Contacts of the strand formed by residues 123 - 130 (chain A) in PDB entry 1AZ7
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 GLY 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER 5.7 0.2 - - - -
116A GLU* 3.8 4.7 - - - -
122A ALA* 1.3 76.4 - - - +
124A CYS* 1.3 61.1 + - - -
172A GLY 3.0 20.3 + - - -
173A LEU* 2.9 23.6 + - - +
205A THR* 4.1 11.2 - - - -
207A GLU* 3.5 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.2 35.0 + - - +
115A PRO* 3.0 31.3 + - + +
116A GLU* 5.0 3.8 - - - -
117A ALA 5.7 0.2 - - - -
122A ALA 5.2 1.3 - - - -
123A GLY* 1.3 75.1 - - - -
125A LEU* 1.3 69.2 + - - +
169A GLU 5.9 0.4 - - - -
170A LEU 3.4 4.0 - - - +
171A CYS* 2.0 48.2 - - - -
172A GLY 4.7 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
111A MET* 4.6 9.4 - - + -
112A ASP 3.4 17.5 - - - +
113A PRO* 3.9 12.3 - - + -
124A CYS* 1.3 80.7 - - - +
126A GLN* 1.3 64.5 + - - +
127A LEU* 3.1 23.7 + - + +
169A GLU* 5.0 0.4 - - - -
170A LEU* 2.8 24.4 + - - +
173A LEU* 3.8 16.8 - - + +
203A LEU* 3.8 27.8 - - + -
204A ARG 3.8 25.4 - - - +
205A THR* 3.9 19.7 - - + +
206A THR* 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 3.4 1.9 - - - -
112A ASP* 2.7 49.0 + - + +
114A SER* 2.8 22.9 + - - +
125A LEU* 1.3 66.4 - - - +
127A LEU* 1.3 60.1 + - - +
128A CYS* 3.7 4.8 + - + +
167A GLN* 3.0 57.5 + - + +
168A TYR 3.1 16.0 + - - +
169A GLU* 4.0 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 4.0 2.2 - - - +
110A THR 3.8 6.1 - - - +
111A MET* 3.6 27.1 - - + -
125A LEU* 3.2 12.3 - - + +
126A GLN* 1.3 70.4 + - - +
128A CYS* 1.3 60.6 + - - +
129A TRP* 3.6 25.9 + - + -
166A LEU 3.5 2.3 - - - +
167A GLN* 3.1 2.9 - - - -
168A TYR 2.8 37.9 + - - +
170A LEU* 3.9 24.5 - - + -
181A LEU* 3.6 31.6 - - + -
203A LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU 4.3 0.7 - - - +
109A ARG* 3.2 2.2 - - - -
110A THR* 2.8 69.2 + - - +
111A MET* 3.9 4.7 - - - -
112A ASP* 4.4 7.6 - - - -
126A GLN* 4.0 10.1 - - + -
127A LEU* 1.3 71.9 - - - +
129A TRP* 1.3 58.3 + - - +
130A GLU* 5.4 5.4 - - - +
166A LEU* 3.3 9.6 - - + +
167A GLN* 4.1 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 5.3 1.1 - - + -
107A MET 4.3 4.3 - - - +
108A LEU 3.8 6.7 - - - -
109A ARG* 3.5 33.0 - - + -
127A LEU* 3.6 31.0 - - + -
128A CYS* 1.3 72.1 - - - +
130A GLU* 1.3 74.0 + - - +
131A PRO* 3.7 6.2 - - - +
144A LEU* 3.8 28.9 - - + -
161A LEU* 4.4 3.4 - - + -
165A ALA 2.7 23.1 + - - -
166A LEU* 2.8 38.6 + - - +
168A TYR* 3.6 31.0 - + + -
181A LEU* 4.1 9.4 - - + -
183A ILE* 3.7 37.2 - - + -
185A CYS* 4.1 19.1 - - - -
201A LEU* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 3.5 4.7 - - - +
107A MET* 2.7 65.9 + - + +
108A LEU* 3.5 24.6 + - + +
128A CYS* 5.4 4.7 - - - +
129A TRP* 1.3 81.2 + - - +
131A PRO* 1.3 68.7 - - + +
132A TRP 3.5 1.1 - - - -
166A LEU* 5.7 4.4 - - - +
----------------------------------------------------------
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