -
273A VAL* 4.2 15.5 - - - -
287A LEU* 4.8 4.9 - - + -
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Residues in contact with PHE 218 (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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181A MET* 3.7 17.9 - - + -
194A ILE* 3.6 20.0 - - + -
195A GLU 3.5 20.2 - - - -
196A GLY* 4.0 8.7 - - - -
198A ALA 3.2 5.2 - - - +
199A ALA* 3.5 18.2 - - + -
216A PHE* 3.5 27.1 - + + -
217A CYS* 1.3 75.9 - - - +
219A ALA* 1.3 63.7 + - - +
220A VAL* 4.3 4.0 - - + -
227A LYS 4.0 0.5 - - - +
228A LEU* 3.6 1.5 - - - +
229A HIS* 2.8 75.2 + + + -
231A ILE* 5.5 5.4 - - + -
245A LYS* 6.1 2.0 - - - -
264A MET* 3.8 3.6 - - - -
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Residues in contact with ALA 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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196A GLY* 3.8 0.7 - - - -
197A HIS* 2.8 23.0 + - - -
198A ALA 2.7 18.3 + - - +
218A PHE* 1.3 74.9 - - - +
220A VAL* 1.3 62.0 + - - +
227A LYS 3.4 7.6 - - - +
228A LEU* 3.8 11.0 - - + -
250A VAL* 4.8 2.0 - - + -
261A PRO* 3.9 9.9 - - + -
264A MET* 3.5 17.2 - - + +
275A LEU* 3.8 26.5 - - + -
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Residues in contact with VAL 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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179A GLY 5.6 0.2 - - - +
195A GLU* 3.5 36.8 - - + +
196A GLY* 3.7 10.8 - - - +
197A HIS* 3.8 16.2 - - + +
218A PHE* 4.3 9.9 - - + -
219A ALA* 1.3 78.1 - - - +
221A ARG* 1.3 61.3 + - - +
222A GLY* 3.6 20.6 - - - +
225A GLY 3.5 1.1 - - - +
226A GLY* 3.1 2.4 - - - -
227A LYS* 2.8 50.3 + - + +
229A HIS* 4.7 2.9 - - + +
250A VAL* 5.0 0.5 - - - +
261A PRO* 3.8 8.5 - - - +
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Residues in contact with ARG 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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177A VAL 5.0 1.4 - - - +
195A GLU* 4.9 0.3 - - - +
197A HIS* 3.1 20.9 + - - +
220A VAL* 1.3 76.0 - - - +
222A GLY* 1.3 60.2 + - - +
225A GLY* 3.5 4.3 - - - -
226A GLY 3.8 11.1 - - - +
252A PHE* 3.4 52.3 + - + +
253A PRO 4.8 1.2 + - - -
256A ALA 3.1 25.1 + - - -
257A GLN* 3.6 8.9 + - - +
259A ASP 2.9 29.6 + - - +
260A PHE* 4.3 5.4 - - + -
261A PRO* 3.8 9.6 - - + +
341B VAL 4.0 6.7 + - - -
342B LEU* 4.0 12.7 + - - +
343B GLN* 3.6 39.2 + - + +
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Residues in contact with GLY 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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195A GLU* 3.4 23.8 - - - -
220A VAL* 3.6 8.3 - - - +
221A ARG* 1.3 75.7 - - - +
223A GLN* 1.3 67.3 + - - +
224A ALA 3.3 2.9 - - - -
225A GLY 3.0 18.7 + - - -
343B GLN 3.4 12.3 - - - +
345B PRO* 4.0 3.0 - - - +
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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