Contacts of the helix formed by residues 113 - 134 (chain B) in PDB entry 2OG9
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 GLY 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 3.2 22.9 - - - -
110A GLY* 5.3 0.2 - - - -
112A SER 3.8 7.9 - - - -
112B SER* 1.3 77.8 - - - +
114B LEU* 1.3 65.1 + - - -
115B SER 3.3 0.9 - - - -
116B THR* 3.3 2.9 + - - -
117B GLN* 2.9 36.1 + - - +
268B THR* 3.8 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.8 0.7 - - - +
79A HIS* 3.6 37.0 - - + +
109A ALA* 3.5 29.2 + - + -
112A SER 5.0 0.2 + - - -
114A LEU* 4.0 23.7 - - + +
115A SER* 3.9 17.0 - - - +
68B SER* 4.7 0.2 - - - +
72B GLY* 3.8 24.7 - - - +
75B GLY* 4.2 14.1 - - - -
76B GLN* 3.8 15.4 - - + +
79B HIS* 5.4 0.2 - - - -
112B SER 4.1 0.4 + - - -
113B GLY* 1.3 70.6 - - - -
115B SER* 1.3 62.5 + - - +
117B GLN* 3.3 15.1 + - - +
118B ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.9 8.6 + - - +
79B HIS* 3.4 34.0 - - - -
106B GLY 5.0 1.1 + - - -
109B ALA* 3.6 34.5 + - - +
110B GLY 3.9 10.6 + - - -
112B SER 4.1 4.5 + - - -
113B GLY 3.3 0.4 + - - -
114B LEU* 1.3 78.7 - - - +
116B THR* 1.3 60.9 + - - +
118B ALA* 3.3 4.9 + - - +
119B ILE* 3.1 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 3.8 25.6 - - + -
103B CYS* 4.4 2.2 - - - -
110B GLY 4.1 6.5 - - - +
111B ARG* 3.4 32.9 + - - +
112B SER* 3.1 27.0 - - - +
113B GLY 3.3 4.0 + - - -
115B SER* 1.3 80.3 + - - +
117B GLN* 1.3 60.6 + - - +
118B ALA 3.2 0.2 - - - -
119B ILE* 3.3 16.8 + - + +
120B GLY 2.8 21.7 + - - -
268B THR 4.4 4.0 + - - -
292B VAL 4.7 1.9 + - - -
293B GLY* 3.2 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 2.9 29.0 + - - +
109A ALA* 4.0 2.7 - - - +
66B SER* 3.1 29.6 + - - +
67B TYR 4.4 2.6 - - - +
76B GLN* 2.7 38.0 + - - +
113B GLY* 2.9 24.8 + - - +
114B LEU* 3.6 16.1 - - - +
116B THR* 1.3 74.7 - - - +
118B ALA* 1.3 64.9 + - - +
120B GLY* 3.2 8.7 + - - +
121B ALA 3.3 1.9 + - - -
268B THR* 3.6 11.3 - - - +
290B PRO 3.8 9.4 - - - +
291B ARG* 3.2 34.5 + - - +
293B GLY* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 12.7 - - - +
76B GLN* 3.5 25.5 - - - +
79B HIS* 4.3 7.6 - - + -
80B ALA* 3.9 17.9 - - + +
83B ILE* 4.9 1.1 - - + -
114B LEU 3.0 12.7 + - - +
115B SER 3.5 9.6 - - - +
116B THR 3.2 0.2 - - - -
117B GLN* 1.3 75.8 - - - +
119B ILE* 1.3 64.9 + - - +
121B ALA* 3.1 16.1 + - - +
122B PHE* 3.4 16.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 5.6 1.1 - - - +
83B ILE* 3.7 17.9 - - + -
99B TRP* 3.4 43.5 - - + +
102B LEU* 3.6 13.0 - - + +
103B CYS* 3.4 41.3 - - + +
115B SER* 3.1 19.5 + - - +
116B THR* 3.4 20.0 - - + +
118B ALA* 1.3 75.6 - - - +
120B GLY* 1.3 58.4 + - - +
