Contacts of the helix formed by residues 116 - 129 (chain D) 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 ARG 116 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG* 4.6 2.2 - - - +
349B GLU* 2.6 43.6 + - - +
113D SER* 3.0 28.8 + - - +
114D GLY 3.3 4.9 - - - +
115D ASN* 1.3 81.4 + - - +
117D PRO* 1.3 65.5 - - - +
118D LEU 3.2 2.2 - - - -
119D THR* 3.4 20.1 + - + -
120D VAL* 3.1 26.1 + - + +
147D MET* 3.7 22.3 + - - +
150D GLU* 3.3 44.3 + - - +
151D ASP* 2.9 28.9 + - - -
508D DMS 4.0 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D VAL* 4.5 5.6 - - + +
109D ILE* 4.2 12.8 - - + -
110D ALA* 3.8 31.2 - - + +
113D SER* 3.4 4.9 - - - +
115D ASN* 3.2 11.4 - - - +
116D ARG* 1.3 89.0 - - - +
118D LEU* 1.3 56.6 + - - +
121D ILE* 2.9 39.1 + - + +
150D GLU* 3.1 10.8 - - - +
162D ASN* 3.5 13.0 - - - +
163D ILE* 4.0 17.0 - - + -
166D ALA* 3.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PRO* 1.3 75.1 - - - +
119D THR* 1.3 67.6 + - - +
122D MET* 2.9 49.6 + - + +
146D LEU* 4.9 2.9 - - + +
149D LEU* 4.0 20.0 - - + -
150D GLU* 3.0 34.3 + - + +
153D TYR* 3.9 29.4 - - + -
162D ASN 4.0 8.3 - - - +
165D ALA* 4.0 5.4 - - + -
166D ALA* 3.7 26.5 - - - +
169D VAL* 4.0 11.9 - - + -
198D ALA* 4.1 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG* 3.7 15.3 - - + -
117D PRO 3.4 0.2 - - - -
118D LEU* 1.3 77.3 - - - +
120D VAL* 1.3 58.5 + - + +
123D HIS* 2.9 29.5 + - + +
143D ILE* 4.6 7.2 - - + -
146D LEU* 3.4 44.3 + - + +
147D MET* 3.5 20.7 + - + -
150D GLU* 2.7 23.0 + - - -
505D EDO 4.5 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 4.2 15.0 - - + -
96D LEU* 3.8 20.0 - - + -
109D ILE* 3.7 29.6 - - + -
113D SER* 4.1 15.3 - - - -
116D ARG* 3.1 17.3 + - + +
117D PRO 4.1 0.2 - - - +
119D THR* 1.3 79.2 - - + +
121D ILE* 1.3 60.0 + - - +
123D HIS* 3.4 2.9 + - - +
124D THR* 2.9 32.4 + - - -
505D EDO 3.3 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.0 19.7 - - + -
99D VAL* 4.7 3.8 - - + -
104D LEU* 3.9 18.4 - - + -
106D VAL* 3.8 28.3 - - + -
109D ILE* 4.1 12.3 - - + -
117D PRO 2.9 22.2 + - - +
118D LEU* 4.4 0.7 - - - +
120D VAL* 1.3 74.4 - - - +
122D MET* 1.3 65.3 + - + +
124D THR* 3.4 5.5 + - - -
125D ILE* 2.9 43.1 + - + +
166D ALA* 3.9 17.3 - - + +
169D VAL* 4.5 4.3 - - + -
170D GLN* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 2.9 39.1 + - + +
121D ILE* 1.3 75.8 - - - +
123D HIS* 1.3 58.9 + - - +
125D ILE* 3.3 3.2 + - - -
126D PHE* 2.8 60.8 + - + -
142D LEU* 5.6 0.2 - - + -
145D TYR* 6.0 0.7 - - + -
146D LEU* 3.6 31.6 - - + -
149D LEU* 5.5 0.4 - - + -
169D VAL* 3.5 24.7 - - + -
194D ILE* 3.6 17.7 - - + +
195D PHE* 4.7 9.6 - - + -
198D ALA* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D THR 2.9 19.5 + - - +
120D VAL* 3.8 3.8 - - - +
121D ILE 3.3 0.2 - - - -
122D MET* 1.3 77.3 - - - +
124D THR* 1.3 58.4 + - - +
126D PHE* 3.2 0.5 + - - -
127D GLN* 2.8 64.0 + - + +
139D VAL* 3.7 10.3 - - + +
142D LEU* 4.1 19.1 - - + -
143D ILE* 4.0 23.2 - - + +
146D LEU* 4.0 8.7 - - + +
505D EDO 3.2 36.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.8 30.7 - - + +
99D VAL* 3.9 30.5 - - + -
120D VAL 2.9 18.9 + - - -
121D ILE* 3.8 6.7 - - - -
123D HIS* 1.3 75.6 - - - +
125D ILE* 1.3 59.1 + - - +
127D GLN* 3.3 6.1 + - - +
128D GLU* 2.8 35.2 + - + +
505D EDO 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 3.7 20.0 - - + -
121D ILE* 2.9 39.4 + - + +
122D MET* 3.8 3.8 - - - +
124D THR* 1.3 78.5 - - - +
126D PHE* 1.3 64.5 + - + +
128D GLU* 4.3 4.7 - - - -
129D ARG* 2.9 26.5 + - - +
169D VAL* 3.8 15.5 - - + -
170D GLN* 4.0 6.1 - - - -
173D HIS* 3.7 44.9 - - + +
194D ILE* 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D MET* 2.8 56.1 + - + +
123D HIS 3.7 2.7 - - - +
125D ILE* 1.3 74.8 - - + +
127D GLN* 1.3 63.3 + - - +
130D ASP* 3.0 3.5 + - - -
131D LEU* 3.0 51.2 + - + -
132D LEU* 3.7 16.0 - - + +
137D ILE* 3.7 26.2 - - + -
142D LEU* 3.9 29.4 - - + -
191D LEU* 3.7 27.1 - - + -
194D ILE* 3.8 19.1 - - + -
195D PHE* 5.6 3.4 - - + -
248D ILE* 5.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D HIS* 2.8 53.5 + - + +
124D THR* 3.7 5.6 - - - +
126D PHE* 1.3 74.1 - - - +
128D GLU* 1.3 64.5 + - - +
130D ASP* 3.0 16.6 + - - +
132D LEU* 3.7 24.0 - - - +
139D VAL* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 5.1 7.0 - - + +
100D ASN* 3.0 33.3 + - - +
124D THR* 2.8 27.6 + - + +
125D ILE* 3.8 4.9 - - - +
127D GLN* 1.3 75.5 - - - +
129D ARG* 1.3 58.1 + - - +
130D ASP* 3.5 1.6 + - - +
173D HIS* 4.6 5.2 - - + +
511D EDO 3.4 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ILE* 2.9 19.2 + - - +
128D GLU* 1.3 75.3 - - - +
130D ASP* 1.3 71.1 + - - +
131D LEU* 3.2 20.9 + - + +
134D THR* 4.7 1.7 + - - -
173D HIS* 2.9 39.0 + - + +
176D LEU* 3.5 17.9 + - - +
177D SER* 3.0 28.7 + - - +
187D ASP* 5.5 2.4 - - - +
190D ILE* 3.8 34.3 - - + +
194D ILE* 3.6 26.5 - - - +
511D EDO 3.8 20.6 + - - +
----------------------------------------------------------
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