Contacts of the helix formed by residues 133 - 149 (chain A) in PDB entry 1I9G
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 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 3.0 14.0 + - - +
132A GLN* 1.3 85.0 - - + +
134A ALA* 1.3 63.5 + - - +
135A ASP* 2.8 36.9 + - - +
136A HIS* 3.4 30.8 + - + +
137A ALA* 2.9 20.6 + - - +
301A SAM 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN 3.8 3.6 + - - -
133A ARG* 1.3 70.6 - - - +
135A ASP* 1.3 59.8 + - - +
137A ALA* 3.3 1.0 + - - -
138A GLU* 2.6 41.3 + - + +
159A VAL* 3.8 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 2.8 49.2 + - - +
134A ALA* 1.3 77.2 - - - +
136A HIS* 1.3 78.6 + - + -
138A GLU* 3.2 17.7 + - - +
139A HIS* 3.3 20.8 + - + +
142A ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.4 29.5 - - + +
109A GLY 3.2 7.6 - - - +
131A GLU* 3.4 18.2 - - - +
133A ARG* 3.3 36.7 + - + +
135A ASP* 1.3 94.2 + - - +
137A ALA* 1.3 62.5 + - - +
139A HIS* 3.0 23.6 + + - +
140A ALA 3.0 10.6 + - - -
301A SAM 2.6 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 3.4 19.7 - - + +
133A ARG 2.9 16.7 + - - +
134A ALA 3.5 5.6 - - - +
135A ASP 3.2 0.2 - - - -
136A HIS* 1.3 77.8 - - - +
138A GLU* 1.3 64.6 + - - +
140A ALA* 3.3 3.0 + - - +
141A ARG* 2.9 30.9 + - - +
157A LEU* 3.5 13.6 - - + +
159A VAL* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 2.6 33.1 + - + +
135A ASP* 3.2 9.6 + - - +
137A ALA* 1.3 79.5 - - - +
139A HIS* 1.3 58.2 + - - +
141A ARG* 2.2 40.9 + - - +
142A ARG* 2.9 53.0 + - - +
159A VAL* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 4.7 12.9 - - + +
78A ARG 3.1 28.5 + - - -
79A GLY* 4.3 7.4 - - - -
80A PRO* 4.5 10.7 - - + +
109A GLY 4.4 4.7 - - - +
110A SER* 4.8 1.1 - - - +
135A ASP* 3.3 22.5 + - + -
136A HIS* 3.0 15.1 + + - +
138A GLU* 1.3 77.5 - - - +
140A ALA* 1.3 56.5 + - - +
142A ARG* 3.3 24.7 + - - +
143A ASN* 2.8 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 4.0 19.5 - - + -
109A GLY 3.3 17.6 + - - +
110A SER 3.8 12.8 - - - -
111A GLY* 3.8 12.3 - - - +
136A HIS 3.0 7.7 + - - +
137A ALA* 3.7 8.3 - - - +
139A HIS* 1.3 74.7 - - - +
141A ARG* 1.3 58.5 + - - +
143A ASN* 3.3 0.3 + - - +
144A VAL* 2.8 36.7 + - - +
155A TRP* 4.0 11.0 - - + -
157A LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 2.9 25.6 + - - +
138A GLU* 2.2 53.0 + - - +
140A ALA* 1.3 77.4 - - - +
142A ARG* 1.3 61.6 + - - +
144A VAL* 4.1 1.2 - - - +
145A SER* 3.1 31.1 + - - +
151A PRO* 6.3 2.9 - - + -
155A TRP* 3.9 16.9 - - + -
157A LEU* 3.6 28.7 + - + +
159A VAL* 3.6 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 6.4 0.2 - - - +
138A GLU* 2.9 45.1 + - - +
139A HIS* 3.6 39.5 + - - +
141A ARG* 1.3 77.2 - - - +
143A ASN* 1.3 60.4 + - - +
145A SER* 3.4 4.4 + - - -
146A GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 2.7 30.7 + - - -
76A MET* 3.6 31.6 - - - +
77A PRO* 3.5 31.2 + - - +
110A SER* 2.8 40.1 + - - +
111A GLY* 5.2 0.4 - - - -
115A LEU* 4.2 1.2 - - - +
139A HIS* 2.8 30.7 + - - +
140A ALA 3.9 0.4 - - - +
142A ARG* 1.3 75.6 - - - +
144A VAL* 1.3 64.5 + - + +
147A CYS* 3.4 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY* 4.1 22.7 - - - +
114A THR* 4.2 9.4 - - - -
115A LEU* 4.0 13.9 - - + -
118A LEU* 3.9 11.7 - - + -
140A ALA 2.8 24.7 + - - +
143A ASN* 1.3 72.3 - - - +
145A SER* 1.3 62.0 + - - +
147A CYS* 3.3 7.6 + - - +
148A TYR* 3.1 23.7 - - - -
152A PRO* 3.7 22.0 - - + -
155A TRP* 3.6 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 3.1 21.9 + - - +
142A ARG* 3.9 4.7 - - - -
144A VAL* 1.3 78.1 - - - +
146A GLY* 1.3 52.9 + - - +
148A TYR 3.1 1.4 + - - -
149A GLY* 2.6 35.6 + - - -
150A GLN* 3.2 18.6 + - - -
151A PRO* 3.2 33.9 - - - +
152A PRO* 4.6 0.3 - - - +
155A TRP* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 4.2 20.6 + - - +
72A TYR* 3.4 21.3 + - - -
142A ARG 2.9 15.0 + - - -
143A ASN 3.4 0.2 + - - -
144A VAL 3.3 0.8 - - - -
145A SER* 1.3 75.1 - - - +
147A CYS* 1.3 60.0 + - - +
148A TYR 3.4 0.2 - - - -
149A GLY* 4.2 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 5.9 1.4 - - - +
69A LEU* 3.8 28.3 - - - -
72A TYR* 3.4 32.1 + - + -
115A LEU* 3.8 18.2 - - + -
144A VAL 3.3 10.9 + - - +
145A SER 3.2 1.0 - - - -
146A GLY* 1.3 77.1 - - - +
148A TYR* 1.3 68.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.5 28.7 + - + +
118A LEU* 3.4 30.0 - - + +
119A ARG* 4.5 3.8 + - - +
144A VAL* 3.1 20.0 - - + -
145A SER 3.1 2.0 + - - +
147A CYS* 1.3 87.5 - - + +
149A GLY* 1.3 57.1 + - - +
150A GLN* 3.3 16.9 + - - +
152A PRO* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 2.6 17.1 + - - -
146A GLY* 4.2 5.2 + - - -
147A CYS 3.7 0.8 - - - -
148A TYR* 1.3 73.8 - - - +
150A GLN* 1.3 62.9 - - - +
----------------------------------------------------------
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