Contacts of the helix formed by residues 156 - 165 (chain A) in PDB entry 2IFG
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 LEU 156 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 4.6 12.8 - - - +
130A LEU* 4.7 9.6 - - + +
150A LEU* 4.8 15.3 - - + +
151A HIS 3.7 24.2 - - - +
152A CYS* 3.9 22.0 - - - -
153A SER* 3.3 15.2 + - - +
154A CYS 2.6 6.7 + - - -
155A ALA* 1.3 79.7 - - - +
157A ARG* 1.3 64.6 + - - +
158A TRP* 3.0 12.1 - - + +
159A LEU* 2.8 48.9 + - + +
160A GLN* 2.8 11.6 + - - +
186A MET* 5.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER 4.2 1.6 + - - -
154A CYS 2.8 15.3 + - - +
156A LEU* 1.3 76.9 - - - +
158A TRP* 1.3 56.7 + - - +
160A GLN* 2.7 45.5 - - - +
161A ARG* 2.7 46.3 + - + +
164A GLU* 3.4 30.9 + - - -
186A MET* 5.4 5.1 - - - -
187A PRO 5.5 2.2 - - - -
188A ASN* 3.9 32.8 + - - +
191A CYS* 4.6 20.5 + - + +
271A VAL* 3.9 10.1 - - + -
1C NAG 3.6 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.2 39.4 + - + -
131A SER 3.9 8.6 + - - -
132A TRP* 4.0 35.2 - + + -
135A VAL* 3.4 34.8 - - + -
143A LEU* 3.8 18.4 - - + -
145A LEU* 4.8 0.7 - - + -
155A ALA 2.9 30.5 + - - -
156A LEU* 3.0 7.3 - - + +
157A ARG* 1.3 78.7 - - - +
159A LEU* 1.3 84.8 + - + +
161A ARG* 3.2 10.5 + - - +
162A TRP* 2.9 65.9 + + + +
271A VAL* 3.5 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.9 3.4 - - + -
145A LEU* 4.2 26.7 - - + -
150A LEU* 5.3 7.6 - - + -
156A LEU* 2.8 39.1 + - + +
158A TRP* 1.3 99.3 - - + +
160A GLN* 1.3 68.3 + - - +
162A TRP* 2.9 16.4 + - + +
163A GLU* 3.1 10.8 + - - +
170A VAL* 4.4 24.5 - - + +
175A LEU* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 2.8 7.0 + - - +
157A ARG* 2.7 48.6 - - - +
159A LEU* 1.3 75.8 - - - +
161A ARG* 1.3 54.2 + - - +
163A GLU* 3.0 43.5 + - - +
164A GLU* 3.4 22.6 + - - +
184A ALA* 4.2 6.6 - - - -
185A HIS* 3.3 28.1 + - - +
186A MET* 3.5 19.6 - - - +
187A PRO 4.9 0.4 + - - -
188A ASN* 3.7 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 2.7 51.6 + - - +
158A TRP* 3.5 12.3 - - - +
160A GLN* 1.3 66.8 - - - +
162A TRP* 1.3 63.1 + - + +
163A GLU 2.7 11.5 + - - -
164A GLU* 3.2 13.0 + - - -
165A GLU* 2.8 62.7 + - + +
1C NAG 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.6 36.3 - - + -
137A GLY* 6.2 0.4 - - - -
140A LEU* 4.6 16.6 - - + -
143A LEU* 4.4 20.2 - - + -
158A TRP* 2.9 52.4 + + + +
159A LEU* 2.9 12.8 + - + +
161A ARG* 1.3 78.9 - - + +
163A GLU* 1.3 56.2 + - - +
165A GLU* 4.3 5.4 - - - -
166A GLY* 3.2 2.8 + - - -
167A LEU* 3.0 44.0 + - + +
168A GLY* 3.6 34.9 + - - +
170A VAL* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU 3.1 7.6 + - - +
160A GLN* 3.0 21.8 + - - +
161A ARG 2.7 2.0 + - - -
162A TRP* 1.3 76.4 - - - +
164A GLU* 1.3 61.1 + - + +
166A GLY* 2.7 25.5 + - - -
170A VAL* 4.4 17.8 - - + +
171A PRO* 3.4 33.6 - - + +
174A LYS* 5.4 1.4 - - - -
175A LEU* 5.0 6.8 + - - +
184A ALA* 2.6 45.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.4 27.5 + - - -
160A GLN* 3.8 27.8 - - - +
161A ARG* 3.2 10.7 + - - +
163A GLU* 1.3 74.3 - - + +
165A GLU* 1.3 67.2 + - + +
166A GLY* 2.9 6.4 + - - -
188A ASN* 4.3 1.6 - - - +
1C NAG 4.2 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.8 64.1 + - + +
162A TRP* 4.3 0.4 - - + +
164A GLU* 1.3 79.6 - - + +
166A GLY* 1.3 62.9 + - - +
167A LEU* 3.2 40.9 + - + +
----------------------------------------------------------
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