Contacts of the helix formed by residues 151 - 167 (chain A) in PDB entry 1C5G
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 GLU 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 3.3 40.3 + - - +
150A SER* 1.3 73.5 - - - +
152A VAL* 1.3 54.0 + - - +
153A GLU 3.4 2.5 - - - -
154A ARG* 2.8 53.9 + - + +
155A ALA 3.1 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE 3.2 20.9 - - - +
150A SER 2.9 12.7 + - - +
151A GLU* 1.3 73.1 - - - +
153A GLU* 1.3 80.4 + - + +
154A ARG 3.2 0.2 + - - -
155A ALA* 3.2 4.7 + - - +
156A ARG* 2.9 32.4 + - - +
180A VAL* 4.2 14.9 - - + +
181A ASP* 3.6 28.7 - - - +
182A GLN* 3.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU 3.2 1.0 + - - -
152A VAL* 1.3 93.1 - - + +
154A ARG* 1.3 60.5 + - - +
156A ARG* 3.1 42.8 + - - +
157A PHE* 3.4 21.5 + - - +
177A LYS* 3.9 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 2.8 37.5 + - + +
153A GLU* 1.3 76.4 - - - +
155A ALA* 1.3 60.9 + - - +
157A PHE* 3.3 13.9 + - - +
158A ILE* 2.9 70.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.8 8.2 - - + +
148A ASP 3.6 23.7 + - - +
149A PHE* 3.9 30.3 - - + -
151A GLU* 3.1 6.7 + - - +
152A VAL* 3.7 7.0 - - - +
154A ARG* 1.3 78.0 - - - +
156A ARG* 1.3 62.8 + - - +
158A ILE* 3.1 18.8 + - - +
159A ILE* 3.1 20.9 + - - +
180A VAL* 4.8 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
152A VAL 2.9 16.8 + - - +
153A GLU* 3.1 37.2 + - - +
155A ALA* 1.3 77.5 - - - +
157A PHE* 1.3 57.9 + - - +
159A ILE* 3.4 1.8 + - - +
160A ASN* 2.9 39.8 + - - +
173A ASN* 4.3 9.2 + - - -
175A LEU* 2.8 43.0 + - + -
176A GLY* 2.8 51.2 - - - -
177A LYS* 2.9 20.1 - - - +
180A VAL* 4.5 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU 3.4 17.9 + - - +
154A ARG* 3.3 16.5 + - - +
155A ALA 3.2 0.4 - - - -
156A ARG* 1.3 81.0 - - - +
158A ILE* 1.3 73.3 + - + +
160A ASN* 4.5 5.2 - - + +
161A ASP* 2.9 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.3 13.6 - - + -
147A VAL* 4.3 30.1 - - + -
154A ARG* 2.9 48.9 + - - +
155A ALA* 3.1 11.9 + - - +
157A PHE* 1.3 87.3 - - + +
159A ILE* 1.3 60.3 + - - +
161A ASP* 4.0 3.5 - - - +
162A TRP* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 4.1 37.7 - - + -
147A VAL* 5.6 1.8 - - + -
149A PHE* 5.2 6.5 - - + -
155A ALA 3.1 17.1 + - - +
156A ARG* 3.8 2.0 - - - +
158A ILE* 1.3 73.3 - - + +
160A ASN* 1.3 66.1 + - - +
161A ASP 3.1 1.3 - - - -
162A TRP* 2.8 23.5 + - - +
163A VAL* 3.0 16.5 + - + +
174A LEU* 4.6 6.7 - - + -
175A LEU* 3.2 45.5 - - + -
187A VAL* 4.0 26.2 - - + -
189A VAL* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.9 29.4 + - - +
157A PHE* 4.0 4.7 - - + +
159A ILE* 1.3 79.0 - - - +
161A ASP* 1.3 57.4 + - - +
163A VAL* 3.5 6.8 + - - +
164A LYS* 3.1 26.9 + - - +
171A ILE 4.6 1.4 - - - +
172A SER* 5.0 0.2 - - - -
173A ASN* 3.7 21.2 + - - +
174A LEU* 3.1 13.9 + - - +
175A LEU* 2.7 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 2.9 51.5 + - + +
158A ILE* 4.0 4.3 - - - +
160A ASN* 1.3 75.1 - - - +
162A TRP* 1.3 62.0 + - - +
163A VAL 3.3 0.2 - - - -
164A LYS* 3.7 22.4 + - - +
165A THR* 3.0 39.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
117A THR* 3.3 52.6 - - + +
118A ASP 3.8 3.1 - - - -
119A ALA* 3.4 24.5 - - + -
121A PHE* 3.9 16.4 - + + -
145A LYS* 4.0 24.3 - - + +
158A ILE 3.3 12.6 + - - +
159A ILE 2.8 11.0 + - - +
161A ASP* 1.3 76.5 - - - +
163A VAL* 1.3 74.6 + - + +
165A THR* 3.4 3.5 + - - -
166A HIS* 2.9 54.2 + + - +
189A VAL* 3.7 26.9 - - + -
191A ALA* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.0 20.3 + - + +
160A ASN* 3.7 7.0 - - - +
162A TRP* 1.3 90.6 - - + +
164A LYS* 1.3 63.8 + - - +
166A HIS* 3.1 3.3 + - - -
167A THR* 2.8 33.5 + - + +
171A ILE* 3.6 30.3 - - + +
174A LEU* 3.7 23.8 - - + +
189A VAL* 4.1 7.6 - - + -
191A ALA* 5.1 2.0 - - + -
361A SER* 3.3 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASN 3.1 17.6 + - - +
161A ASP* 3.7 23.8 + - - +
162A TRP 3.3 0.2 - - - -
163A VAL* 1.3 78.6 - - - +
165A THR* 1.3 76.6 + - - +
167A THR* 3.5 1.0 + - - -
168A LYS 3.4 1.6 + - - -
169A GLY* 2.6 48.5 + - - +
171A ILE 3.3 10.9 + - - +
172A SER* 3.7 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP* 3.0 24.2 + - - +
162A TRP* 3.4 2.9 + - - -
163A VAL 3.3 0.2 - - - -
164A LYS* 1.3 89.3 - - - +
166A HIS* 1.3 84.0 + - - +
168A LYS* 3.4 20.9 + - - +
169A GLY 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 4.9 6.6 + - - -
117A THR* 3.0 38.0 + - + +
162A TRP* 2.9 52.5 + + + +
163A VAL 3.1 3.3 + - - +
165A THR* 1.3 91.9 + - - +
167A THR* 1.3 60.2 + - - +
168A LYS* 3.3 11.1 - - - +
191A ALA* 3.5 29.0 - - + +
193A TYR* 4.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 2.8 26.5 + - + +
164A LYS 3.5 2.9 + - - -
166A HIS* 1.3 80.1 - - - +
168A LYS* 1.3 61.2 + - - +
170A MET* 2.8 33.6 + - - +
171A ILE* 3.0 43.7 + - + -
191A ALA* 4.3 6.7 - - + -
192A LEU 4.3 2.5 - - - +
193A TYR* 3.9 5.4 - - - -
359A SER* 3.2 23.0 + - - +
360A SER 4.0 17.5 - - - +
----------------------------------------------------------
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