Contacts of the helix formed by residues 147 - 162 (chain A) in PDB entry 1LD7
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 ASP 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN 3.8 1.0 + - - -
146A LYS* 1.3 75.0 - - - +
148A LEU* 1.3 59.9 + - - +
149A HIS* 3.0 20.2 + - - +
150A GLU* 2.8 63.5 + - + +
151A GLU* 3.1 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.4 17.0 - - + +
146A LYS 3.2 13.6 + - - +
147A ASP* 1.3 71.5 + - - +
149A HIS* 1.3 61.6 + - - +
151A GLU* 3.1 5.1 + - - +
152A MET* 2.8 30.5 + - - +
175A LEU* 4.3 12.8 - - + +
178A TRP* 3.7 54.7 - - + +
179A LEU* 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 3.0 15.5 + - - +
148A LEU* 1.3 77.6 - - - +
150A GLU* 1.3 62.9 + - - +
152A MET* 3.3 8.8 + - - +
153A ASN* 3.1 29.4 + - - +
179A LEU* 3.9 30.5 - - + +
181A ASP* 3.9 22.9 + - + -
184A GLN* 5.0 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 2.8 32.6 + - + +
149A HIS* 1.3 80.3 - - - +
151A GLU* 1.3 61.5 + - - +
153A ASN* 3.2 26.7 + - + +
154A TYR* 3.2 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 4.1 4.9 - - - -
137A ARG* 2.7 41.9 + - - -
141A LEU* 3.6 27.5 - - + +
147A ASP 3.1 9.1 + - - +
148A LEU* 3.1 11.6 + - - +
150A GLU* 1.3 79.8 - - - +
152A MET* 1.3 55.7 + - - +
154A TYR* 3.1 13.4 + - - +
155A ILE* 2.9 27.4 + - - +
171A HIS* 2.7 25.6 + - - +
175A LEU* 3.5 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU 2.8 16.7 + - - +
149A HIS* 3.5 13.0 - - - +
150A GLU 3.2 0.2 - - - -
151A GLU* 1.3 77.2 - - - +
153A ASN* 1.3 53.9 + - - +
155A ILE* 3.2 6.7 - - - +
156A THR* 2.6 38.3 + - - -
172A ARG* 3.7 23.1 + - - +
175A LEU* 3.9 26.9 - - + +
176A VAL* 4.0 14.8 - - + -
179A LEU* 3.9 20.0 - - + -
181A ASP* 4.9 7.9 - - - +
184A GLN* 4.5 25.1 - - + +
185A GLU* 3.2 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A HIS* 3.1 18.7 + - - +
150A GLU* 3.2 23.3 + - - +
152A MET* 1.3 78.1 - - - +
154A TYR* 1.3 62.9 + - - +
156A THR* 3.5 8.8 + - - +
157A ALA* 3.3 20.1 + - - +
184A GLN* 4.7 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.4 55.7 + - + +
124A ILE* 3.6 33.3 - - - +
134A TRP* 4.1 13.7 - + - -
137A ARG* 3.5 34.5 - - - +
150A GLU 3.2 10.9 + - - +
151A GLU* 3.1 23.5 + - - +
153A ASN* 1.3 75.7 - - - +
155A ILE* 1.3 69.9 + - + +
157A ALA* 3.1 8.8 + - + +
158A ILE* 3.0 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 3.7 23.3 - - + -
151A GLU 2.9 17.2 + - - +
152A MET* 3.2 17.9 - - - +
154A TYR* 1.3 74.8 - - + +
156A THR* 1.3 61.4 + - - +
158A ILE* 3.7 5.6 - - + -
159A ILE* 2.9 32.7 + - + +
168A VAL* 3.5 34.1 - - + +
171A HIS* 3.7 20.9 - - + -
172A ARG* 3.7 38.4 - - + +
175A LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 2.6 22.7 + - - +
153A ASN* 3.5 10.7 + - - -
154A TYR 3.1 0.2 - - - -
155A ILE* 1.3 77.7 - - - +
157A ALA* 1.3 62.9 + - - +
159A ILE 3.6 0.2 + - - -
160A GLU* 3.1 32.5 + - + +
172A ARG* 3.0 23.1 + - - +
184A GLN* 4.8 6.6 + - - -
188A PHE* 3.6 26.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN 3.3 8.8 + - - +
154A TYR* 3.1 10.8 + - + +
156A THR* 1.3 81.2 - - - +
158A ILE* 1.3 67.5 + - + +
160A GLU* 3.3 10.3 + - - +
161A GLU* 3.2 34.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124A ILE* 5.0 7.2 - - + -
125A GLU* 6.4 1.8 - - + -
128A ALA* 5.3 4.5 - - + -
134A TRP* 4.4 8.5 - - + -
154A TYR* 3.0 55.5 + - + +
155A ILE* 3.7 9.4 - - + +
157A ALA* 1.3 79.0 - - + +
159A ILE* 1.3 58.0 + - - +
161A GLU* 3.0 21.5 + - - +
162A GLN* 2.9 30.7 + - + +
168A VAL* 3.4 30.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
155A ILE* 2.9 24.7 + - + +
158A ILE* 1.3 74.5 - - - +
160A GLU* 1.3 59.8 + - - +
162A GLN 4.1 6.7 - - - -
163A PRO* 2.8 31.3 - - + +
168A VAL* 3.7 38.6 - - + +
169A TRP* 3.5 35.9 - - + +
172A ARG* 3.8 30.7 - - + -
188A PHE* 3.5 25.8 - - + -
192A ILE* 4.0 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
156A THR* 3.1 27.5 + - + +
157A ALA* 3.4 11.2 - - - +
158A ILE 3.2 0.4 - - - -
159A ILE* 1.3 77.8 - - - +
161A GLU* 1.3 62.9 + - + +
163A PRO* 3.8 8.1 - - - +
188A PHE* 3.7 13.9 - - + -
191A ASP* 2.6 22.7 - - - +
192A ILE* 3.6 18.6 - - - +
195A GLN* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 6.0 1.9 - - - +
157A ALA* 3.2 24.2 + - - +
158A ILE* 3.0 20.7 + - - +
160A GLU* 1.3 80.2 - - + +
162A GLN* 1.3 73.3 + - + +
163A PRO* 3.5 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE 4.8 3.6 + - - -
125A GLU* 4.9 8.5 + - - +
128A ALA* 3.4 32.7 + - + +
158A ILE* 2.9 13.5 + - - +
159A ILE* 3.2 4.2 - - - -
161A GLU* 1.3 94.0 + - + +
163A PRO* 1.3 60.9 - - - +
164A LYS 3.2 6.9 + - - +
165A ASN* 3.5 21.7 + - + +
168A VAL* 3.5 19.4 - - + +
----------------------------------------------------------
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