Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 1C7G
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 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 3.3 6.5 + - - +
159A ASP* 1.3 72.3 + - - +
161A ASN* 1.3 61.1 + - - +
163A LEU* 3.7 11.2 - - + +
164A ALA* 2.9 29.5 + - - +
196A ASN* 4.2 12.1 - - - +
199A ALA* 3.6 33.9 - - + +
200A VAL* 3.8 27.1 - - + -
203A MET* 3.7 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASP* 2.8 15.5 + - - +
160A LEU* 1.3 78.3 - - - +
162A LYS* 1.3 62.0 + - + +
164A ALA* 3.9 6.1 - - - +
165A THR* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 4.5 7.3 + - - +
140A ILE* 4.1 23.3 - - + +
141A VAL 3.3 20.8 + - - +
143A ASP* 2.9 36.9 + - - +
146A HIS* 5.4 3.8 - - - -
159A ASP* 3.0 37.1 + - + +
161A ASN* 1.3 76.7 - - + +
163A LEU* 1.3 64.3 + - - +
165A THR* 3.5 6.2 + - - -
166A LEU* 3.0 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118A ALA* 4.9 4.7 - - + -
140A ILE* 4.0 23.0 - - + +
158A ILE* 4.6 2.9 - - + -
159A ASP 3.1 11.5 + - - +
160A LEU* 3.7 22.7 - - + +
162A LYS* 1.3 75.3 - - - +
164A ALA* 1.3 67.0 + - - +
166A LEU* 3.0 12.3 + - + +
167A ILE* 2.9 39.1 + - + +
175A ILE* 5.6 2.0 - - + -
178A ILE* 3.6 35.7 - - + -
200A VAL* 4.2 15.5 - - + +
203A MET* 4.0 25.6 - - + -
204A ALA 5.2 0.9 - - - +
209A ILE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU 2.9 18.8 + - - +
161A ASN* 3.9 7.0 - - - +
163A LEU* 1.3 76.1 - - - +
165A THR* 1.3 58.2 + - - +
167A ILE* 3.4 8.8 + - - +
168A LYS* 2.9 33.9 + - - +
203A MET* 3.7 21.5 - - + -
207A TYR* 6.3 0.4 - - - -
----------------------------------------------------------
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 ASN* 2.8 23.0 + - - +
162A LYS* 3.6 7.4 - - - +
164A ALA* 1.3 74.2 - - - +
166A LEU* 1.3 56.8 + - - +
168A LYS* 3.0 15.0 + - + +
169A GLU* 2.7 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.9 6.5 - - + -
118A ALA* 3.5 32.3 - - + +
138A VAL* 4.1 32.1 - - + -
140A ILE* 4.6 3.4 - - + -
162A LYS 3.0 14.1 + - - +
163A LEU* 3.0 13.4 + - + +
165A THR* 1.3 77.3 - - - +
167A ILE* 1.3 58.3 - - - +
169A GLU* 4.5 2.5 - - - +
170A LYS* 2.8 59.1 + - + +
175A ILE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 2.9 31.2 + - + +
164A ALA* 3.5 7.9 - - - +
166A LEU* 1.3 75.5 - - - +
168A LYS* 1.3 58.8 + - - +
171A GLY* 2.8 26.9 + - - +
172A ALA 4.4 10.1 - - - +
175A ILE* 3.8 15.2 - - + +
203A MET* 4.1 18.4 - - + +
204A ALA* 5.4 0.7 - - - -
207A TYR* 3.8 51.6 - - + -
209A ILE* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 2.9 22.0 + - - +
165A THR* 3.0 14.0 + - + +
167A ILE* 1.3 80.1 - - - +
169A GLU* 1.3 84.5 + - + +
170A LYS 3.6 0.2 + - - -
171A GLY* 4.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 2.7 43.3 + - + +
166A LEU* 4.2 2.2 - - - +
168A LYS* 1.3 91.5 - - + +
170A LYS* 1.3 75.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.3 49.8 + - + -
166A LEU* 2.8 40.8 + - + +
168A LYS 4.9 0.2 - - - -
169A GLU* 1.3 86.0 + - + +
171A GLY* 1.3 61.6 + - - +
174A ASN* 2.5 36.9 + - + +
175A ILE* 5.1 2.9 - - + -
----------------------------------------------------------
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