Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 1LC7
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 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU 3.3 4.3 + - - -
163A PRO* 1.3 75.3 - - - +
165A ARG* 1.3 67.6 + - - +
166A PRO* 4.0 12.6 - - + -
167A LEU* 3.2 15.7 + - + +
168A LEU* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PRO 3.7 1.4 + - - -
164A GLU* 1.3 70.5 - - - +
166A PRO* 1.3 67.4 - - + +
168A LEU* 3.0 8.0 + - - +
169A GLN* 2.8 51.1 + - + +
195A GLU* 5.5 9.3 + - - +
196A THR* 4.2 9.1 + - - -
197A GLY 3.9 15.8 + - - +
198A PHE* 3.4 40.6 - - - -
201A ALA* 4.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 3.5 10.3 - - + -
165A ARG* 1.3 95.9 - - + +
167A LEU* 1.3 56.8 + - - +
169A GLN* 3.3 7.4 + - + +
170A ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.4 44.0 - - + +
136A THR* 3.9 8.5 - - - +
137A ASP* 3.8 29.6 - - + +
140A LEU* 4.8 7.4 - - + -
163A PRO* 4.5 8.5 - - + -
164A GLU* 3.2 17.2 + - + +
166A PRO* 1.3 79.4 - - - +
168A LEU* 1.3 58.2 + - - +
170A ALA* 3.1 5.6 + - + +
171A ILE* 2.9 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.8 0.2 - - + -
152A LEU* 3.8 28.5 - - + -
154A THR* 4.1 25.6 - - + +
162A LEU* 5.4 2.5 - - + -
163A PRO* 3.7 33.7 - - + +
164A GLU 3.0 16.4 + - - +
165A ARG* 3.7 9.9 - - - +
167A LEU* 1.3 76.1 - - - +
169A GLN* 1.3 57.3 + - - +
171A ILE* 3.7 7.0 - - + +
172A ALA* 2.9 29.8 + - - +
182A LEU* 4.7 2.9 - - + +
184A LEU* 4.8 5.4 - - + -
198A PHE* 3.8 32.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 2.8 42.0 + - + +
166A PRO* 3.6 8.5 - - + +
167A LEU 3.2 0.2 - - - -
168A LEU* 1.3 77.0 - - - +
170A ALA* 1.3 58.4 + - - +
172A ALA* 3.3 8.4 + - - +
173A ASP* 2.8 62.7 + - - +
198A PHE* 4.0 11.6 - - - -
201A ALA* 5.8 2.2 - - - +
205A ASN* 5.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.7 23.5 - - + +
166A PRO 2.9 17.5 + - - +
167A LEU* 3.5 8.3 - - + +
169A GLN* 1.3 77.5 - - - +
171A ILE* 1.3 62.4 + - - +
173A ASP* 3.5 8.1 + - - +
174A ARG* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.0 16.4 - - + -
139A ILE* 3.7 26.9 - - + -
140A LEU* 3.8 19.7 - - + -
143A LEU* 4.3 5.6 - - + +
150A LEU* 3.5 29.8 - - + -
152A LEU* 4.1 15.9 - - + -
167A LEU* 2.9 37.2 + - + +
168A LEU* 3.7 6.5 - - - +
170A ALA* 1.3 75.8 - - - +
172A ALA* 1.3 59.7 + - - +
174A ARG* 3.3 3.2 + - - +
175A CYS* 2.8 34.3 + - - -
182A LEU* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU 2.9 17.5 + - - +
169A GLN* 3.5 16.8 - - - +
171A ILE* 1.3 77.1 - - - +
173A ASP* 1.3 58.2 + - - +
175A CYS* 3.3 1.1 + - - +
176A LYS* 2.9 23.9 + - - +
182A LEU* 3.6 22.4 - - + +
198A PHE* 4.3 6.1 - - + -
205A ASN* 5.8 1.3 - - - +
207A HIS* 3.1 14.1 - - + -
208A ILE* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 2.8 46.4 + - - +
170A ALA* 3.8 7.4 - - - +
172A ALA* 1.3 78.3 - - - +
174A ARG* 1.3 61.9 + - - +
176A LYS* 3.3 11.4 + - - +
177A SER* 3.1 23.0 + - - -
205A ASN* 5.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 2.8 44.8 + - + -
141A GLU* 4.2 6.1 + - - +
143A LEU* 2.7 42.4 + - + -
145A PRO* 6.0 1.0 - - - +
170A ALA 3.0 17.8 + - - +
171A ILE 3.8 3.1 - - - +
173A ASP* 1.3 78.6 - - - +
175A CYS* 1.3 58.3 + - - +
177A SER* 3.3 6.5 + - - -
178A LEU* 2.9 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.2 7.9 - - - -
150A LEU* 4.1 22.9 - - - -
171A ILE* 2.8 26.7 + - - +
172A ALA* 3.5 6.5 - - - +
174A ARG* 1.3 75.4 - - - +
176A LYS* 1.3 65.9 + - - +
179A ASN* 3.0 5.4 + - - -
180A ILE* 2.8 68.8 + - - +
182A LEU* 4.2 14.1 - - + -
207A HIS* 4.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA 2.9 13.4 + - - +
173A ASP* 3.5 14.6 - - - +
175A CYS* 1.3 77.9 - - - +
177A SER* 1.3 62.8 + - - +
179A ASN* 3.5 8.9 + - - +
204A ASP* 3.0 28.4 + - - +
205A ASN* 3.5 11.3 + - - +
206A PRO* 5.3 4.5 - - - -
207A HIS* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 3.1 16.6 + - - -
174A ARG* 3.6 7.4 - - - -
175A CYS 3.2 0.2 - - - -
176A LYS* 1.3 79.2 - - - +
178A LEU* 1.3 67.4 + - - +
179A ASN 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU 3.6 32.3 - - - +
144A THR* 3.8 9.4 - - - +
145A PRO* 3.6 42.0 - - + +
174A ARG* 2.9 52.4 + - + +
175A CYS 3.2 0.2 + - - -
177A SER* 1.3 86.2 - - - +
179A ASN* 1.3 70.8 - - - +
180A ILE* 3.3 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO 5.1 0.8 - - - +
147A LEU 3.7 9.0 - - - +
148A ASP* 4.3 5.7 - - - +
175A CYS 3.0 4.6 + - - -
176A LYS 3.5 7.4 + - - +
177A SER 3.4 4.2 + - - +
178A LEU* 1.3 80.9 - - - +
180A ILE* 1.3 58.3 + - - +
181A ASN* 4.3 1.6 + - - -
207A HIS* 6.4 0.7 - - - -
----------------------------------------------------------
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