Contacts of the helix formed by residues 123 - 144 (chain B) in PDB entry 3MI9
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 SER 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 3.9 5.6 - - - +
120B ASP* 2.6 40.6 + - - -
122B ARG* 1.3 84.6 - - - +
124B GLU* 1.3 66.5 + - - +
125B ALA* 3.9 6.2 + - - +
126B TYR* 3.1 16.6 + - - +
127B LEU* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG 3.8 0.9 + - - +
123B SER* 1.3 74.4 - - - +
125B ALA* 1.3 67.4 + - - +
126B TYR 2.9 1.0 + - - -
127B LEU* 3.1 15.6 + - - +
128B GLN* 2.8 24.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
119B PRO* 4.9 9.6 - - + -
123B SER* 4.1 7.9 - - - +
124B GLU* 1.3 78.3 - - - +
126B TYR* 1.3 65.2 + - - +
128B GLN* 3.0 19.3 - - - +
129B GLN* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 5.7 0.7 - - - -
102B GLU* 3.1 43.5 + - + +
105B ILE* 3.9 21.1 - - + +
118B LEU* 6.4 2.5 - - + -
119B PRO* 4.0 21.7 - - + +
120B ASP 3.1 20.4 - - - +
121B THR* 3.4 43.9 - - + +
123B SER* 3.1 9.8 + - - +
124B GLU 2.9 1.8 + - - -
125B ALA* 1.3 72.0 - - - +
127B LEU* 1.3 71.4 + - + +
128B GLN 2.6 15.8 + - - -
129B GLN* 2.6 39.5 + - - +
130B VAL* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR 4.5 13.5 - - - +
122B ARG* 4.3 11.2 - - - +
123B SER 3.3 11.0 + - - +
124B GLU* 3.1 19.9 + - - +
126B TYR* 1.3 86.9 - - + +
128B GLN* 1.3 61.4 + - - +
130B VAL* 3.4 10.6 + - + +
131B GLN* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU 2.8 13.3 + - - +
125B ALA* 3.0 17.9 - - - +
126B TYR 2.6 4.4 + - - -
127B LEU* 1.3 73.2 - - - +
129B GLN* 1.3 57.2 + - - +
131B GLN* 2.9 31.4 + - - +
132B ASP* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 2.9 36.4 + - + +
109B HIS* 5.5 8.1 - - - +
119B PRO* 4.6 17.8 - - - +
125B ALA* 3.6 8.9 - - - +
126B TYR* 2.6 44.2 + - + +
128B GLN* 1.3 71.7 - - - +
130B VAL* 1.3 62.3 + - - +
131B GLN 2.8 5.2 - - - -
132B ASP* 2.7 25.7 + - + +
133B LEU* 2.7 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 3.5 31.9 - - - +
101B LEU* 3.6 11.5 - - + +
105B ILE* 3.4 24.7 - - + -
126B TYR* 3.1 45.4 + - + +
127B LEU* 3.6 14.8 - - + +
129B GLN* 1.3 75.8 - - + +
131B GLN* 1.3 61.7 + - + +
133B LEU* 3.8 3.0 + - - +
134B VAL* 3.1 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.2 16.5 + - + +
128B GLN* 2.9 21.0 + - - +
129B GLN 2.8 0.2 - - - -
130B VAL* 1.3 78.1 + - + +
132B ASP* 1.3 59.1 + - - +
133B LEU 3.1 1.6 - - - -
134B VAL* 3.0 21.2 + - - +
135B ILE* 2.8 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN* 3.0 37.6 + - - +
129B GLN* 2.7 18.0 + - + +
131B GLN* 1.3 72.6 - - - +
133B LEU* 1.3 55.2 + - - +
135B ILE* 3.4 19.7 + - - +
136B LEU* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PRO* 4.5 12.3 - - + -
86B ALA* 4.3 15.5 - - + +
89B PHE* 3.8 28.0 - - + -
101B LEU* 3.4 32.5 - - + -
104B VAL* 4.2 16.4 - - + -
105B ILE* 3.6 19.7 - - + -
129B GLN 2.7 13.4 + - - +
130B VAL* 3.9 6.5 - - - +
132B ASP* 1.3 74.4 - - - +
134B VAL* 1.3 69.7 + - - +
136B LEU* 3.0 9.1 + - - +
137B GLU* 2.9 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 6.2 3.6 - - + -
56A LYS* 4.3 4.0 - - - +
58A GLY* 4.0 24.7 - - - -
59A PHE 5.0 0.7 - - - +
89B PHE* 6.1 0.2 - - + -
101B LEU* 3.8 19.3 - - + -
130B VAL* 3.1 19.1 - - + +
131B GLN* 3.0 20.3 + - - +
133B LEU* 1.3 81.6 - - + +
135B ILE* 1.3 65.1 + - + +
137B GLU* 3.2 11.6 + - - +
