Contacts of the strand formed by residues 213 - 223 (chain A) in PDB entry 2YTZ
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 LEU 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.7 26.9 - - - +
151A LEU* 4.3 6.5 - - + +
156A ARG* 3.4 46.2 - - + +
205A ALA 4.9 1.2 - - - +
208A ALA* 3.3 33.1 + - + +
209A ALA* 3.4 8.5 + - - +
211A TYR* 3.2 26.2 - - + +
212A ASP* 1.3 76.0 - - - +
214A GLY* 1.3 62.9 + - - +
233A LEU* 4.4 16.6 - - + -
234A LYS 3.1 20.2 - - - +
235A ASP* 3.7 3.8 - - - -
236A GLY 4.4 0.2 - - - -
240A GLY* 3.7 8.9 - - - -
243A THR* 5.2 0.2 - - - -
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Residues in contact with GLY 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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205A ALA 5.9 0.2 - - - -
208A ALA* 5.3 0.2 - - - -
213A LEU* 1.3 76.0 - - - +
215A ILE* 1.3 71.8 + - - +
233A LEU* 3.5 5.7 - - - +
234A LYS* 2.9 33.0 + - - +
239A LYS 3.8 10.3 - - - -
240A GLY* 3.9 3.2 - - - +
243A THR* 3.0 21.3 - - - -
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Residues in contact with ILE 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 VAL* 3.8 32.8 - - + +
204A ILE* 4.8 3.8 - - + -
205A ALA* 4.0 21.3 - - + +
208A ALA* 4.4 13.0 - - + -
214A GLY* 1.3 81.4 - - - +
216A ASP* 1.3 69.9 + - - +
217A VAL* 4.2 5.8 - - + -
231A VAL* 4.0 25.1 - - + -
232A LYS 3.2 8.5 - - - +
233A LEU* 3.9 18.6 - - + -
234A LYS* 4.1 3.4 - - - +
243A THR* 3.0 25.5 + - + -
277A TRP* 4.0 15.2 - - + -
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Residues in contact with ASP 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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215A ILE* 1.3 80.3 - - - +
217A VAL* 1.3 65.3 + - - +
218A ILE* 3.2 2.9 + - + +
231A VAL* 3.4 2.8 - - - -
232A LYS* 2.8 41.1 + - + +
234A LYS* 2.9 36.4 + - - +
246A LYS* 5.9 0.9 + - - -
277A TRP* 5.6 0.9 - - - -
283A ASP* 5.8 3.8 - - - +
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Residues in contact with VAL 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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201A VAL* 3.6 22.7 - - + -
215A ILE* 4.2 4.9 - - + -
216A ASP* 1.3 72.0 - - - +
218A ILE* 1.3 62.0 + - - +
219A LEU 3.9 4.5 - - - +
220A ALA* 3.8 20.6 - - + -
230A PHE 3.8 5.8 - - - +
231A VAL* 4.3 4.3 - - + -
277A TRP* 3.5 22.7 - - + +
280A PRO* 3.5 24.0 - - + +
281A LEU* 3.5 28.7 - - - +
282A LYS 3.5 16.1 - - - +
283A ASP* 3.6 4.3 + - - +
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Residues in contact with ILE 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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42A LEU* 3.7 29.6 - - + -
46A LEU* 3.5 25.4 - - + -
159A ILE* 3.9 19.7 - - + -
216A ASP* 4.0 9.9 - - + +
217A VAL* 1.3 73.8 - - - +
219A LEU* 1.3 66.7 + - + +
230A PHE* 2.8 14.7 + - + +
231A VAL 4.0 1.6 - - - -
232A LYS* 3.9 24.9 - - + +
282A LYS* 3.4 1.8 - - - +
283A ASP* 2.9 29.5 + - + +
286A ILE* 4.0 27.8 - - + -
287A VAL* 4.0 5.0 - - - +
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Residues in contact with LEU 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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38A ILE* 4.0 26.5 - - + -
42A LEU* 5.6 1.1 - - + -
217A VAL* 3.4 1.3 - - - -
218A ILE* 1.3 87.2 - - + +
220A ALA* 1.3 67.2 + - - +
221A TYR* 3.9 16.8 - - + -
229A ALA 3.7 0.2 - - - -
230A PHE* 2.7 48.3 + - + +
281A LEU 3.7 6.1 - - - -
282A LYS* 4.5 3.1 - - + -
287A VAL* 3.9 14.4 - - + -
290A MET* 4.1 20.0 - - + -
309A LEU* 4.8 6.5 - - + -
312A ILE* 3.8 38.6 - - + -
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Residues in contact with ALA 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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197A THR* 3.9 18.6 - - + +
201A VAL* 4.0 14.8 - - + -
217A VAL* 3.8 17.7 - - + -
219A LEU* 1.3 81.2 - - - +
221A TYR* 1.3 65.6 + - - +
228A ARG 3.1 12.8 - - - +
229A ALA* 4.2 2.5 - - - -
281A LEU* 3.0 28.4 + - + +
312A ILE* 5.4 1.2 - - - +
356A HIS* 4.3 4.7 + - - -
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Residues in contact with TYR 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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35A ASN* 4.4 4.9 + - - -
38A ILE* 3.8 27.3 - - + +
197A THR* 4.0 11.4 + - - +
219A LEU* 3.9 28.5 - - + -
220A ALA* 1.3 79.3 - - - +
222A TYR* 1.3 71.7 + - - +
223A LYS* 3.8 19.1 - - + -
226A TYR* 4.1 14.6 + + - +
227A PHE* 3.7 2.1 - - - -
228A ARG* 2.9 65.4 + - + +
230A PHE* 4.4 3.8 - + - -
308A LEU* 3.8 21.3 - - + -
312A ILE* 3.6 15.3 - - + -
356A HIS* 3.3 21.1 - - + +
357A PHE* 4.6 0.2 - - - -
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Residues in contact with TYR 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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171A CYS* 5.6 0.4 - - - -
193A HIS* 3.4 52.8 + + + +
197A THR* 3.9 12.6 - - - +
221A TYR* 1.3 78.3 - - - +
223A LYS* 1.3 72.3 + - - +
224A ASP 4.6 1.3 - - - -
225A HIS* 3.0 58.7 + - - -
226A TYR 3.2 20.6 - - - -
227A PHE* 3.8 25.4 - + + +
308A LEU* 5.0 1.7 - - - +
356A HIS* 3.2 23.5 + - - +
357A PHE* 3.9 20.8 - + + -
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Residues in contact with LYS 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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31A ARG* 4.7 5.6 - - - +
34A LEU* 3.6 23.4 - - + +
221A TYR* 3.8 17.2 - - + -
222A TYR* 1.3 88.2 - - - +
224A ASP* 1.3 100.9 + - - +
225A HIS 3.1 2.0 - - - -
226A TYR* 2.9 41.3 + - + +
304A GLN* 5.0 5.3 + - - +
307A LYS* 5.1 10.7 - - - +
308A LEU* 4.5 20.6 - - + +
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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