Contacts of the strand formed by residues 226 - 242 (chain B) in PDB entry 4O8M
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.3 7.0 - - - -
154B THR* 2.8 37.4 + - - +
155B LYS 3.0 27.3 + - - -
156B LYS* 3.5 12.7 - - - +
157B PRO* 3.6 22.2 - - - +
224B ALA 3.7 0.6 - - - -
225B LYS* 1.3 82.9 + - - +
227B LEU* 1.3 60.5 + - - +
228B ASN* 3.4 10.5 + - - +
289B THR* 3.5 14.2 - - - +
291B ASN* 3.1 24.0 + - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 4.0 11.7 - - + -
152B LEU 3.5 11.9 - - - +
153B LEU* 3.9 5.6 - - + -
212B THR* 4.0 12.3 - - + -
215B LEU* 3.5 31.9 - - + -
226B ASN* 1.3 70.9 - - - +
228B ASN* 1.3 58.8 + - - +
229B LEU* 3.9 16.5 + - + -
280B LEU* 3.3 34.3 - - + -
283B LEU* 4.1 10.5 - - + -
288B VAL* 3.6 17.9 - - + +
289B THR 2.8 9.9 + - - +
290B VAL* 3.4 9.4 - - + +
291B ASN 2.8 27.9 + - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.6 2.6 - - - +
152B LEU* 2.9 47.7 + - + +
154B THR* 2.8 27.3 + - - +
158B VAL* 3.1 44.3 + - + +
226B ASN* 3.4 8.5 + - - +
227B LEU* 1.3 71.8 - - - +
229B LEU* 1.3 52.0 + - - +
230B THR* 2.8 18.9 + - - -
291B ASN* 2.8 35.5 + - - -
293B VAL* 4.0 4.9 - - + -
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.3 31.9 - - + +
227B LEU* 3.9 27.6 - - + -
228B ASN* 1.3 66.1 - - - +
230B THR* 1.3 61.7 + - - +
231B ALA* 3.3 6.4 + - - +
280B LEU* 4.5 10.5 - - + -
290B VAL* 3.5 26.2 - - + -
291B ASN 3.0 14.1 + - - +
292B ASP* 3.9 22.4 - - - +
293B VAL* 3.7 16.2 + - - +
295B LEU* 3.7 8.8 - - - +
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 2.8 27.3 + - - -
151B HIS* 3.6 0.4 + - - -
152B LEU* 3.5 36.3 + - + +
184B MET* 3.9 11.9 - - + -
228B ASN 2.8 9.1 + - - +
229B LEU* 1.3 70.0 - - - +
231B ALA* 1.3 71.9 + - - +
232B HIS* 2.8 32.2 + - - -
293B VAL* 3.9 22.2 - - + -
295B LEU* 3.3 5.5 - - - +
298B PHE* 4.0 13.9 - - + -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.6 10.7 - - + -
112B GLN* 4.8 12.2 + - - +
149B THR* 3.6 24.4 - - + +
150B ARG 3.2 10.5 + - - -
151B HIS* 3.2 16.6 + - + -
229B LEU 4.1 4.3 - - - +
230B THR* 1.3 80.1 + - - +
232B HIS* 1.3 62.4 + - - +
233B THR 3.3 4.6 + - - -
234B LYS* 4.9 9.6 - - - +
295B LEU* 5.0 5.8 - - + -
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 3.2 12.6 - - + +
109B TYR* 2.9 57.1 + - + +
150B ARG* 3.2 22.0 + - + +
151B HIS 3.9 1.3 - - - -
152B LEU* 4.1 5.8 - - + -
177B PHE* 5.3 3.1 - + - -
180B THR* 5.0 8.3 - - + -
181B ILE* 5.3 2.3 - - + +
184B MET* 4.2 20.9 - - + +
209B GLU* 2.9 45.3 + - + +
230B THR* 2.8 27.9 + - - -
231B ALA* 1.3 77.1 - - - +
233B THR* 1.3 80.9 + - - +
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Residues in contact with THR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 3.4 44.6 + - + +
107B ALA 5.3 1.6 - - - -
108B PRO* 4.6 2.6 - - - +
109B TYR 5.2 0.2 - - - +
117B LYS* 4.7 0.7 - - - +
148B GLY 3.6 0.2 - - - +
149B THR* 3.4 2.9 - - - +
150B ARG* 2.9 43.4 + - - +
177B PHE* 3.7 9.8 - - + -
180B THR* 5.9 0.7 - - - +
231B ALA 4.7 2.0 - - - -
232B HIS* 1.3 95.9 + - - +
234B LYS* 1.3 63.3 + - - +
235B HIS* 3.4 27.5 + - + +
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Residues in contact with LYS 234 (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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106B ASN* 3.4 0.3 - - - +
111B SER 3.4 25.6 + - - +
112B GLN* 3.8 44.6 + - - +
114B PHE* 3.5 30.4 - - + +
117B LYS* 2.9 33.8 + - + +
148B GLY 4.0 0.9 - - - -
149B THR* 2.8 42.3 + - - +
231B ALA* 4.9 8.3 + - - +
232B HIS 4.4 0.2 - - - -
233B THR* 1.3 70.3 - - - +
235B HIS* 1.3 61.6 + - - +
236B MET 3.4 1.2 + - - -
