Contacts of the helix formed by residues 132 - 148 (chain A) in PDB entry 2A79
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 SER 132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR 5.2 1.6 + - - -
129A ARG 5.1 3.2 + - - -
130A GLY* 3.4 3.0 + - - -
131A LEU* 1.3 80.6 - - - +
133A ARG* 1.3 65.6 + - - +
134A LYS* 3.2 10.5 + - - +
135A HIS* 2.9 24.7 + - - +
136A ILE* 2.8 22.8 + - - +
164A THR* 3.8 11.2 + - - -
168A GLU* 3.2 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 3.8 0.6 + - - -
132A SER* 1.3 71.8 - - - +
134A LYS* 1.3 63.1 + - - +
137A ILE* 3.1 43.3 + - + +
168A GLU* 2.7 31.9 + - + +
171A ARG* 3.8 21.0 + - - +
172A ALA* 3.8 20.3 - - + +
175A HIS* 3.4 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR* 3.6 41.5 - - + +
132A SER* 3.0 9.2 + - - +
133A ARG* 1.3 79.3 - - - +
135A HIS* 1.3 59.3 + - - +
137A ILE* 4.0 2.8 - - - +
138A GLU* 2.8 75.9 + - - +
168A GLU* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 2.9 35.6 + - - -
119A ILE* 3.8 8.1 - - + +
120A PHE 3.6 11.7 + - - -
122A GLY* 4.0 6.5 - - - -
127A THR 4.1 10.0 + - - +
128A GLU* 3.5 33.3 + - + +
129A ARG 3.8 9.0 - - - +
130A GLY 3.2 26.9 - - - +
132A SER* 2.9 17.6 + - - +
134A LYS* 1.3 77.2 - - - +
136A ILE* 1.3 58.4 + - - +
138A GLU* 4.6 5.8 + - + +
139A GLY* 2.5 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 4.4 13.3 - - + +
130A GLY 4.8 1.3 - - - +
131A LEU* 3.4 37.2 - - + +
132A SER 2.8 19.5 + - - +
135A HIS* 1.3 70.1 - - - +
137A ILE* 1.3 58.9 + - - +
140A LEU* 2.9 32.3 + - + +
155A VAL* 5.8 3.4 - - + -
169A THR* 4.0 13.2 - - + +
172A ALA* 3.9 28.9 - - + -
173A MET* 3.7 39.7 - - + -
176A VAL* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 3.1 44.7 + - + +
134A LYS* 4.0 2.5 - - - +
136A ILE* 1.3 73.8 - - - +
138A GLU* 1.3 72.0 + - + +
140A LEU* 3.9 1.0 - - - +
141A LYS* 2.9 29.4 + - + +
172A ALA* 5.1 3.8 - - + -
175A HIS* 3.4 37.7 - - + +
176A VAL* 4.2 13.9 - - + -
181A MET* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR 4.7 3.8 - - - +
128A GLU* 5.7 3.5 - - - +
134A LYS* 2.8 62.1 + - + +
135A HIS* 4.2 5.9 + - - +
137A ILE* 1.3 77.8 - - + +
139A GLY* 1.3 64.7 + - - +
141A LYS* 3.1 9.6 + - + +
142A ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.8 16.9 - - - +
119A ILE* 3.6 9.7 - - - +
135A HIS* 2.5 34.9 + - - -
138A GLU* 1.3 74.7 - - - +
140A LEU* 1.3 61.7 + - - -
142A ALA* 3.3 6.2 + - - +
143A SER* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 4.1 19.7 - - + -
119A ILE* 3.7 11.8 - - + +
136A ILE* 2.9 22.5 + - + +
139A GLY* 1.3 71.9 - - - +
141A LYS* 1.3 59.0 + - - +
143A SER* 3.2 1.4 + - - -
144A LEU* 2.8 50.0 + - + +
152A VAL* 4.1 8.1 - - + -
155A VAL* 4.0 24.9 - - + -
176A VAL* 3.8 34.8 - - + -
181A MET* 3.8 30.1 - - + +
182A ALA* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 2.9 21.8 + - + +
138A GLU* 3.4 8.5 - - - +
140A LEU* 1.3 77.0 - - - +
142A ALA* 1.3 62.7 + - - +
144A LEU* 3.2 8.1 + - + +
145A GLU* 2.9 32.7 + - - +
181A MET* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 5.5 0.9 - - - +
138A GLU 2.9 13.4 + - - +
139A GLY* 3.5 10.8 - - - +
141A LYS* 1.3 76.7 - - - +
143A SER* 1.3 62.2 + - - +
145A GLU* 3.2 9.7 + - - +
146A ARG* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.6 8.5 - - - +
96A GLU* 2.8 27.6 + - - -
117A THR* 4.3 13.2 - - - -
119A ILE* 3.7 6.6 - - - +
139A GLY 3.1 9.7 + - - -
140A LEU* 3.5 11.2 - - - -
142A ALA* 1.3 77.5 - - - +
144A LEU* 1.3 65.5 + - - +
146A ARG* 3.2 20.3 + - - +
147A LEU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 2.8 30.7 + - + +
141A LYS* 3.5 6.3 - - + +
143A SER* 1.3 72.6 - - - +
145A GLU* 1.3 62.0 + - - +
147A LEU* 3.5 3.7 + - + -
148A GLN 3.0 16.1 + - - -
149A LEU* 3.1 27.4 + - + +
150A GLU 3.5 19.5 - - - +
151A TYR* 3.5 19.1 - - - +
152A VAL* 3.5 33.4 - - + +
181A MET* 3.7 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 2.9 22.8 + - - +
142A ALA* 3.4 12.0 - - - +
143A SER 3.1 0.2 - - - -
144A LEU* 1.3 75.3 - - - +
146A ARG* 1.3 67.8 + - + +
148A GLN* 2.9 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.4 19.4 + - - +
93A GLY* 3.4 30.2 - - - -
96A GLU* 2.7 39.7 + - + -
97A VAL* 3.9 32.8 - - + +
100A GLY* 4.8 0.2 - - - -
101A ASN* 5.6 0.2 - - - +
142A ALA* 3.0 34.0 + - - +
143A SER* 3.3 26.0 + - - +
145A GLU* 1.3 77.9 - - + +
147A LEU* 1.3 62.1 + - - +
148A GLN* 3.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 4.5 1.1 - - + -
96A GLU* 3.6 38.1 - - + +
99A LEU* 3.8 30.3 - - + -
100A GLY* 3.3 21.3 - - - +
104A LYS* 5.2 0.3 + - - -
115A ILE* 4.5 6.5 - - + -
117A THR* 4.9 4.9 - - - -
143A SER* 2.9 29.5 + - - +
144A LEU* 3.9 5.2 - - - +
146A ARG* 1.3 73.0 - - - +
148A GLN* 1.3 69.9 + - - +
149A LEU* 3.5 29.4 - - + +
152A VAL* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 4.5 1.8 - - - +
101A ASN* 3.2 29.3 + - - +
104A LYS* 3.4 50.4 + - - +
144A LEU 3.0 1.5 + - - -
145A GLU* 2.9 21.0 + - - +
146A ARG 3.0 5.9 - - - +
147A LEU* 1.3 82.8 - - - +
149A LEU* 1.3 59.6 + - - +
----------------------------------------------------------
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