Contacts of the helix formed by residues 159 - 174 (chain A) in PDB entry 5L0P
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 SER 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 5.2 0.5 + - - -
69A ARG* 4.2 3.4 - - - +
129A LEU* 3.4 43.8 - - - +
130A ARG 4.3 5.9 + - - -
132A ILE* 5.0 4.3 - - - +
156A SER* 3.2 13.2 + - - -
158A HIS* 1.3 88.8 + - - +
160A GLY* 1.3 66.9 + - - +
161A ASP* 3.3 3.6 - - - -
162A VAL* 3.2 9.0 + - - +
163A LEU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.3 36.9 - - - +
153A ARG 4.1 0.7 - - - -
156A SER* 2.8 25.0 + - - -
157A PRO 4.8 0.4 + - - -
158A HIS 3.9 0.4 - - - -
159A SER* 1.3 76.7 - - - +
161A ASP* 1.3 57.8 + - - +
163A LEU* 3.5 5.1 + - - -
164A TYR* 2.9 24.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
61A LEU* 3.5 16.1 - - - +
65A ASP* 3.7 27.4 - - - +
68A TYR* 5.3 0.9 - - - -
69A ARG* 2.8 48.7 + - - +
149A LYS* 3.8 10.7 - - - +
153A ARG* 3.9 27.3 + - - +
159A SER 4.0 1.0 - - - -
160A GLY* 1.3 76.2 - - - +
162A VAL* 1.4 62.5 + - - +
164A TYR* 3.5 3.1 + - - +
165A GLU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.7 30.5 - - + -
57A ALA* 4.0 22.0 - - + +
60A LEU* 4.2 15.6 - - + +
61A LEU* 3.7 23.8 - - + -
69A ARG* 4.6 1.1 - - - +
127A PHE* 4.7 7.9 - - + -
129A LEU* 4.5 20.0 - - + -
159A SER* 3.2 8.0 + - - +
161A ASP* 1.4 82.0 + - - +
163A LEU* 1.3 59.1 + - + +
165A GLU* 3.4 5.2 + - - +
166A LEU* 2.7 33.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
119A TRP* 3.7 18.7 - - + -
120A LEU* 4.1 13.5 - - + -
123A ALA* 3.8 29.4 - - + -
129A LEU* 4.3 6.7 - - + -
132A ILE* 4.2 20.9 - - + -
137A PHE* 4.1 27.1 - - + -
152A PHE* 3.7 12.1 - - + -
156A SER* 4.4 9.0 - - - +
159A SER* 3.0 25.7 + - - +
160A GLY* 3.6 4.3 - - - +
162A VAL* 1.3 76.5 - - + +
164A TYR* 1.3 66.0 + - - +
166A LEU* 3.1 9.2 + - + +
167A LEU 2.9 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU 4.0 13.9 - - - -
148A THR* 4.6 1.3 - - - -
149A LYS* 3.7 43.1 + - + -
152A PHE* 3.3 38.9 - + + -
160A GLY 2.9 18.0 + - - +
161A ASP 3.7 4.5 - - - +
162A VAL 3.4 0.2 - - - -
163A LEU* 1.3 74.9 - - - +
165A GLU* 1.3 73.9 + - - +
167A LEU* 3.3 3.3 + - + +
168A GLN* 2.9 69.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.4 33.3 - - + +
61A LEU* 4.6 0.2 - - - -
62A THR* 3.7 15.7 - - + +
65A ASP* 3.8 4.9 - - - +
149A LYS* 2.8 34.0 + - - +
161A ASP 3.0 22.0 + - - +
162A VAL* 3.7 4.7 - - - +
163A LEU 3.2 0.2 - - - -
164A TYR* 1.3 88.1 - - - +
166A LEU* 1.3 66.5 + - - +
168A GLN* 3.3 12.6 + - - +
169A HIS* 3.0 39.4 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
60A LEU* 4.2 11.1 - - + +
98A ILE* 4.2 16.8 - - + -
119A TRP* 3.6 26.7 - - + +
122A TRP* 4.1 10.1 - - + -
123A ALA* 3.6 31.4 - - + -
127A PHE* 3.9 30.1 - - + -
162A VAL* 2.7 19.4 + - + +
163A LEU* 3.1 13.9 - - + +
165A GLU* 1.3 71.4 - - - +
167A LEU* 1.3 62.6 - - - +
169A HIS* 3.1 6.2 + - - +
170A ILE* 3.0 37.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
108A PRO* 3.7 35.0 - - + -
111A TRP* 4.6 14.1 - - + -
119A TRP* 4.0 9.8 - - + -
144A LEU* 4.2 17.9 - - + +
145A LEU* 3.8 21.3 - - + -
152A PHE* 4.0 22.4 - - + -
163A LEU 2.9 15.1 + - - +
164A TYR* 3.5 9.6 - - + +
166A LEU* 1.3 74.5 - - - +
168A GLN* 1.3 72.7 + - - +
170A ILE* 3.2 6.1 + - + +
171A LEU* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 2.9 79.4 + - + +
165A GLU* 3.3 18.6 + - - +
167A LEU* 1.3 86.0 - - - +
169A HIS* 1.3 61.5 + - + +
171A LEU* 3.2 20.2 + - - +
172A LYS* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU 5.5 2.5 - - - -
60A LEU* 3.5 36.4 + - + +
98A ILE* 4.7 13.6 - - + +
165A GLU* 3.0 36.6 + - - +
166A LEU* 3.1 8.3 + - - +
168A GLN* 1.3 78.4 - - + +
170A ILE* 1.3 65.6 + - - +
172A LYS* 3.0 19.4 + - + +
173A GLN* 3.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 4.4 12.5 - - + +
100A LEU* 3.9 36.6 - - + -
106A LEU 5.5 1.8 - - - +
108A PRO* 3.9 27.3 - - + +
111A TRP* 4.2 7.6 - - + -
119A TRP* 3.5 28.7 - - + +
166A LEU* 3.0 27.8 + - + +
167A LEU* 3.2 9.4 + - + +
169A HIS* 1.3 75.9 - - + +
171A LEU* 1.3 59.1 + - - +
173A GLN* 3.6 8.2 + - + +
174A ARG* 3.6 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 3.8 28.7 - - + -
145A LEU* 3.9 29.8 - - + -
167A LEU* 3.1 24.0 + - + +
168A GLN* 3.5 27.1 - - - +
169A HIS 3.1 0.4 - - - -
170A ILE* 1.3 73.9 - - - +
172A LYS* 1.3 65.6 + - - +
174A ARG* 3.4 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN 3.0 12.6 + - - +
169A HIS* 3.0 10.1 + - + +
171A LEU* 1.3 77.3 - - - +
173A GLN* 1.3 60.1 + - - +
174A ARG 3.3 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 5.9 3.1 - - - +
169A HIS 3.1 15.0 + - - +
170A ILE* 3.9 10.3 - - - +
171A LEU 3.3 0.2 - - - -
172A LYS* 1.3 76.1 - - - +
174A ARG* 1.3 59.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
107A GLN* 4.5 24.2 - - + -
108A PRO* 5.9 1.6 - - + -
170A ILE 3.6 9.3 + - - +
171A LEU* 3.4 20.8 + - + +
172A LYS 3.2 7.9 - - - +
173A GLN* 1.3 82.1 - - - +
----------------------------------------------------------
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