Contacts of the helix formed by residues 138 - 152 (chain B) in PDB entry 4OGB
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 PRO 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS 3.4 10.3 - - - +
137B ILE* 1.3 88.2 - - + +
139B VAL* 1.3 60.1 + - - +
140B ASP* 3.2 18.8 - - - +
141B THR* 3.0 19.3 + - + +
142B LEU* 2.9 24.1 + - - +
247B ASP 5.6 0.4 - - - +
248B ILE 5.7 0.7 - - - +
250B GLN* 4.0 16.8 - - + +
251B ASN* 4.1 9.4 - - - +
511B EDO 4.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 4.5 8.1 - - + -
127B GLN* 4.0 20.2 - - - +
132B LEU* 3.6 28.0 - - + -
133B LYS* 6.2 2.7 - - - +
137B ILE 3.3 1.7 + - - +
138B PRO* 1.3 71.7 - - - +
140B ASP* 1.3 62.1 + - + +
142B LEU* 3.8 1.8 - - - +
143B ILE* 3.0 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 3.2 11.8 - - - +
139B VAL* 1.3 84.4 + - + +
141B THR* 1.3 60.1 + - - +
143B ILE* 3.9 4.8 - - - +
144B THR* 2.7 38.0 + - - +
245B ASN* 3.0 15.2 + - - +
511B EDO 2.7 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 3.0 30.2 + - + +
140B ASP* 1.3 78.7 + - - +
142B LEU* 1.3 64.4 + - - +
145B TYR* 3.0 22.7 + - - +
245B ASN* 2.6 44.1 + - - +
246B CYS 3.9 0.7 - - - -
247B ASP 3.3 35.0 - - - +
248B ILE* 4.1 4.7 - - + +
250B GLN* 3.8 7.0 + - - +
511B EDO 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 4.0 18.4 - - - +
126B PHE* 3.9 45.5 - - + -
132B LEU* 3.6 23.3 - - + -
137B ILE* 3.9 10.5 - - + -
138B PRO 2.9 14.7 + - - +
139B VAL 3.8 4.9 - - - +
141B THR* 1.3 77.2 - - - +
143B ILE* 1.3 57.9 + - - +
145B TYR* 3.3 2.4 + - - +
146B LEU* 2.9 58.2 + - + +
248B ILE* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 4.1 18.6 - - + -
123B HIS* 3.8 39.5 - - + +
139B VAL* 3.0 22.8 + - + +
140B ASP* 4.0 5.6 - - - +
142B LEU* 1.3 76.8 - - + +
144B THR* 1.3 56.9 + - - +
146B LEU* 4.5 4.7 - - + -
147B MET* 3.0 53.6 + - + +
349D GLU 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP* 2.7 21.6 + - - +
143B ILE* 1.3 77.7 - - - +
145B TYR* 1.3 60.0 + - - +
147B MET* 3.8 11.3 - - - +
148B THR* 2.9 29.8 + - - -
244B GLU 3.3 25.8 - - - +
245B ASN* 3.3 23.7 + - + +
246B CYS* 3.8 5.8 - - - -
349D GLU 5.4 0.2 + - - -
350D ARG* 4.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 6.1 0.9 - - + -
141B THR 3.0 15.3 + - - +
142B LEU 3.7 2.9 - - - +
144B THR* 1.3 73.4 - - - +
146B LEU* 1.3 71.6 + - + +
148B THR* 2.9 4.0 + - - -
149B LEU* 2.7 61.1 + - + +
195B PHE* 3.3 29.3 - + - -
199B ILE* 3.5 9.4 - - - +
237B GLY 2.8 20.4 + - - -
240B LEU* 3.8 17.9 - - + -
241B LEU* 3.5 30.3 - - + -
246B CYS* 3.2 36.5 - - - +
248B ILE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.6 3.8 - - + +
119B THR* 3.4 43.9 + - + +
122B MET* 3.6 44.4 - - + -
123B HIS* 3.8 9.2 - - + +
142B LEU* 2.9 50.4 + - + +
143B ILE* 4.0 2.2 - - + +
145B TYR* 1.3 86.3 - - + +
147B MET* 1.3 58.3 + - - +
149B LEU* 3.7 7.5 - - + +
150B GLU* 2.9 32.1 + - - +
248B ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.0 33.1 + - - +
119B THR* 3.5 15.9 - - + +
143B ILE* 3.0 35.6 + - + +
144B THR* 3.8 14.6 - - - +
146B LEU* 1.3 74.5 - - - +
148B THR* 1.3 59.5 + - - +
151B ASP* 2.7 33.2 + - - +
349D GLU* 3.3 57.7 - - + +
350D ARG* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR 2.9 16.7 + - - -
145B TYR* 2.9 10.2 + - + -
147B MET* 1.3 73.6 - - - +
149B LEU* 1.3 67.2 + - - +
151B ASP* 2.8 13.8 + - - +
152B HIS* 3.1 22.3 + - + +
240B LEU* 4.0 27.6 - - + +
243B GLU* 3.8 22.2 + - - +
246B CYS* 3.6 17.1 - - - -
350D ARG* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 13.9 - - + -
145B TYR* 2.7 47.7 + - + +
146B LEU* 3.7 9.4 - - + +
148B THR* 1.3 71.1 - - - +
150B GLU* 1.3 64.2 + - - +
152B HIS* 2.9 15.6 + - - +
153B TYR* 3.5 14.6 - - + -
198B ALA* 3.6 34.1 - - + +
199B ILE* 3.7 23.8 - - + -
202B VAL* 3.9 25.8 - - + +
237B GLY* 4.5 2.7 - - - -
240B LEU* 4.0 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN 3.9 1.8 - - - +
116B ARG* 3.2 38.5 + - - +
117B PRO* 3.1 5.7 - - - +
118B LEU* 2.8 42.8 + - + +
119B THR* 2.6 28.1 + - - -
146B LEU 2.9 13.4 + - - +
149B LEU* 1.3 76.3 - - - +
151B ASP* 1.3 60.9 + - - +
153B TYR* 3.2 22.8 + - - +
162B ASN* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 2.9 26.8 + - - -
147B MET 2.7 23.6 + - - +
148B THR 2.8 10.3 + - - +
150B GLU* 1.3 75.3 - - - +
152B HIS* 1.3 60.4 + - - +
153B TYR 3.3 8.1 + - - +
346D ARG* 3.3 45.0 + - - +
350D ARG* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 3.1 21.9 + - + -
149B LEU 2.9 12.2 + - - +
151B ASP* 1.3 78.1 - - - +
153B TYR* 1.3 59.6 + - - +
154B HIS* 3.9 4.4 - - - -
202B VAL* 3.7 7.6 - - + -
203B ASP* 2.8 34.8 + - + +
236B VAL* 4.4 9.4 - - + -
240B LEU* 3.5 43.2 - - + +
243B GLU* 4.3 10.3 + - - -
346D ARG* 4.7 13.5 - - - -
350D ARG* 6.0 0.2 - - - -
----------------------------------------------------------
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