122B PHE* 3.0 15.0 + - - +
123B ASP* 2.9 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE 4.7 2.2 - - - -
66B SER* 5.1 0.7 - - - -
116B THR 2.8 11.1 + - - -
117B GLN 3.2 6.0 + - - -
118B ALA 3.1 0.6 - - - -
119B ILE* 1.3 78.0 - - - +
121B ALA* 1.3 60.7 + - - +
123B ASP* 3.4 2.1 - - - +
124B VAL* 2.9 31.6 + - - +
290B PRO* 5.3 2.7 - - - -
293B GLY* 3.1 31.0 - - - -
294B GLY* 3.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 6.3 0.2 - - + -
50B LEU* 3.9 33.7 - - + +
52B ALA* 3.6 21.7 - - + +
64B GLY* 3.5 12.6 - - - -
65B PHE* 3.9 18.2 - - - +
66B SER* 4.0 2.8 - - - +
117B GLN 3.3 4.0 + - - -
118B ALA 3.1 12.5 + - - +
120B GLY* 1.3 75.3 - - - +
122B PHE* 1.3 63.9 + - + +
125B ALA 3.2 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.6 26.9 - - + -
20B ILE* 3.6 22.4 - - + -
52B ALA* 3.8 12.8 - - + -
54B ILE* 3.7 7.7 - - + +
80B ALA* 3.6 34.8 - - + -
83B ILE* 4.1 13.0 - - + -
84B ALA* 4.0 8.5 - - + -
87B LEU* 3.5 25.6 - - + -
102B LEU* 3.8 21.5 - - + -
118B ALA 3.4 22.7 - - - -
119B ILE* 3.0 7.2 + - - +
121B ALA* 1.3 75.1 - - + +
123B ASP* 1.3 66.3 + - - +
125B ALA* 3.2 4.0 + - - +
126B LEU* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.2 14.0 - - - +
99B TRP* 3.6 17.5 - - + +
119B ILE* 2.9 13.2 + - + +
120B GLY* 3.2 14.1 + - - +
122B PHE* 1.3 77.4 - - - +
124B VAL* 1.3 61.7 + - - +
126B LEU* 3.2 10.6 + - - +
127B TRP* 3.1 30.9 + - - -
293B GLY 4.1 0.9 - - - +
295B ILE* 2.9 14.4 + - - -
296B THR* 2.7 51.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY* 3.6 16.2 - - - -
65B PHE* 4.1 15.0 - - + +
120B GLY 2.9 21.4 + - - +
121B ALA 3.9 0.2 - - - +
123B ASP* 1.3 76.1 - - - +
125B ALA* 1.3 57.7 + - - +
127B TRP* 3.2 2.9 + - - +
128B ASP* 2.9 26.5 + - - +
290B PRO* 5.8 1.6 - - + -
294B GLY* 4.2 11.4 - - - -
295B ILE* 4.2 21.1 - - + -
320B LEU* 4.2 23.6 - - + -
363B LEU* 3.4 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA 3.8 9.9 - - - +
54B ILE* 3.8 18.4 - - + -
62B GLY* 3.4 16.5 - - - +
63B LEU 3.6 14.8 - - - -
64B GLY* 3.6 15.6 - - - +
121B ALA 3.2 8.6 + - - +
122B PHE* 3.2 10.0 + - - +
124B VAL* 1.3 79.1 - - - +
126B LEU* 1.3 57.5 + - - +
128B ASP* 3.2 2.9 + - - +
129B LEU* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.9 9.4 - - + -
54B ILE* 3.9 22.9 - - + -
87B LEU* 4.8 6.1 - - + -
92B PRO* 3.7 37.2 - - + +
95B ILE* 3.7 30.4 - - + +
98B LEU* 3.9 28.3 - - + -
99B TRP 5.9 0.2 - - - +
122B PHE* 2.9 23.1 + - + +
123B ASP* 3.2 7.6 + - - +
125B ALA* 1.3 75.8 - - - +
127B TRP* 1.3 59.0 + - - +
129B LEU* 3.4 7.8 + - + +
130B LYS* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.5 26.1 - - + +
123B ASP* 3.1 29.2 + - - -
