Contacts of the helix formed by residues 124 - 142 (chain B) in PDB entry 1MHQ
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 THR 124 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PRO 5.8 1.8 - - - +
76B GLU* 2.5 44.8 + - + +
122B TRP 3.9 4.2 + - - +
123B ALA* 1.3 77.7 - - - +
125B GLY* 1.3 54.6 + - - +
126B LYS* 3.6 2.3 + - - -
127B VAL* 3.1 23.4 + - + +
128B LYS* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 1.3 74.0 - - - +
126B LYS* 1.3 52.0 + - - +
128B LYS* 3.6 13.6 - - - +
129B GLY* 2.7 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 3.8 23.0 + - - +
80B LEU* 4.4 26.8 - - + +
124B THR* 3.1 1.2 - - - -
125B GLY* 1.3 75.4 - - - +
127B VAL* 1.3 65.3 + - - +
129B GLY* 3.1 1.9 + - - -
130B ARG* 3.0 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE 4.5 3.4 - - - +
73B SER 5.7 0.4 - - - +
76B GLU* 4.0 20.2 - - + -
79B ALA* 4.0 25.6 - - + -
80B LEU* 4.0 17.9 - - + -
83B LEU* 4.1 14.5 - - + +
113B VAL* 4.1 12.8 - - + -
123B ALA* 4.0 16.2 - - + -
124B THR* 3.1 27.2 + - - +
126B LYS* 1.3 76.7 - - - +
128B LYS* 1.3 64.6 + - - +
130B ARG* 3.2 4.0 + - - +
131B VAL* 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.5 25.4 - - - +
114B LEU* 3.7 32.9 + - + +
116B PRO* 4.8 10.1 - - - +
120B GLY 5.7 0.2 - - - -
121B SER* 3.1 31.3 + - - -
123B ALA* 4.0 8.7 + - + +
124B THR 2.8 19.2 + - - +
125B GLY* 3.6 12.8 - - - +
127B VAL* 1.3 78.0 - - - +
129B GLY* 1.3 62.7 + - - +
131B VAL* 3.1 5.0 + - - +
132B ILE* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 2.7 21.9 + - - -
126B LYS* 3.1 2.7 + - - -
128B LYS* 1.3 74.2 - - - +
130B ARG* 1.3 60.9 - - - +
132B ILE* 3.3 13.4 + - - +
133B GLU* 3.1 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.6 48.5 + - + +
83B LEU* 3.5 16.2 - - + +
84B THR* 2.8 26.1 + - - +
87B GLU* 2.7 41.3 + - - -
126B LYS 3.0 12.7 + - - +
127B VAL* 3.7 7.9 - - - +
129B GLY* 1.3 72.6 - - - +
131B VAL* 1.3 67.7 + - - +
133B GLU* 3.3 15.9 + - + +
134B ILE* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.5 5.8 - - + -
83B LEU* 4.0 23.3 - - + -
110B LEU* 4.2 25.5 - - + +
113B VAL* 4.2 20.4 - - + -
114B LEU* 3.7 28.7 - - + -
127B VAL* 2.9 19.3 + - + +
128B LYS 3.1 7.6 + - - +
130B ARG* 1.3 78.0 - - - +
132B ILE* 1.3 51.4 + - - +
134B ILE* 3.3 8.2 + - + +
135B LEU* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.9 16.8 - - + -
128B LYS* 3.0 22.6 + - + +
129B GLY* 3.4 12.3 - - - +
131B VAL* 1.3 75.9 - - - +
133B GLU* 1.3 53.8 + - + +
135B LEU* 3.3 6.8 + - - +
136B PHE* 2.8 36.6 + - - +
152B TYR* 4.0 9.1 - - - +
160B ILE 5.2 2.9 - - - +
161B ILE* 3.8 50.0 - - + -
162B LYS 5.9 0.4 - - - +
164B ASP* 5.1 7.2 - - + -
165B PRO* 5.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY* 3.1 21.5 + - - +
130B ARG* 3.3 17.9 + - + +
132B ILE* 1.3 74.7 - - + +
134B ILE* 1.3 62.0 + - + +
136B PHE* 3.2 7.2 + - - +
137B SER* 2.8 31.2 + - - -
