Contacts of the helix formed by residues 118 - 144 (chain A) in PDB entry 3KWO
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 ASP 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.6 14.2 - - + +
57A ARG* 2.9 26.6 + - - -
61A LEU* 3.9 10.0 - - - +
113A ALA* 2.9 21.2 + - - +
116A GLU* 3.1 12.4 - - + +
117A SER* 1.3 74.4 - - - +
119A THR* 1.3 56.4 + - - +
120A THR* 3.4 2.6 + - - -
121A THR* 2.6 31.3 + - - -
122A ALA* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.3 12.0 + - - +
118A ASP* 1.3 69.4 + - - +
120A THR* 1.3 69.4 + - - +
122A ALA* 3.7 6.5 - - - +
123A ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 3.5 40.0 + - - +
60A GLN* 5.2 1.3 - - - +
118A ASP* 3.3 1.8 + - - -
119A THR* 1.3 84.0 + - - +
121A THR* 1.3 63.9 + - - +
123A ALA* 3.3 4.8 + - - +
124A PHE* 3.0 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.8 12.3 - - + +
7A LEU* 4.5 7.2 - - + -
57A ARG* 3.0 23.5 + - + +
109A LEU* 3.8 37.7 - - + -
113A ALA* 3.9 8.1 - - + -
118A ASP* 2.6 30.1 + - - -
120A THR* 1.3 75.4 - - - +
122A ALA* 1.3 61.1 + - - +
124A PHE* 3.2 8.6 + - + +
125A ALA* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 3.8 15.5 - - - +
113A ALA* 3.5 14.5 - - + +
114A GLU* 4.7 9.0 - - + -
118A ASP 3.0 19.8 + - - +
119A THR* 3.7 7.9 - - - +
120A THR 3.3 0.2 - - - -
121A THR* 1.3 77.0 - - - +
123A ALA* 1.3 56.9 + - - +
125A ALA* 3.2 3.0 + - - +
126A GLN* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR 2.9 17.8 + - - +
120A THR* 3.7 6.3 - - - +
122A ALA* 1.3 76.0 - - - +
124A PHE* 1.3 57.8 + - - +
126A GLN* 3.8 7.2 - - - +
127A GLU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.2 16.2 - - + -
50A LEU* 3.6 26.5 - - + -
53A SER* 4.1 26.2 - - - -
54A CYS* 4.3 4.9 - - - -
57A ARG* 5.8 5.8 - - + -
106A PHE* 4.3 6.5 - + - -
109A LEU* 4.0 25.4 - - + -
120A THR* 3.0 15.7 + - + +
121A THR* 3.5 11.9 - - + +
123A ALA* 1.3 78.0 - - - +
125A ALA* 1.3 63.7 + - - +
127A GLU* 3.5 10.1 + - - +
128A ASN* 3.0 46.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.7 21.1 - - - +
109A LEU* 4.0 10.8 - - + -
110A ASN* 3.6 34.5 - - + +
121A THR 2.8 19.5 + - - +
122A ALA 3.6 4.3 - - - +
124A PHE* 1.3 74.9 - - - +
126A GLN* 1.3 57.7 + - - +
128A ASN* 3.2 4.9 + - - +
129A ILE* 2.8 32.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
110A ASN* 2.8 32.0 + - - +
114A GLU* 3.6 16.6 + - - +
122A ALA* 2.9 28.5 + - - +
123A ALA* 3.9 5.9 - - - +
125A ALA* 1.3 72.8 - - - +
127A GLU* 1.3 67.3 + - - +
129A ILE* 3.6 11.8 - - + +
130A ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 2.9 17.2 + - - +
124A PHE* 3.7 11.7 - - - +
126A GLN* 1.3 76.9 - - - +
128A ASN* 1.3 66.4 + - - +
130A ALA* 3.4 7.1 + - - +
131A LYS* 3.1 21.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
50A LEU* 4.9 2.9 - - - +
106A PHE* 3.5 38.1 - - + -
124A PHE* 3.0 43.9 + - - -
125A ALA 3.2 8.4 + - - +
126A GLN 3.1 0.8 - - - -
127A GLU* 1.3 83.7 + - - +
129A ILE* 1.3 65.6 + - - +
131A LYS* 3.2 13.7 + - - +
132A TYR* 3.0 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.9 18.2 - - + +
106A PHE* 3.7 32.8 - - + +
107A LYS* 3.9 21.3 - - + -
110A ASN* 4.0 18.2 - - + +
125A ALA 2.8 24.1 + - - +
126A GLN* 3.1 12.1 + - + +
128A ASN* 1.3 73.8 - - - +
130A ALA* 1.3 62.9 + - - +
132A TYR 3.3 0.5 + - - -
133A GLU* 3.0 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN 2.9 12.7 + - - +
127A GLU* 3.5 11.4 - - - +
129A ILE* 1.3 77.9 - - - +
131A LYS* 1.3 61.4 + - - +
133A GLU* 3.9 9.1 - - - +
134A LYS* 3.2 24.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
46A GLU* 2.9 43.0 + - - -
127A GLU* 3.1 13.5 + - + +
