Contacts of the helix formed by residues 122 - 131 (chain A) in PDB entry 1ZQN
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 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 4.3 21.0 - - + -
103A VAL* 5.4 1.3 - - + -
121A THR* 1.4 77.0 + - - +
123A GLU* 1.3 61.8 + - + +
125A LEU* 3.0 21.6 + - + +
126A ARG* 3.1 58.5 + - - +
140A LEU* 4.2 16.1 - - + +
143A PHE* 3.7 50.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.1 8.7 + - - +
122A LEU* 1.3 73.2 - - + +
124A ASP* 1.4 61.4 + - - +
125A LEU 3.0 1.6 - - - -
126A ARG* 2.6 46.4 + - - +
127A LYS* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 3.0 13.1 - - - +
119A ILE* 3.4 19.0 - - + +
120A LYS* 2.4 24.9 + - - +
121A THR* 2.8 40.0 + - - +
123A GLU* 1.4 77.2 - - - +
125A LEU* 1.3 62.7 + - - +
127A LYS* 4.2 5.8 - - - -
128A ASN* 2.4 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.8 26.0 - - + -
103A VAL* 3.9 14.8 - - + -
106A ILE* 3.9 14.8 - - + -
114A PHE* 4.1 15.9 - - + -
119A ILE* 3.8 19.1 - - + -
121A THR 2.8 12.7 + - - +
122A LEU* 3.2 13.2 - - + +
123A GLU 3.0 0.2 - - - -
124A ASP* 1.3 79.8 - - - +
126A ARG* 1.3 62.7 + - - +
128A ASN* 3.1 12.1 + - + +
129A GLU* 3.4 10.7 + - - -
132A LEU* 3.4 32.8 - - + +
140A LEU* 3.7 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.1 42.9 + - + +
123A GLU* 2.6 42.3 + - - +
125A LEU* 1.3 68.0 - - - +
127A LYS* 1.3 58.7 + - + +
128A ASN 2.7 14.5 + - - -
129A GLU* 2.7 28.8 + - - +
140A LEU* 4.5 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.9 30.0 + - + +
124A ASP* 3.9 4.0 - - - +
126A ARG* 1.3 77.5 - - + +
128A ASN* 1.3 75.3 + - - +
129A GLU 3.5 0.6 + - - -
130A ASP* 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.8 26.4 - - + +
124A ASP* 2.4 33.4 + - - +
125A LEU* 3.1 8.4 + - + +
126A ARG 2.7 2.2 + - - -
127A LYS* 1.3 94.9 - - - +
129A GLU* 1.3 51.7 - - - +
130A ASP* 2.7 29.6 + - - +
131A LYS* 2.8 36.2 + - + +
132A LEU* 3.9 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 3.4 4.7 + - - +
126A ARG* 2.7 26.5 + - - +
127A LYS 3.5 1.0 + - - -
128A ASN* 1.3 69.3 - - - +
130A ASP* 1.3 56.1 + - - +
131A LYS 3.4 0.2 - - - -
132A LEU* 3.2 18.1 + - + +
137A ARG* 2.8 59.4 + - + +
140A LEU* 4.9 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS 4.5 2.1 - - - +
128A ASN* 2.7 18.9 + - - +
129A GLU* 1.3 75.3 + - - +
131A LYS* 1.3 72.1 + - - +
132A LEU 3.0 11.2 + - - +
137A ARG* 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 4.3 8.6 + - - -
114A PHE* 3.7 24.3 - - + -
117A GLU* 3.5 39.7 - - - +
119A ILE* 4.4 8.6 - - + +
128A ASN* 2.8 39.4 + - + +
130A ASP* 1.3 86.6 + - - +
132A LEU* 1.3 59.7 + - + +
136A GLN* 4.5 1.0 + - - -
----------------------------------------------------------
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