Contacts of the strand formed by residues 138 - 154 (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 ILE 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.7 29.6 - - + -
81B LYS* 4.5 20.6 - - + +
95B LEU* 4.4 4.7 - - + -
98B ILE* 3.5 31.4 - - + -
133B LEU* 3.1 50.2 + - + +
134B ASP* 3.4 2.6 + - - +
136B HIS 3.4 6.8 - - - +
137B ASP* 1.3 84.8 - - - +
139B HIS* 1.3 62.1 + - - +
240B VAL* 3.9 29.2 - - + -
241B ALA 3.7 5.4 - - - +
242B GLY* 5.4 0.4 - - - -
243B THR* 3.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 4.5 7.6 + - - -
134B ASP* 2.7 32.6 + - - +
138B ILE* 1.3 74.3 - - - +
140B ILE* 1.3 85.9 + - - +
141B ILE* 3.4 6.9 + - + +
240B VAL* 3.2 6.1 - - - -
241B ALA 2.8 39.1 + - - +
243B THR* 3.8 13.0 - - + +
246B TRP* 3.3 52.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 4.0 15.0 - - + -
95B LEU* 4.8 1.6 - - + -
102B LEU* 4.8 4.7 - - + -
126B PHE* 3.8 24.7 - - + -
130B SER* 4.3 20.9 + - - +
133B LEU* 3.7 29.3 - - + +
134B ASP* 4.4 1.2 + - - -
138B ILE 4.2 0.8 + - - -
139B HIS* 1.3 91.5 + - - +
141B ILE* 1.3 63.2 + - - +
142B VAL 3.6 26.2 - - - +
143B PRO* 3.9 14.6 - - + -
238B PRO* 4.1 8.1 - - + -
239B PHE 3.8 4.0 - - - +
240B VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.3 13.5 - - + -
87B ILE* 3.9 20.9 - - + -
139B HIS* 4.0 15.0 - - + +
140B ILE* 1.3 76.2 - - - +
142B VAL* 1.3 62.2 + - + +
143B PRO* 4.4 2.4 - - - +
239B PHE 2.9 10.9 + - - +
240B VAL 4.2 2.7 - - - -
241B ALA* 3.8 24.0 - - + +
246B TRP* 3.4 50.9 - - + -
257B ILE* 4.1 13.9 - - + -
258B VAL* 4.2 20.3 - - + +
261B SER* 4.3 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.0 17.7 - - + -
140B ILE* 3.6 3.8 - - - +
141B ILE* 1.3 76.9 - - - +
143B PRO* 1.3 67.7 - - - +
144B ASP* 3.6 2.9 - - - +
145B VAL* 4.3 2.5 - - + -
237B SER 4.1 0.5 - - - +
238B PRO* 3.2 3.3 - - - +
239B PHE* 3.0 52.8 + - + +
261B SER* 3.5 19.1 - - - +
262B ARG* 3.7 14.1 - - - +
264B MET* 4.0 10.3 - - + -
265B VAL* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 2.7 34.9 + - - +
121B LEU* 3.5 31.4 - - + +
122B HIS* 4.5 7.4 - - + +
126B PHE* 3.6 23.3 - - + -
140B ILE* 3.9 5.4 - - + -
141B ILE 4.4 2.7 - - - +
142B VAL* 1.3 88.7 - - + +
144B ASP* 1.3 75.5 + - + +
237B SER 3.5 12.0 + - - +
262B ARG* 4.1 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 3.0 17.2 + - - +
121B LEU* 3.8 13.7 - - + -
122B HIS* 3.0 16.3 - - - -
142B VAL* 3.6 0.8 - - - +
143B PRO* 1.3 82.7 - - + +
145B VAL* 1.3 64.3 + - - +
146B ILE* 3.4 3.8 + - - +
236B MET* 3.1 26.6 - - + +
262B ARG* 2.8 44.4 + - - -
265B VAL* 3.6 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.7 29.8 - - + -
44B ALA* 5.7 2.9 - - + -
45B MET* 5.5 0.4 - - + -
142B VAL* 4.3 5.8 - - + -
144B ASP* 1.3 76.1 - - - +
146B ILE* 1.3 69.7 + - - +
147B TYR 3.3 1.0 + - - -
236B MET* 3.5 2.8 - - - -
237B SER* 2.8 42.8 + - - +
239B PHE* 3.7 23.1 - - + -
264B MET* 3.6 40.6 - - + -
265B VAL* 3.9 12.1 - - + +
268B GLY* 6.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.5 4.2 - - - +
114B PHE* 3.6 57.7 - - + +
144B ASP 3.4 3.1 + - - +
145B VAL* 1.3 79.8 - - - +
147B TYR* 1.3 61.6 + - - +
148B GLY 4.0 1.1 - - - +
235B HIS 4.1 2.5 - - - -
236B MET* 4.1 12.3 - - + -
265B VAL* 5.2 9.1 + - + +