165B PRO* 4.4 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.6 33.2 - - + +
86B LEU* 4.1 10.3 - - + -
87B GLU* 3.3 40.8 - - + +
110B LEU* 5.7 3.8 - - + -
130B ARG* 3.0 31.3 + - + +
131B VAL* 3.6 5.2 - - - +
133B GLU* 1.3 77.8 - - + +
135B LEU* 1.3 63.0 + - - +
137B SER* 2.7 23.8 + - - +
138B TRP* 3.1 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.0 27.1 - - + -
110B LEU* 4.1 20.6 - - + -
111B ILE* 5.6 1.6 - - + -
114B LEU* 5.1 3.6 - - + -
131B VAL* 2.8 24.6 + - + +
132B ILE* 3.7 5.6 - - - +
134B ILE* 1.3 76.7 - - - +
136B PHE* 1.3 61.4 + - - +
138B TRP* 3.4 13.2 + - + +
139B THR* 3.3 21.3 + - - +
148B ILE* 4.4 7.1 - - + +
151B ALA* 4.8 5.4 - - + -
152B TYR* 3.7 27.4 - - + +
155B LEU* 3.3 34.5 - - + -
161B ILE* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE 2.8 20.9 + - - +
133B GLU 3.2 4.7 + - - +
135B LEU* 1.3 72.2 - - - +
137B SER* 1.3 67.9 + - - +
139B THR* 2.4 35.7 + - - -
140B VAL* 3.2 27.1 + - + +
152B TYR* 3.3 39.9 - + + +
164B ASP 4.7 2.7 - - - -
165B PRO* 3.7 31.6 - - + -
168B PRO* 4.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU 2.8 16.5 + - - -
134B ILE* 2.7 24.0 + - - -
136B PHE* 1.3 77.3 - - - +
138B TRP* 1.3 59.8 + - - +
140B VAL* 2.9 10.9 + - - +
141B TRP* 2.7 59.2 + - - -
168B PRO* 6.4 0.7 - - - -
170B ASP 4.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.9 16.4 - - + -
90B MET* 3.5 43.3 - - + +
101B VAL* 3.1 45.3 - - + -
106B PHE* 4.0 4.3 - + - -
107B LEU* 4.5 6.7 - - + -
110B LEU* 4.0 17.3 - - + -
134B ILE* 3.1 36.8 + - + +
135B LEU* 3.5 22.4 - - + +
136B PHE 3.1 0.2 - - - -
137B SER* 1.3 84.8 + - - +
139B THR* 1.3 61.6 + - - +
140B VAL 3.0 1.6 - - - -
141B TRP* 4.2 7.1 - + - -
142B PHE* 2.7 53.4 + + + +
148B ILE* 4.1 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 3.3 15.0 + - - +
136B PHE* 2.4 31.4 + - - +
138B TRP* 1.3 78.7 - - - +
140B VAL* 1.3 66.1 + - - +
142B PHE 4.7 2.7 - - - -
143B PRO* 3.3 23.7 - - - +
148B ILE* 3.7 21.3 - - + +
149B ARG* 4.9 4.7 - - - +
152B TYR* 3.8 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.4 37.7 - - + +
137B SER* 2.9 13.1 + - - +
139B THR* 1.3 85.7 - - - +
141B TRP* 1.3 80.9 - - + +
143B PRO* 3.3 13.6 - - - +
168B PRO* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 5.8 2.2 - - + -
137B SER* 2.7 37.9 + - - +
138B TRP* 4.3 12.8 - + - -
140B VAL* 1.3 95.6 - - + +
142B PHE* 1.3 90.6 + + + +
143B PRO* 3.2 8.2 - - - +
170B ASP 3.9 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.9 29.8 - - + -
95B GLU* 5.5 2.9 - - - -
98B HIS* 4.2 30.3 - + + -
101B VAL* 6.0 0.9 - - + -
102B ALA* 6.2 1.3 - - + -
138B TRP* 2.7 45.0 + + + +
139B THR* 3.8 3.0 - - - +
141B TRP* 1.3 100.9 - + + +
143B PRO* 1.3 59.6 - - - +
144B GLU* 2.9 11.5 + - - -
145B ASP* 2.9 23.4 + - + +
148B ILE* 3.8 24.9 - - + +
----------------------------------------------------------
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