128A ASN* 3.2 17.9 + - - +
130A ALA* 1.3 78.8 - - - +
132A TYR* 1.3 89.6 + - + +
134A LYS* 3.6 3.8 + - - +
135A SER* 3.1 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 4.5 2.3 + - - +
47A MSE 3.2 28.6 - - - +
50A LEU* 5.3 0.3 - - - +
99A TYR* 3.6 57.8 - + + +
102A LEU* 3.9 8.5 - - + -
103A LEU* 4.3 21.1 - - + -
106A PHE* 3.6 32.0 - + - -
128A ASN* 3.0 38.0 + - - +
129A ILE 4.4 1.3 - - - +
131A LYS* 1.3 101.2 - - + +
133A GLU* 1.3 61.3 + - - +
135A SER* 4.2 3.8 - - - -
136A LEU* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.1 15.2 - - + +
107A LYS* 4.1 17.0 + - - -
129A ILE* 3.0 48.3 + - + +
130A ALA* 3.9 7.8 - - - +
132A TYR* 1.3 75.5 - - - +
134A LYS* 1.3 61.7 + - - +
136A LEU* 4.0 4.1 - - - +
137A TRP* 3.1 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
130A ALA 3.2 14.5 + - - +
131A LYS* 3.8 4.9 - - - +
133A GLU* 1.3 79.6 - - - +
135A SER* 1.3 61.9 + - - +
137A TRP* 3.2 26.7 + - + +
138A MSE 3.2 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 5.0 4.1 + - - -
99A TYR* 4.2 25.6 - - - -
131A LYS* 3.1 28.5 + - - +
132A TYR* 3.9 7.4 - - - -
134A LYS* 1.3 75.1 - - - +
136A LEU* 1.3 58.1 + - - +
138A MSE 3.2 18.7 + - - +
139A ILE* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS* 3.8 24.7 - - + +
99A TYR* 3.7 40.6 - - + +
100A GLU* 3.7 28.9 - - + +
103A LEU* 3.9 27.1 - - + -
132A TYR* 2.8 26.2 + - + +
133A GLU* 4.0 3.6 - - - +
135A SER* 1.3 70.6 - - - +
137A TRP* 1.3 61.1 + - - +
139A ILE* 4.1 5.1 - - + +
140A GLY* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU 3.1 15.3 + - - +
134A LYS* 3.2 22.0 + - + +
136A LEU* 1.3 77.8 - - - +
138A MSE 1.3 84.6 + - + +
140A GLY* 3.3 2.0 + - - -
141A ALA* 3.0 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 3.2 43.6 + - + +
135A SER* 3.2 21.3 + - - +
137A TRP* 1.3 98.3 - - + +
139A ILE* 1.3 61.3 + - - +
141A ALA* 3.2 7.9 + - - +
142A THR* 2.7 33.0 + - - -
158A ACY 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.9 13.2 - - + +
92A ILE* 3.8 22.2 - - + +
95A ILE* 4.0 11.9 - - + -
96A LYS* 3.6 32.5 - - + +
99A TYR* 3.5 32.1 - - + -
135A SER 2.8 22.5 + - - +
136A LEU* 4.1 7.4 - - + +
138A MSE 1.3 76.4 - - - +
140A GLY* 1.3 62.6 + - - +
142A THR* 3.1 17.1 + - - -
143A LEU* 3.1 15.4 + - + +
158A ACY 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS* 4.7 15.7 - - - +
136A LEU 2.9 18.0 + - - -
137A TRP* 3.7 1.6 - - - -
139A ILE* 1.3 77.3 - - - +
141A ALA* 1.3 63.0 + - - +
143A LEU* 3.2 6.2 + - - +
144A GLN* 3.0 33.3 + - - +
----------------------------------------------------------
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 TRP* 3.0 27.4 + - + +
138A MSE 3.2 8.3 + - - +
140A GLY* 1.3 77.6 - - - +
142A THR* 1.3 60.8 + - - +
143A LEU 3.4 0.3 + - - -
144A GLN* 3.4 29.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
89A LEU* 4.8 6.9 - - + +
92A ILE* 4.1 31.6 - - + -
138A MSE 2.7 18.9 + - - -
139A ILE* 3.3 11.7 - - - -
141A ALA* 1.3 78.3 - - - +
143A LEU* 1.3 61.0 + - + +
144A GLN 4.4 2.6 - - - +
158A ACY 2.8 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.9 23.0 - - + +
92A ILE* 3.5 23.8 - - + -
93A GLU* 3.8 35.2 - - + +
96A LYS* 3.8 28.9 - - + -
139A ILE* 3.1 23.3 + - + +
140A GLY* 3.8 5.2 - - - +
141A ALA 3.2 0.2 - - - -
142A THR* 1.3 78.8 - - - +
144A GLN* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 3.0 21.2 + - - +
141A ALA* 3.4 30.3 + - - +
142A THR 4.4 2.9 - - - +
143A LEU* 1.3 83.5 - - - +
145A GLY* 1.3 67.3 + - - +
146A ALA 4.3 0.5 + - - -
----------------------------------------------------------
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