138B SER* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 2.8 28.7 + - + +
132B ASP* 3.5 25.1 - - - +
134B VAL* 1.3 74.2 - - + +
136B LEU* 1.3 67.0 + - + +
138B SER* 3.0 17.7 + - - -
139B ILE* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 6.0 1.1 - - + -
78B PHE* 4.2 27.4 - - + -
82B SER* 3.3 47.6 - - - +
83B VAL* 3.5 15.7 - - + +
86B ALA* 3.8 9.6 - - + -
132B ASP* 2.9 19.2 + - + +
133B LEU* 3.4 6.5 - - - +
135B ILE* 1.3 75.5 - - + +
137B GLU* 1.3 67.2 + - - +
139B ILE* 3.0 12.2 + - + +
140B ILE* 2.9 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 3.5 7.6 - - - -
59A PHE* 2.9 30.7 + - + +
86B ALA* 4.0 9.3 - - + +
89B PHE* 3.5 13.2 - - - -
90B LEU* 3.8 22.5 - - + +
93B LYS* 2.5 35.6 + - - +
133B LEU* 2.9 14.5 + - + +
134B VAL* 3.2 13.5 + - - +
136B LEU* 1.3 76.0 - - - +
138B SER* 1.3 57.6 + - - +
140B ILE* 3.1 14.1 + - - +
141B LEU* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MET* 6.1 1.2 - - - +
59A PHE* 5.0 10.5 + - - +
99A ILE* 6.3 1.8 - - - -
134B VAL* 3.2 15.1 + - - +
135B ILE* 3.0 12.3 + - - -
137B GLU* 1.3 79.9 + - - +
139B ILE* 1.3 59.3 + - - +
141B LEU* 3.4 11.3 + - - +
142B GLN* 2.9 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.6 17.5 - - + -
69B PHE* 4.1 13.0 - - + -
73B GLN* 5.0 0.2 - - - +
78B PHE* 4.1 34.5 - - + -
135B ILE* 3.1 30.0 + - + +
136B LEU* 3.0 14.9 + - + +
138B SER* 1.3 74.9 - - - +
140B ILE* 1.3 54.4 + - - +
142B GLN* 3.8 9.0 - - - +
143B THR* 2.6 50.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
65B TYR* 4.9 8.7 - - + +
69B PHE* 3.8 29.6 - - + -
83B VAL* 4.0 14.8 - - + +
86B ALA* 3.6 32.1 - - + -
87B ALA* 3.6 18.2 - - + +
90B LEU* 3.9 15.7 - - + -
136B LEU* 2.9 17.5 + - + +
137B GLU* 3.4 7.9 - - - +
139B ILE* 1.3 75.9 - - - +
141B LEU* 1.3 58.2 + - - +
143B THR* 3.1 1.4 + - - -
144B LEU* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.6 45.5 - - + -
64A LEU* 3.9 7.4 - - + -
90B LEU* 3.7 22.4 - - + -
137B GLU* 2.9 24.2 + - + +
138B SER* 3.6 11.0 - - - +
140B ILE* 1.3 78.8 - - - +
142B GLN* 1.3 59.8 + - - +
144B LEU* 3.5 4.3 + - + -
145B GLY 3.2 2.3 + - - -
146B PHE* 2.8 54.1 + - + +
148B LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS* 3.6 23.7 - - - -
12A PHE* 4.4 1.7 + - - +
13A CYS* 3.7 15.3 + - + +
86A ARG* 3.1 36.8 + - - +
99A ILE* 4.1 15.9 - - + +
138B SER* 2.9 38.5 + - - +
139B ILE* 3.8 9.4 - - - +
141B LEU* 1.3 73.3 - - - +
143B THR* 1.3 67.0 + - - +
145B GLY* 3.0 13.0 + - - -
146B PHE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU 4.7 1.7 + - - -
10A CYS* 4.7 5.1 - - - +
11A PRO* 5.4 0.6 - - - +
12A PHE* 3.6 10.9 + - - -
12B TRP* 3.5 13.1 - - + -
69B PHE* 3.8 33.6 - - + +
72B ILE* 3.6 36.9 - - + +
73B GLN* 3.2 20.7 + - - +
139B ILE* 2.6 31.9 + - - +
140B ILE 3.5 3.6 - - - -
142B GLN* 1.3 74.5 - - - +
144B LEU* 1.3 59.5 + - - +
145B GLY 3.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 5.3 1.0 + - - -
12B TRP* 3.9 19.9 + - + -
65B TYR* 3.4 50.0 - - + +
68B ARG* 3.5 37.7 - - + -
69B PHE* 4.1 7.0 - - - +
90B LEU* 5.1 2.9 - - + -
140B ILE* 2.8 34.6 + - + +
141B LEU* 4.0 5.2 - - - +
143B THR* 1.3 76.2 - - - +
145B GLY* 1.3 64.3 + - - +
146B PHE* 2.9 4.0 + - - +
147B GLU* 3.0 28.5 + - + +
148B LEU* 5.7 3.1 - - + -
----------------------------------------------------------
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