Contacts of the helix formed by residues 155 - 171 (chain A) in PDB entry 5IZL
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 LYS 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.0 3.3 - - - +
152A PRO* 3.1 20.2 + - + +
154A GLY* 1.3 71.2 - - - +
156A ARG* 1.3 63.9 + - - +
157A GLN 3.9 0.2 - - - -
158A ALA* 4.3 11.6 - - + +
159A ALA* 3.3 19.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
148A ILE* 3.6 30.0 + - + +
149A ASP* 4.1 13.7 + - - +
151A LEU* 3.3 44.7 + - + +
152A PRO 2.9 9.1 + - - +
153A GLU* 3.4 31.5 - - + +
154A GLY 3.2 4.4 + - - -
155A LYS* 1.3 73.8 - - - +
157A GLN* 1.3 62.4 + - - +
158A ALA 3.1 0.9 - - - -
159A ALA* 2.8 21.7 + - - +
160A ILE* 3.2 17.1 + - + +
200A GLN* 3.7 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU 4.7 1.2 + - - -
154A GLY 5.1 0.8 + - - -
156A ARG* 1.3 79.1 - - - +
158A ALA* 1.3 61.6 + - - +
159A ALA 3.4 0.3 + - - -
160A ILE* 3.5 24.2 + - - +
161A ASP* 2.6 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY 5.3 3.3 + - - +
155A LYS* 4.5 13.7 - - + +
156A ARG 3.1 1.2 - - - +
157A GLN* 1.3 80.5 - - - +
159A ALA* 1.3 60.9 + - - +
161A ASP* 3.8 9.2 + - - +
162A LYS* 3.7 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 6.0 0.7 - - - -
151A LEU* 4.2 23.3 - - + -
155A LYS* 3.3 18.7 + - + +
156A ARG 2.8 5.8 + - - +
158A ALA* 1.3 78.5 - - - +
160A ILE* 1.3 65.9 + - - +
162A LYS* 3.1 15.8 + - - +
163A MET* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 5.0 4.5 - - + -
145A LEU* 4.4 11.2 - - + -
148A ILE* 4.5 21.3 - - + -
151A LEU* 4.6 11.9 - - + -
156A ARG* 3.2 17.2 + - + +
157A GLN* 4.0 22.9 - - - +
158A ALA 3.5 0.2 - - - -
159A ALA* 1.3 77.8 - - - +
161A ASP* 1.3 55.9 + - - +
163A MET* 3.1 8.3 + - - +
164A THR* 2.6 51.4 + - - +
183A PRO* 4.3 31.6 - - + -
----------------------------------------------------------
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 GLN* 2.6 43.3 + - - +
158A ALA* 4.1 9.0 - - - +
159A ALA 3.3 0.8 - - - -
160A ILE* 1.3 79.7 - - - +
162A LYS* 1.3 58.7 + - - +
164A THR* 3.7 8.1 + - - -
165A LYS* 2.9 30.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
158A ALA 3.7 9.1 + - - +
159A ALA* 3.1 12.2 + - - +
161A ASP* 1.3 75.8 - - - +
163A MET* 1.3 60.5 + - - +
165A LYS* 3.3 4.4 + - - +
166A LYS* 2.8 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.9 0.4 - - + -
119A VAL* 4.3 22.4 - - + +
122A GLY* 3.7 31.9 - - - -
123A MET* 4.7 3.1 - - + +
145A LEU* 4.0 28.3 - - + -
159A ALA 3.1 8.5 + - - +
160A ILE 3.1 7.5 + - - +
162A LYS* 1.3 74.6 - - - +
164A THR* 1.3 68.0 + - - +
166A LYS* 3.3 23.2 + - + -
167A MET* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.0 7.2 - - - +
160A ILE* 2.6 42.5 + - - +
161A ASP* 3.7 9.2 + - - -
163A MET* 1.3 71.7 - - - +
165A LYS* 1.3 58.2 + - - +
167A MET* 2.9 18.4 + - - +
168A GLN* 3.0 27.1 + - - +
181A ILE* 3.6 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP 2.9 19.6 + - - +
162A LYS* 3.9 4.5 - - - +
164A THR* 1.3 77.1 - - - +
166A LYS* 1.3 62.7 + - - +
168A GLN* 3.4 17.5 + - - +
169A LYS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 2.8 25.9 + - + +
163A MET* 3.5 25.8 - - + +
165A LYS* 1.3 76.8 - - - +
167A MET* 1.3 52.0 + - - +
169A LYS* 3.6 6.7 + - + +
170A THR* 2.4 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.9 3.1 - - + -
117A ILE* 4.6 13.2 - - + -
123A MET* 4.0 33.7 - - + -
143A VAL* 4.2 25.8 - - + -
145A LEU* 4.6 7.4 - - + -
163A MET* 2.9 41.6 + - + +
164A THR* 2.9 7.6 + - - +
166A LYS* 1.3 73.7 - - - +
168A GLN* 1.3 67.0 + - - +
169A LYS 3.1 1.6 - - - -
170A THR* 2.9 24.3 + - + -
171A LEU* 2.9 33.7 + - + +
181A ILE* 3.6 16.6 - - + -
----------------------------------------------------------
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 THR* 3.0 26.9 + - - +
165A LYS* 3.4 17.9 + - - +
167A MET* 1.3 75.6 - - - +
169A LYS* 1.3 61.7 + - - +
171A LEU* 3.4 8.3 + - - +
172A GLU* 3.1 21.3 + - - +
177A ARG 4.6 10.3 - - - +
179A ALA 5.7 1.1 - - - +
181A ILE* 3.8 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS 3.1 16.4 + - - +
166A LYS* 3.7 8.3 - - + +
167A MET 3.1 0.6 - - - -
168A GLN* 1.3 77.4 - - - +
170A THR* 1.3 63.3 + - - +
172A GLU* 3.0 23.5 + - - +
173A ASN 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET* 4.0 32.4 - - + +
131A LEU* 4.6 9.5 - - + +
166A LYS* 2.4 27.5 + - - +
167A MET* 2.9 19.7 + - + +
169A LYS* 1.3 75.9 - - - +
171A LEU* 1.3 61.3 + - - +
172A GLU 3.6 0.2 + - - -
173A ASN* 4.6 3.6 + - - +
174A THR* 4.2 10.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
115A LEU* 6.0 0.4 - - + -
131A LEU* 4.1 35.4 - - + -
141A LEU* 4.1 9.4 - - + -
143A VAL* 4.1 16.6 - - + -
167A MET* 2.9 34.6 + - + +
168A GLN* 3.6 6.5 - - - +
170A THR* 1.3 75.2 - - - +
172A GLU* 1.3 64.1 + - - +
173A ASN 3.3 2.9 - - - -
174A THR* 3.1 20.9 + - - +
176A PHE 3.5 22.0 - - - +
177A ARG* 3.2 19.7 - - - +
179A ALA* 4.0 24.0 - - + +
181A ILE* 5.0 3.1 - - + -
----------------------------------------------------------
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