124B VAL 3.6 2.0 - - - +
126B LEU* 1.3 73.0 - - - +
128B ASP* 1.3 66.7 + - - +
130B LYS* 3.3 11.6 + - + +
131B ALA* 2.9 25.3 + - - +
138B LEU* 4.2 13.8 - - + +
141B LEU* 3.9 29.6 - - + +
142B LEU* 3.6 18.8 - - + -
295B ILE* 3.5 47.8 - - + +
296B THR* 3.2 23.5 + - - -
299B LEU* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY* 3.5 1.6 - - - -
63B LEU* 2.9 30.7 + - - +
124B VAL 2.9 13.5 + - - +
125B ALA 3.3 8.3 - - - +
127B TRP* 1.3 76.6 - - - +
129B LEU* 1.3 57.7 + - - +
131B ALA* 3.4 1.7 + - - +
132B LYS* 2.8 69.9 + - - +
138B LEU* 5.7 0.2 - - - -
362B GLY* 3.3 4.1 - - - -
363B LEU* 2.7 47.0 + - + +
364B GLY 4.3 0.7 + - - -
365B LEU 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.1 16.4 - - + +
56B THR* 3.8 24.5 - - + -
60B HIS* 3.8 18.3 + - + +
61B GLN 3.6 30.7 - - - +
62B GLY* 3.9 3.8 - - - +
92B PRO* 4.4 15.7 - - + +
125B ALA 2.9 14.9 + - - +
126B LEU* 3.6 8.1 - - + +
128B ASP* 1.3 78.4 - - - +
130B LYS* 1.3 61.4 + - - +
132B LYS* 3.4 3.3 + - - +
133B ARG* 2.9 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO 5.8 0.9 - - - +
93B SER* 2.8 47.9 + - - +
95B ILE* 4.0 18.9 - - + +
126B LEU 3.0 16.2 + - - +
127B TRP* 3.8 13.3 - - + +
129B LEU* 1.3 78.4 - - + +
131B ALA* 1.3 66.8 + - - +
133B ARG* 3.2 27.8 + - + +
134B ALA* 3.3 9.2 + - - +
141B LEU* 4.0 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP 2.9 17.9 + - - +
130B LYS* 1.3 77.8 - - - +
132B LYS* 1.3 62.1 + - - +
134B ALA* 3.0 12.8 + - - +
136B LEU 3.0 36.3 + - - +
137B SER 4.1 1.1 - - - +
138B LEU* 4.1 13.0 - - + -
141B LEU* 3.6 22.8 - - + +
362B GLY* 3.5 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 5.5 1.8 - - - +
61B GLN* 3.6 24.9 + - + +
62B GLY* 4.7 1.8 - - - -
63B LEU* 4.7 3.4 - - - +
128B ASP* 2.8 49.7 + - - +
129B LEU* 3.7 4.7 - - - +
131B ALA* 1.3 72.3 - - - +
133B ARG* 1.3 66.4 + - - +
135B GLY* 2.9 14.6 + - - -
361B PRO* 3.9 28.1 - - + +
362B GLY 3.9 11.0 - - - +
363B LEU 5.1 0.2 - - - +
364B GLY* 5.3 2.2 - - - +
365B LEU 4.6 12.2 + - - +
366B THR* 5.9 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 4.4 9.8 + - - -
13B ASP* 3.3 35.2 + - - +
60B HIS* 3.1 47.8 + - + +
92B PRO* 3.9 7.7 - - - +
93B SER* 4.1 16.7 + - - -
129B LEU* 2.9 36.5 + - - +
130B LYS* 3.2 18.6 - - - +
131B ALA 3.2 0.2 - - - -
132B LYS* 1.3 76.8 - - - +
134B ALA* 1.3 58.7 + - - +
135B GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS 3.3 6.7 + - - +
131B ALA 3.0 9.8 + - - +
133B ARG* 1.3 77.9 - - - +
135B GLY* 1.3 64.2 + - - +
136B LEU* 3.4 28.4 + - + +
141B LEU* 4.7 8.7 - - + -
----------------------------------------------------------
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