Contacts of the helix formed by residues 145 - 158 (chain A) 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 ASP 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A HIS* 2.6 35.6 + - - -
102A ALA* 4.0 17.8 - - + +
142A PHE* 2.9 28.5 + - - +
143A PRO 3.1 2.9 - - - +
144A GLU* 1.3 84.1 - - - +
146A ILE* 1.3 59.9 + - - +
147A LYS 3.5 1.6 - - - +
148A ILE* 3.3 26.8 + - + +
149A ARG* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PRO 5.4 0.7 - - - -
144A GLU 3.3 11.3 + - - +
145A ASP* 1.3 68.5 - - - +
147A LYS* 1.3 72.8 + - + +
149A ARG* 3.1 28.7 + - - +
150A ASP* 2.7 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.4 21.1 - - - +
103A LYS* 4.9 1.8 - - - -
104A PHE* 4.2 26.5 - - + +
107A LEU* 3.8 9.9 - - + +
145A ASP 3.5 0.4 - - - -
146A ILE* 1.3 91.5 - - + +
148A ILE* 1.3 57.8 + - - +
150A ASP* 3.8 8.5 + - - +
151A ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 4.3 8.5 - - + -
102A ALA* 4.0 18.6 + - + -
107A LEU* 3.7 24.7 - - + -
135A LEU* 4.5 6.9 - - + +
138A TRP* 3.9 48.5 - - + +
139A THR* 4.2 15.7 - - + +
142A PHE* 5.2 1.6 - - + +
145A ASP* 3.3 36.9 + - + +
146A ILE 3.1 0.6 - - - -
147A LYS* 1.3 78.1 - - - +
149A ARG* 1.3 62.8 + - - +
151A ALA* 3.4 2.8 + - - +
152A TYR* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 4.5 16.1 - - + +
143A PRO* 5.5 8.7 - - + +
145A ASP 3.0 13.1 + - - +
146A ILE* 3.5 32.1 + - - +
148A ILE* 1.3 75.8 - - - +
150A ASP* 1.3 88.9 + - - +
151A ALA 3.2 0.3 + - - -
152A TYR* 3.2 3.6 + - - +
153A GLN* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 6.5 0.7 - - + -
146A ILE* 2.7 38.6 + - - +
147A LYS* 3.8 9.2 + - - +
149A ARG* 1.3 106.1 + - - +
151A ALA* 1.3 56.5 + - - +
153A GLN* 3.5 5.5 + - - +
154A MET* 2.9 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 4.7 7.4 - - + -
107A LEU* 4.5 16.2 - - + -
111A ILE* 4.1 23.7 - - + +
135A LEU* 5.9 5.4 - - + -
147A LYS 2.9 18.2 + - - +
148A ILE* 3.8 4.0 - - - +
149A ARG 3.2 0.2 - - - -
150A ASP* 1.3 73.3 - - - +
152A TYR* 1.3 67.1 + - - +
154A MET* 3.0 13.4 + - - +
155A LEU* 2.8 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.3 5.4 - - + -
135A LEU* 4.0 11.1 - - + +
136A PHE* 3.5 42.5 - + + -
139A THR* 3.4 28.5 - - + -
148A ILE 3.1 4.7 + - - +
149A ARG 3.7 4.0 - - - +
151A ALA* 1.3 79.3 - - - +
153A GLN* 1.3 72.8 + - - +
155A LEU* 3.3 9.6 + - - +
156A LYS* 2.9 36.6 + - + +
161A ILE* 3.6 34.2 - - + +
164A ASP* 2.8 43.4 + - - -
165A PRO* 3.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.0 31.0 + - + +
150A ASP* 3.8 6.5 - - - +
152A TYR* 1.3 91.7 - - - +
154A MET* 1.3 54.9 + - - +
156A LYS* 2.9 25.8 + - - +
157A LYS* 2.7 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 3.7 32.8 - - + -
111A ILE* 6.2 1.6 - - + -
150A ASP* 2.9 31.1 + - + +
151A ALA* 3.3 9.4 - - - +
153A GLN* 1.3 76.2 - - - +
155A LEU* 1.3 63.7 + - + +
157A LYS* 3.0 13.1 + - + +
158A GLN* 2.8 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.6 37.9 - - + -
114A LEU* 3.7 16.2 - - + -
135A LEU* 3.8 17.9 - - + -
151A ALA 2.8 17.8 + - - +
152A TYR* 3.5 9.4 - - - +
154A MET* 1.3 77.1 - - + +
156A LYS* 1.3 63.5 + - - +
158A GLN* 3.2 11.0 + - - +
160A ILE* 3.1 53.3 + - + +
161A ILE* 3.5 32.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 2.9 23.8 + - + +
153A GLN* 2.9 33.2 + - - +
155A LEU* 1.3 77.7 - - - +
157A LYS* 1.3 60.6 + - + +
159A GLY* 3.2 13.2 + - - -
161A ILE* 3.4 41.7 - - + +
162A LYS 4.2 3.6 - - - +
163A GLN* 3.9 6.7 - - - +
164A ASP* 2.4 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 2.7 34.1 + - - +
154A MET* 3.0 13.0 + - + +
156A LYS* 1.3 75.6 - - + +
158A GLN* 1.3 58.5 + - + +
159A GLY 3.1 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 5.8 0.8 - - - +
154A MET* 2.8 34.5 + - + +
155A LEU* 3.2 8.3 + - - +
157A LYS* 1.3 76.7 - - + +
159A GLY* 1.3 58.4 + - - +
160A ILE* 3.1 34.5 + - + +
----------------------------------------------------------
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