Contacts of the helix formed by residues 129 - 142 (chain A) in PDB entry 2AUW
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 PRO 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 5.7 0.2 - - - -
121A TYR* 3.5 27.1 - - + +
126A LYS* 3.9 11.0 - - - +
127A ILE* 3.2 11.4 - - + +
128A ILE* 1.4 90.0 - - - +
130A ARG* 1.3 65.9 + - - +
131A THR* 3.9 16.2 - - - +
132A ILE* 3.1 23.7 + - + +
133A TRP* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 5.4 5.2 - - - -
128A ILE 3.6 2.4 + - - -
129A PRO* 1.3 71.1 - - - +
131A THR* 1.3 64.6 + - - +
133A TRP* 3.2 7.4 + - - +
134A LEU* 3.1 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PRO* 3.1 11.0 - - - +
130A ARG* 1.3 79.0 - - - +
132A ILE* 1.3 68.5 + - + +
134A LEU* 3.5 11.0 + - + +
135A ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.1 25.1 - - + -
111A LEU* 4.4 8.7 - - + +
113A ILE* 4.0 28.3 - - + -
121A TYR* 3.7 32.3 - - + +
128A ILE* 4.2 7.6 - - + -
129A PRO* 3.1 26.9 + - + +
131A THR* 1.3 81.7 - - + +
133A TRP* 1.3 59.5 + - - +
135A ALA* 3.3 9.6 + - + +
136A CYS* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.6 47.0 - - + +
92A MSE 3.5 45.6 - - + -
93A PHE* 4.0 8.7 - + - -
96A TRP* 3.7 22.7 - + + -
99A ARG* 4.1 13.7 - - - -
128A ILE* 4.5 1.3 - - + -
129A PRO 3.3 4.9 + - - +
130A ARG* 3.2 7.4 + - - +
132A ILE* 1.3 78.0 - - - +
134A LEU* 1.3 66.4 + - + +
136A CYS* 3.3 19.4 + - + +
137A LEU* 3.0 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 3.1 58.8 + - + +
131A THR* 3.6 9.0 - - + +
133A TRP* 1.3 77.6 - - + +
135A ALA* 1.3 51.0 + - - +
137A LEU* 3.4 14.7 + - + +
138A GLY* 2.7 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 23.1 - - + +
131A THR 3.1 14.5 + - - +
132A ILE* 3.3 15.7 - - + +
134A LEU* 1.3 73.6 - - - +
136A CYS* 1.3 59.7 + - - +
138A GLY* 4.4 1.8 - - - +
139A TRP* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.7 26.2 - - - -
96A TRP* 3.1 55.0 + - + +
111A LEU* 3.6 12.3 - - - +
132A ILE 2.9 23.3 + - - -
133A TRP* 3.3 29.1 + - + +
135A ALA* 1.3 75.8 - - - +
137A LEU* 1.3 61.8 + - - +
139A TRP* 3.3 1.0 + - - +
140A GLU* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.3 4.7 - - - +
133A TRP* 3.0 54.8 + - + +
134A LEU* 3.8 14.8 - - + +
136A CYS* 1.3 73.3 - - - +
138A GLY* 1.3 59.8 + - - +
140A GLU* 3.1 23.4 + - + +
141A ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU 2.7 21.0 + - - -
135A ALA* 3.7 2.7 - - - -
137A LEU* 1.3 72.1 - - - +
139A TRP* 1.3 61.6 + - - +
141A ALA* 3.3 7.3 + - - +
142A THR* 3.1 31.1 + - - +
153A LEU* 5.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 4.1 18.2 - + + -
100A ASN* 3.4 34.3 - - + -
102A LEU* 4.0 22.9 - - + -
110A ALA* 3.4 48.7 - - + +
111A LEU* 4.9 1.8 - - + -
135A ALA 2.8 21.0 + - - +
136A CYS* 3.5 5.6 - - - +
137A LEU 3.2 0.2 - - - -
138A GLY* 1.3 71.2 - - - +
140A GLU* 1.3 65.2 + - + +
142A THR* 3.2 9.9 + - - -
143A ARG* 2.6 78.0 + - + +
145A GLU* 3.6 12.2 + - - +
149A LEU* 5.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.7 8.8 - - - +
99A ARG* 2.7 48.2 + - - +
100A ASN* 2.9 33.1 + - - +
136A CYS 3.1 12.1 + - - +
137A LEU* 3.1 21.8 + - + +
139A TRP* 1.3 81.8 - - + +
141A ALA* 1.3 59.2 + - - +
142A THR 3.4 0.7 + - - -
143A ARG* 3.8 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU 2.9 15.3 + - - +
138A GLY* 3.7 7.9 - - - +
139A TRP 3.2 0.8 - - - -
140A GLU* 1.3 75.2 - - - +
142A THR* 1.3 57.7 + - - +
143A ARG 3.6 1.5 - - - +
153A LEU* 4.1 21.8 - - + -
154A PRO* 3.3 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY* 3.1 19.1 + - - +
139A TRP* 3.2 3.5 + - - -
141A ALA* 1.3 82.1 - - + +
143A ARG* 1.3 90.5 + - - +
144A PRO 2.9 15.8 - - - +
146A THR* 5.0 5.0 - - - +
149A LEU* 4.4 7.6 - - + +
150A PRO* 3.8 34.4 - - + +
152A THR 5.4 0.4 - - - +
153A LEU* 4.9 7.9 - - + -
154A PRO* 4.5 12.1 - - + -
----------------------------------------------------------
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