268B GLY 5.2 2.4 - - - +
269B GLY* 3.9 28.0 - - - +
272B ILE* 3.8 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 5.8 0.2 - - - -
35B ASN* 3.0 37.4 + - - -
41B ILE* 3.8 24.7 - - + +
89B ILE* 4.0 11.4 - - + -
145B VAL 3.3 1.2 + - - -
146B ILE* 1.3 73.9 - - - +
148B GLY* 1.3 56.4 + - - +
150B ARG* 3.9 8.5 - - - -
193B LEU* 5.4 4.2 - - - +
210B ASN* 3.8 20.1 + - - -
211B PRO* 3.5 22.1 - - + +
213B VAL* 4.5 5.2 - - - +
214B VAL* 3.6 20.1 - - + +
235B HIS* 2.9 35.5 + + + +
237B SER* 3.4 26.7 - - - +
272B ILE* 3.9 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.6 12.8 - - - -
146B ILE* 3.6 4.7 - - - +
147B TYR* 1.3 80.9 - - - +
149B THR* 1.3 62.1 + - - -
150B ARG 3.6 0.3 + - - -
211B PRO* 3.7 6.5 - - - +
235B HIS* 2.8 31.5 + - - +
272B ILE* 4.5 2.5 - - - -
276B GLU* 3.1 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.8 5.2 - - - -
148B GLY* 1.3 71.3 - - - -
150B ARG* 1.3 62.5 + - - +
151B HIS* 3.5 24.6 - - + +
211B PRO* 3.2 17.1 - - - +
212B THR 4.3 0.2 + - - -
231B ALA* 3.6 29.6 - - + -
233B THR 3.4 7.4 - - - +
234B LYS* 2.8 42.6 + - - +
276B GLU* 2.8 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.9 12.7 - - - -
149B THR* 1.3 70.3 - - - +
151B HIS* 1.3 61.5 + - - +
170B ARG* 4.9 2.6 - - - +
172B GLN* 3.6 18.8 - - - +
177B PHE* 3.6 19.5 - - - -
209B GLU* 2.7 43.2 + - - +
210B ASN* 3.1 37.1 + - - +
211B PRO* 4.0 9.4 - - + -
231B ALA* 3.2 6.8 - - - -
232B HIS* 3.2 41.1 + - + +
233B THR* 2.9 24.9 + - - +
235B HIS* 3.2 42.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 3.5 42.5 + - + +
150B ARG* 1.3 72.4 - - - +
152B LEU* 1.3 61.7 + - - +
153B LEU 3.7 0.3 + - - -
209B GLU* 3.1 9.1 - - - -
210B ASN 3.0 31.0 + - - +
212B THR* 4.3 21.5 - - + +
215B LEU* 4.4 1.6 - - - +
227B LEU* 4.0 15.7 - - + -
228B ASN 3.6 7.6 - - - +
229B LEU* 3.3 36.3 - - + +
230B THR* 3.7 5.4 - - - -
231B ALA* 3.2 29.8 + - + -
232B HIS* 3.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 1.3 74.1 - - - +
153B LEU* 1.3 58.5 + - - +
154B THR* 4.3 7.0 - - + -
158B VAL* 4.0 24.7 - - + -
164B LEU* 4.1 22.0 - - + -
169B VAL* 4.1 18.6 - - + -
181B ILE* 4.3 12.8 - - + -
184B MET* 4.4 5.4 - - + -
208B LEU 3.5 11.7 - - - +
209B GLU* 4.1 10.8 - - + -
227B LEU* 3.5 7.7 - - - +
228B ASN* 2.9 46.1 + - - +
230B THR* 3.5 28.5 + - + +
232B HIS* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS 3.7 1.2 + - - -
152B LEU* 1.3 73.8 - - - +
154B THR* 1.3 61.2 + - - +
207B GLY* 3.0 3.6 - - - -
208B LEU* 2.9 42.7 + - + +
215B LEU* 3.9 30.7 - - + -
220B PHE* 3.6 33.0 - - + +
221B PHE* 4.1 2.0 - - - +
224B ALA* 3.4 36.1 - - + +
226B ASN 3.3 20.6 - - - +
227B LEU* 3.8 17.9 - - + +
283B LEU* 5.4 3.1 - - + -
288B VAL* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.3 14.1 - - + -
153B LEU* 1.3 84.5 - - - +
155B LYS* 1.3 62.4 + - - +
156B LYS 2.6 25.1 + - - -
158B VAL* 3.9 4.1 - - + +
164B LEU* 5.1 0.2 - - + -
167B MET* 3.8 26.0 - - - -
169B VAL* 5.2 2.2 - - + -
206B ASP 3.5 7.9 - - - -
207B GLY* 4.0 6.5 - - - -
208B LEU 4.8 0.7 - - - +
224B ALA* 3.9 6.5 - - - -
225B LYS 3.4 3.5 + - - -
226B ASN* 2.8 32.8 + - - +
228B ASN* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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