Contacts of the strand formed by residues 236 - 248 (chain B) in PDB entry 4YZS
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 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 4.0 15.7 - - + -
128B TRP* 3.6 33.4 - - + -
203B TYR 3.5 1.2 - - - +
205B LEU* 2.6 47.5 + - + +
207B ALA* 3.6 21.1 - - + -
235B ILE* 1.3 77.9 - - - +
237B LEU* 1.3 59.2 + - - +
238B LEU* 5.8 2.0 - - + -
266B LEU* 3.6 32.1 - - + -
267B ARG 3.9 0.9 - - - +
268B TYR* 3.6 30.5 - - + -
345B LEU* 3.8 13.7 - - + -
350B VAL* 5.8 0.4 - - + -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 3.6 31.9 - - + -
250A PRO* 3.8 19.5 - - + +
202B THR* 4.3 16.6 - - + -
203B TYR 3.8 2.2 - - - +
204B GLY* 4.8 5.4 - - - -
214B TYR* 4.1 5.8 - - + +
235B ILE* 4.7 3.6 - - - +
236B LEU* 1.3 77.1 - - - +
238B LEU* 1.3 59.4 + - - +
239B GLN 4.2 0.4 - - - -
265B GLU 4.0 0.2 - - - +
266B LEU* 3.1 9.7 - - - +
267B ARG* 2.7 59.0 + - + +
269B ILE* 3.8 30.7 - - + -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.9 4.7 - - + -
115B ILE* 3.6 43.1 - - + -
128B TRP* 5.3 3.4 - - + -
130B LEU* 3.7 22.7 - - + -
202B THR* 4.3 2.5 - - - +
203B TYR* 2.8 55.9 + - + +
205B LEU* 4.9 8.3 - - + -
236B LEU* 4.9 1.3 - - + +
237B LEU* 1.3 74.2 - - - +
239B GLN* 1.3 56.7 + - - +
264B PHE* 3.5 30.3 - - + -
265B GLU 3.7 2.7 - - - +
266B LEU* 3.8 28.5 - - + -
343B TRP* 5.2 1.3 - - + -
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 5.8 5.5 - - - -
194A LEU 3.8 13.2 - - - +
200B LEU* 3.3 30.6 - - - +
201B THR 3.4 12.1 - - - +
202B THR* 3.9 15.5 + - + +
237B LEU 4.2 0.4 - - - -
238B LEU* 1.3 72.0 - - - +
240B ARG* 1.3 70.4 + - - +
241B THR* 3.9 12.1 + - - +
263B HIS 3.7 0.9 - - - +
264B PHE* 3.1 6.6 - - - -
265B GLU* 2.8 70.5 + - + +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY* 3.6 24.5 + - - -
134B SER* 2.8 47.6 + - - -
135B GLY 4.1 0.4 + - - -
136B SER 3.1 27.7 + - - -
137B LEU* 3.7 14.9 - - - +
199B SER* 3.7 1.7 + - - +
200B LEU* 3.7 2.8 - - - -
201B THR* 2.9 36.5 + - + +
203B TYR* 4.4 11.4 - - + +
238B LEU 3.9 2.0 + - - -
239B GLN* 1.3 72.2 - - - +
241B THR* 1.3 71.2 + - - +
242B GLN* 2.9 30.3 + - + +
263B HIS 3.5 6.1 - - - -
264B PHE* 3.4 35.1 - - + -
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Residues in contact with THR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LYS* 4.3 14.4 - - + -
199B SER 3.3 10.5 - - - +
200B LEU* 4.0 18.9 - - + +
239B GLN* 3.9 19.1 + - - +
240B ARG* 1.3 77.1 - - - +
242B GLN* 1.3 66.5 + - - +
243B LYS* 3.3 22.9 - - - +
262B GLY* 3.1 23.9 - - - -
263B HIS* 3.0 35.0 + - + -
265B GLU* 5.1 0.9 + - - +
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Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B SER 4.8 7.3 + - - +
