Contacts of the helix formed by residues 155 - 166 (chain A) in PDB entry 2YG9
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 GLY 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 3.6 10.5 - - - +
153A GLY 4.0 1.0 - - - -
154A ILE* 1.3 74.6 - - - +
156A ARG* 1.3 66.3 + - - -
157A TRP 3.3 2.6 + - - -
158A THR 3.5 0.5 + - - -
159A ALA* 3.1 22.5 + - - +
1227A CL 3.1 22.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 2.4 43.4 + - - -
145A ILE* 3.8 20.7 - - + +
149A VAL* 3.5 18.5 - - + +
155A GLY* 1.3 71.6 - - - -
157A TRP* 1.3 58.0 + - - +
159A ALA* 3.3 3.1 + - - +
160A GLU* 2.8 65.2 + - + +
175A SER* 5.8 3.7 + - - -
1227A CL 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 4.4 13.9 - - + -
155A GLY 3.3 0.8 - - - -
156A ARG* 1.3 79.3 - - - +
158A THR* 1.3 83.7 + - - +
160A GLU* 3.3 10.1 + - - +
161A MET* 2.9 58.8 + - + +
174A SER* 3.3 21.8 - - - +
176A GLY* 4.0 9.4 - - - +
177A ASP* 2.8 46.9 + - - +
1227A CL 3.9 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.9 7.6 - - + -
68A SER* 4.3 11.9 + - - +
69A VAL* 5.2 2.5 - - + -
72A GLN* 3.2 30.8 + - - +
153A GLY 4.5 3.6 + - - +
154A ILE* 4.0 27.6 - - + -
155A GLY 3.9 4.3 - - - -
157A TRP* 1.3 88.6 - - - +
159A ALA* 1.3 58.1 + - - +
161A MET* 3.4 5.0 + - + +
162A PHE* 3.0 28.6 + - + +
1227A CL 2.9 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 6.4 0.2 - - - -
145A ILE* 4.1 25.1 - - + +
148A LEU* 3.9 36.3 - - + -
149A VAL* 4.4 0.9 - - + -
154A ILE* 4.2 1.7 - - + +
155A GLY 3.1 18.1 + - - +
156A ARG* 3.5 4.0 - - - +
158A THR* 1.3 75.7 - - - +
160A GLU* 1.3 57.4 + - - +
162A PHE* 3.2 4.9 + - - +
163A LEU* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.0 17.8 - - + +
156A ARG* 2.8 59.0 + - + +
157A TRP* 3.6 4.5 - - - +
159A ALA* 1.3 75.0 - - - +
161A MET* 1.3 61.0 + - - +
163A LEU* 3.5 7.9 + - - +
164A LEU* 3.0 28.2 + - - +
172A VAL* 3.8 19.9 - - + +
173A PHE 4.2 8.5 - - - +
174A SER* 2.5 43.0 + - - +
175A SER* 4.3 3.5 + - - -
176A GLY* 4.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 6.0 2.0 - - - +
157A TRP* 2.9 56.0 + - + +
158A THR* 3.7 6.5 - - - +
160A GLU* 1.3 78.0 - - - +
162A PHE* 1.3 57.9 + - - +
164A LEU* 4.5 6.7 - - + -
165A PHE* 2.8 51.0 + - + +
172A VAL* 5.6 0.4 - - + -
174A SER* 3.5 34.5 - - - +
212A TRP* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.3 35.2 - - + -
64A ARG 4.6 1.8 - - - -
65A LEU* 3.6 35.9 - - + -
68A SER* 5.4 6.7 - - - +
133A PHE* 4.9 3.6 - + - -
136A LEU* 4.4 9.0 - - + -
144A VAL* 5.0 0.4 - - + -
148A LEU* 3.7 29.6 - - + -
158A THR* 3.0 15.3 + - + +
159A ALA* 3.3 9.4 - - - +
161A MET* 1.3 74.7 - - - +
163A LEU* 1.3 63.0 + - + +
166A ALA* 2.8 50.6 + - + +
167A LEU* 3.0 41.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 3.7 31.2 - - + +
144A VAL* 3.6 31.0 - - + -
145A ILE* 3.6 34.5 - - + -
148A LEU* 4.5 1.6 - - + -
159A ALA 3.0 23.8 + - - +
160A GLU* 3.6 9.0 - - - +
162A PHE* 1.3 79.7 - - + +
164A LEU* 1.3 58.2 + - - +
167A LEU* 3.4 15.3 - - + +
168A ALA 3.1 11.1 + - - -
169A ARG* 2.9 37.5 + - + +
172A VAL* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.8 7.2 - - + +
160A GLU 3.0 16.8 + - - +
161A MET* 4.0 7.2 - - + +
163A LEU* 1.3 77.2 - - - +
165A PHE* 1.3 87.3 + - + +
168A ALA* 3.2 23.0 - - - -
169A ARG 4.0 8.0 - - - +
172A VAL* 3.7 30.1 - - + +
174A SER 6.0 0.7 - - - +
205A SER* 3.7 25.6 - - - +
208A SER* 4.2 1.8 - - - -
209A ARG* 3.9 23.6 - - + -
212A TRP* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.0 27.5 - - + +
56A ALA 5.0 2.4 - - - +
64A ARG* 3.3 19.3 + - - +
161A MET* 2.8 45.2 + - + +
164A LEU* 1.3 90.3 - - + +
166A ALA* 1.3 61.2 + - - +
168A ALA 4.2 1.4 + - - -
209A ARG* 4.5 12.1 - - + -
212A TRP* 3.5 36.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 4.0 2.3 - - - +
57A PRO* 3.6 1.6 - - - +
58A THR* 2.8 32.2 + - + +
64A ARG* 3.6 29.1 + - + +
161A MET 4.0 0.4 + - - -
162A PHE* 2.8 51.5 + - + +
165A PHE* 1.3 75.6 - - - +
167A LEU* 1.3 62.1 + - - +
168A ALA 3.2 1.0 + - - -
----------------------------------------------------------
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