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Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER 5.2 1.4 + - - -
91B ASP* 3.2 29.5 + - - +
106B ASN* 3.6 11.0 + - - -
114B PHE* 3.5 4.8 - - - -
146B ILE 3.9 0.2 - - - -
147B TYR* 2.9 42.2 + + + +
148B GLY 2.8 22.5 + - - +
150B ARG* 3.2 41.7 + - + -
172B GLN* 5.1 1.8 - - - -
177B PHE* 3.7 15.3 - + - -
233B THR* 3.7 8.2 - - + +
234B LYS* 1.3 71.2 - - - +
236B MET* 1.3 68.5 + - - +
237B SER* 3.4 25.8 + - - -
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Residues in contact with MET 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 5.2 0.2 - - - +
92B TYR* 3.7 9.0 - - + -
105B ILE* 4.5 5.4 - - + -
106B ASN* 3.0 28.0 + - - +
114B PHE* 3.7 38.4 - - - +
117B LYS* 3.7 35.4 - - + -
118B SER* 4.6 3.6 - - - +
121B LEU* 3.9 19.5 - - + -
143B PRO 4.6 0.9 - - - +
144B ASP* 3.1 45.1 - - + +
145B VAL 3.5 4.5 - - - +
146B ILE* 4.1 11.0 - - + -
235B HIS* 1.3 77.9 + - - +
237B SER* 1.3 60.8 + - - +
238B PRO* 4.1 0.5 - - - +
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.0 22.7 - - - +
90B SER 4.6 1.5 + - - -
143B PRO 3.5 7.7 - - - +
145B VAL* 2.8 47.6 + - - +
147B TYR* 3.4 20.3 - - - +
235B HIS* 3.4 21.1 + - - -
236B MET* 1.3 72.2 - - - +
238B PRO* 1.4 65.3 - - - +
239B PHE* 4.7 1.1 - - - -
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Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.6 4.9 - - - +
90B SER* 3.0 54.8 + - - +
91B ASP* 4.0 5.8 - - - +
92B TYR* 3.5 45.8 - - + +
95B LEU* 4.2 7.4 - - + -
140B ILE* 4.1 11.9 - - + -
142B VAL 3.2 10.8 - - - +
143B PRO 4.0 0.2 - - - -
236B MET 4.1 0.4 - - - +
237B SER* 1.4 85.2 - - - +
239B PHE* 1.3 62.2 + - - +
240B VAL* 4.2 5.8 - - + -
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Residues in contact with PHE 239 (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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31B VAL* 4.8 2.9 - - + -
32B ALA 4.5 5.4 - - - -
33B TYR* 4.8 2.0 - - + -
41B ILE* 4.3 9.0 - - + -
45B MET* 3.4 36.6 - - + -
48B TRP* 4.2 14.6 - + + -
87B ILE* 4.1 15.3 - - + -
88B THR* 3.4 6.5 - - - -
89B ILE* 3.6 51.6 - - + -
140B ILE* 3.8 0.3 - - - -
141B ILE* 2.9 27.4 + - - +
142B VAL* 3.0 25.3 + - + +
145B VAL* 3.7 37.5 - - + -
237B SER* 4.7 0.4 - - - -
238B PRO* 1.3 75.5 - - - +
240B VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.5 31.9 - - + -
80B ALA* 5.8 0.4 - - + -
87B ILE* 3.3 5.2 - - - +
88B THR* 2.9 46.4 + - + +
90B SER* 4.1 16.6 - - - -
95B LEU* 4.8 2.7 - - + -
138B ILE* 3.9 13.7 - - + -
139B HIS 3.2 10.3 - - - +
140B ILE* 3.9 25.4 - - + -
141B ILE* 4.2 4.9 - - - +
238B PRO* 4.2 7.0 - - + -
239B PHE* 1.3 82.4 - - - +
241B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 6.4 0.2 - - - -
80B ALA* 4.5 4.9 - - - -
86B ILE 3.4 20.0 - - - +
87B ILE* 4.4 2.5 - - + -
138B ILE* 3.7 4.5 - - - +
139B HIS* 2.8 31.6 + - - +
141B ILE* 3.8 19.2 - - + +
240B VAL* 1.3 76.3 - - - +
242B GLY* 1.3 67.6 + - - +
245B PHE* 4.3 14.8 - - + -
246B TRP* 4.5 8.3 - - + -
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Residues in contact with GLY 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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80B ALA* 3.3 35.4 + - - +
81B LYS* 4.2 2.7 - - - -
84B ALA 5.4 0.2 + - - -
86B ILE 4.6 0.6 + - - -
137B ASP 3.4 11.4 - - - -
138B ILE* 4.6 1.3 - - - -
241B ALA* 1.3 75.3 - - - +
243B THR* 1.3 60.3 + - - -
244B ALA* 3.2 3.4 - - - -
245B PHE* 3.2 7.4 + - - +
246B TRP* 2.9 26.9 + - - +
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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
------------------------------------------------------------
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