136B SER 4.3 6.1 + - - -
197B GLY 3.5 1.9 - - - +
198B LYS* 3.2 4.9 - - - -
199B SER* 2.9 50.1 + - - +
240B ARG* 2.9 44.5 + - + +
241B THR* 1.3 73.7 - - - +
243B LYS* 1.3 62.7 + - - +
244B THR* 4.2 10.8 - - - +
260B SER* 3.2 24.2 + - - -
261B VAL 3.5 15.5 + - - -
262B GLY* 3.4 6.1 - - - +
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ASP 3.1 26.2 + - - -
160B GLY* 4.4 2.5 - - - -
178B THR* 5.8 0.7 - - + -
179B VAL* 3.6 22.6 - - + +
180B GLU* 3.2 40.9 + - + +
183B LEU* 6.2 0.7 - - + -
197B GLY 3.5 4.3 - - - +
198B LYS* 4.2 13.0 - - + +
241B THR* 3.3 26.7 + - - +
242B GLN* 1.3 75.4 - - - +
244B THR* 1.3 61.2 + - - +
260B SER* 3.1 4.2 + - - -
261B VAL* 2.8 53.0 + - + -
263B HIS* 3.7 20.3 + - - -
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA* 3.7 34.3 + - + +
179B VAL* 3.8 3.7 - - - +
183B LEU* 3.8 4.5 - - - +
196B GLY* 3.2 1.6 - - - -
197B GLY 2.8 37.7 + - - +
242B GLN* 4.2 9.9 - - - +
243B LYS* 1.3 74.4 - - - +
245B VAL* 1.3 64.1 + - - +
246B ARG* 4.2 15.7 - - + +
258B ASN* 4.9 3.4 - - - +
259B PHE 3.4 7.9 - - - +
260B SER* 2.6 25.9 + - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B VAL* 3.6 34.1 - - + +
182B LEU* 4.0 33.9 - - + -
183B LEU* 4.2 6.5 - - + -
194B LEU* 4.3 15.9 - - + -
195B VAL 3.4 8.5 - - - +
244B THR* 1.3 75.2 - - - +
246B ARG* 1.3 64.3 + - - +
257B TRP* 4.1 10.6 - - + -
258B ASN* 3.1 4.5 - - - +
259B PHE* 2.9 47.1 + - + +
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER 3.6 15.7 - - - -
218A ALA* 2.6 30.6 + - - +
219A LEU 3.7 4.6 + - - -
220A GLY* 3.7 16.3 - - - +
221A CYS* 5.4 2.5 - - - +
193B VAL 3.5 1.6 - - - +
194B LEU* 3.6 0.4 - - - -
195B VAL* 2.6 53.5 + - + +
244B THR* 4.2 10.5 - - + +
245B VAL* 1.3 76.6 - - - +
247B ALA* 1.3 62.4 + - - +
248B VAL* 4.6 5.8 - - + -
255B GLU* 3.6 18.8 + - + +
257B TRP 3.5 6.7 - - - +
258B ASN* 3.6 19.1 - - + +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B VAL* 4.9 6.7 - - + -
193B VAL 3.6 5.4 - - - +
194B LEU* 3.7 12.8 - - + -
246B ARG* 1.3 69.4 - - - +
248B VAL* 1.3 55.0 + - - +
255B GLU* 3.3 3.6 - - - -
256B LYS* 2.5 45.1 + - + -
257B TRP* 2.8 52.3 + - + -
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A THR* 4.8 0.7 - - - +
214A TYR* 4.8 8.5 - - + -
216A CYS* 4.1 10.3 - - + -
221A CYS* 3.4 31.6 - - - -
192B VAL* 3.5 3.6 - - - -
193B VAL* 2.6 64.7 + - + +
195B VAL* 4.3 12.6 - - + -
246B ARG* 4.0 11.9 - - + +
247B ALA* 1.3 78.3 - - - +
249B GLY* 1.3 58.4 + - - +
250B PRO* 3.4 2.6 - - + +
252B SER 4.3 14.1 - - - +
255B GLU* 4.2 10.3 - - - +
256B LYS 4.2 2.7 - - - +
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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