Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 4XZ0
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 ALA 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS 3.1 12.8 + - - +
120A ASP* 1.3 80.7 - - - +
122A MET* 1.3 61.1 + - - +
123A VAL 3.6 0.4 - - - -
124A ARG* 3.6 4.6 - - - +
125A ASP* 3.2 27.4 + - - +
301A 4N5 3.6 46.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS* 3.4 4.9 + - - +
118A LEU* 3.2 11.6 + - - +
121A ALA* 1.3 73.2 - - - +
123A VAL* 1.3 63.3 + - - +
124A ARG 3.2 0.9 - - - -
125A ASP* 3.3 5.8 + - - +
126A TYR* 3.0 26.5 + - - +
153A ILE* 3.7 27.1 - - + +
157A ALA* 4.0 17.5 - - + +
160A ARG* 5.6 2.9 - - + -
161A MET* 3.5 24.0 - - + -
233A TRP* 3.3 41.5 - - + -
301A 4N5 3.3 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 2.7 36.1 + - + +
119A ARG* 3.6 14.8 - - + +
122A MET* 1.3 68.4 - - - +
124A ARG* 1.3 60.6 + - - +
126A TYR* 3.1 10.0 + - + +
127A VAL* 2.8 37.8 + - + +
142A ILE* 3.8 16.4 - - - +
145A GLN* 3.7 29.6 - - + -
150A GLU* 4.3 16.8 - - + -
153A ILE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A HIS* 3.7 9.3 - - - +
119A ARG 3.1 7.2 + - - +
120A ASP* 2.7 54.1 + - - +
121A ALA* 3.6 5.6 - - - +
123A VAL* 1.3 76.3 - - - +
125A ASP* 1.3 56.5 + - - +
127A VAL* 3.3 2.6 + - - +
128A ARG* 2.9 40.0 + - - +
134A GLU 5.3 1.0 + - - -
138A LEU* 3.8 31.9 - - + +
139A GLU* 3.6 26.1 + - - +
142A ILE* 3.6 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA 3.2 15.5 + - - +
122A MET* 3.8 5.8 - - - +
123A VAL 3.2 0.2 - - - -
124A ARG* 1.3 76.2 - - - +
126A TYR* 1.3 66.4 + - - +
128A ARG* 3.4 18.7 + - - +
129A GLN* 2.9 46.0 + - - +
301A 4N5 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET 3.0 13.3 + - - +
123A VAL* 3.4 9.2 - - + +
125A ASP* 1.3 78.8 + - - +
127A VAL* 1.3 72.7 + - + +
129A GLN* 3.3 5.1 + - - +
130A THR* 3.1 47.0 + - + +
131A TRP* 4.3 16.6 - + - -
145A GLN* 3.8 21.4 + - - -
149A VAL* 3.9 23.2 - - + +
152A LEU* 6.4 2.0 - - + -
153A ILE* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 2.8 39.6 + - + +
126A TYR* 1.3 73.6 - - + +
128A ARG* 1.3 59.6 + - - +
130A THR* 3.7 5.8 - - - -
131A TRP* 2.8 36.2 + - + -
132A LYS 3.4 3.3 + - - -
133A LEU* 3.9 25.6 - - + -
138A LEU* 3.3 27.6 - - + -
141A ALA* 4.2 10.3 - - + +
142A ILE* 4.6 5.4 - - + -
145A GLN* 4.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 2.9 30.8 + - - +
125A ASP* 3.7 22.3 + - - +
127A VAL* 1.3 75.0 - - - +
129A GLN* 1.3 73.2 + - - +
132A LYS* 3.1 33.2 + - - +
133A LEU 4.2 9.3 + - - +
138A LEU* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 2.9 44.6 + - - +
126A TYR* 3.7 6.1 - - - +
128A ARG* 1.3 90.0 + - - +
130A THR* 1.3 63.3 + - + +
132A LYS* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.1 41.0 + - + +
127A VAL 3.3 0.7 + - - -
129A GLN* 1.3 84.6 - - + +
131A TRP* 1.3 96.7 + - - +
132A LYS* 4.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 4.3 13.9 - + - -
127A VAL* 2.8 26.7 + - + +
130A THR* 1.3 101.8 + - - +
132A LYS* 1.3 76.1 + - - +
133A LEU* 3.3 29.0 + - + +
141A ALA* 6.0 0.9 - - + -
145A GLN* 3.9 32.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL 3.4 1.4 + - - -
128A ARG* 3.1 23.9 + - - +
129A GLN* 2.9 31.1 + - - +
130A THR 4.4 6.7 - - - +
131A TRP* 1.3 83.1 - - - +
133A LEU* 1.3 65.7 + - - +
134A GLU* 4.5 6.8 - - - +
----------------------------------------------------------
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