Contacts of the helix formed by residues 128 - 150 (chain A) in PDB entry 4ICK
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 PHE 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS* 5.3 12.1 - + + +
80A LEU* 4.5 2.0 - - + -
82A TYR* 3.4 53.4 - + + -
83A VAL 6.1 0.4 - - - -
126A ALA 2.7 14.1 + - - +
127A GLN* 1.3 82.9 + - - +
129A LYS* 1.3 76.1 + - + +
130A GLU* 3.2 40.6 - - + -
131A MET* 3.1 23.6 + - + +
132A LYS* 3.0 24.8 + - - +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN 3.4 5.1 + - - +
128A PHE* 1.3 84.7 - - + +
130A GLU* 1.3 71.6 + - + +
132A LYS* 3.5 10.9 + - + +
133A ALA* 3.0 27.2 + - - +
79B GLU* 4.7 6.9 - - - +
81B ASN* 3.9 31.6 - - - +
90B THR* 5.0 4.0 + - - -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.0 14.4 + - - +
80A LEU* 3.6 15.2 - - + +
81A ASN 3.0 37.7 + - - +
82A TYR* 3.4 11.3 - - - +
128A PHE* 3.2 28.8 + - + -
129A LYS* 1.3 81.6 - - + +
131A MET* 1.3 60.8 + - - +
133A ALA* 3.7 7.4 + - - +
134A ALA* 3.1 25.8 + - - +
81B ASN* 3.8 35.2 - - - +
130B GLU* 4.7 3.1 - - - +
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.5 0.9 - - - -
38A TRP 4.7 5.2 - - - +
39A THR* 4.9 7.0 - - + -
40A PRO* 3.6 27.4 - - + -
80A LEU* 3.5 14.1 - - + +
82A TYR* 6.1 0.9 - - - +
93A TYR* 3.3 41.1 - - + +
126A ALA* 3.6 25.8 - - + +
128A PHE* 3.1 25.3 + - + +
130A GLU* 1.3 75.0 - - - +
132A LYS* 1.3 65.4 + - - +
134A ALA* 3.2 4.7 + - - +
135A LEU* 3.0 33.2 + - + +
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A CYS* 3.0 55.7 - - + +
124A GLN* 4.3 7.3 - - - +
126A ALA* 4.8 0.9 - - + +
127A GLN* 3.2 29.5 + - - +
128A PHE 3.0 13.8 + - - +
129A LYS* 3.5 13.2 - - + +
131A MET* 1.3 77.3 - - - +
133A ALA* 1.3 62.9 + - - +
135A LEU* 3.4 2.8 + - - -
136A GLN* 3.0 37.0 + - - +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.2 8.5 - - - +
129A LYS 3.0 17.7 + - - +
130A GLU* 3.8 8.3 - - - +
132A LYS* 1.3 74.3 - - - +
134A ALA* 1.3 57.5 + - - +
136A GLN* 3.2 13.1 + - - +
137A GLU* 2.9 50.2 + - - +
79B GLU* 4.5 19.3 - - + +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.1 15.3 - - + +
76A PHE* 3.8 6.4 - - - -
78A ARG* 3.8 23.1 - - + +
80A LEU* 3.9 11.2 - - + -
130A GLU 3.1 19.0 + - - +
131A MET* 3.2 11.4 + - + +
133A ALA* 1.3 75.0 - - - +
135A LEU* 1.3 59.4 + - - +
137A GLU* 3.5 12.1 + - - +
138A GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 33.0 - - + -
26A PHE* 3.9 22.8 - - + -
28A LEU* 4.7 6.7 - - + -
40A PRO* 4.5 11.2 - - + -
119A LEU* 3.5 18.9 - - + +
122A ALA* 4.0 36.1 - - + +
123A CYS* 4.3 4.9 - - - +
126A ALA* 4.2 12.8 - - + -
131A MET* 3.0 26.0 + - + +
132A LYS 3.8 3.1 - - - +
134A ALA* 1.3 74.3 - - - +
136A GLN* 1.3 64.2 + - - +
138A GLY* 3.3 2.1 + - - -
139A HIS* 3.0 19.6 + - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.8 20.1 - - + +
120A GLU* 5.4 4.4 + - - -
123A CYS* 3.8 24.3 - - - +
132A LYS* 3.0 29.9 + - - +
133A ALA* 3.6 12.0 + - - +
135A LEU* 1.3 74.1 - - - +
137A GLU* 1.3 59.4 + - + +
139A HIS* 3.4 3.3 + - - +
140A GLN* 2.9 30.5 + - - +
77B LYS* 6.0 3.9 - - - -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.7 6.4 - - + -
78A ARG* 2.6 48.0 + - - +
133A ALA* 2.9 27.0 + - - +
134A ALA* 3.8 4.0 - - - +
136A GLN* 1.3 77.0 - - + +
138A GLY* 1.3 59.3 + - - +
140A GLN* 3.4 10.4 + - - +
141A PHE* 3.0 28.8 + - - +
75B GLY 4.6 2.4 - - - +
77B LYS* 3.1 40.2 - - + +
78B ARG* 3.4 14.2 + - - +
79B GLU* 3.3 15.1 + - - +
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.6 1.1 - - - -
26A PHE* 4.9 2.7 - - - -
76A PHE* 3.6 23.7 - - - -
95A LEU* 4.1 10.8 - - - +
134A ALA 2.9 15.5 + - - -
135A LEU* 3.3 2.2 + - - -
136A GLN 3.3 0.2 - - - -
137A GLU* 1.3 73.5 - - - +
139A HIS* 1.3 63.8 + - - +
141A PHE* 3.2 3.8 + - - +
142A LEU* 3.0 31.2 + - - +
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.5 31.1 - - + +
26A PHE* 3.9 18.4 - + + -
119A LEU* 4.0 25.8 - - + +
135A LEU 3.0 16.5 + - - +
136A GLN 3.7 4.5 - - - +
138A GLY* 1.3 74.8 - - - +
140A GLN* 1.3 65.6 + - - +
142A LEU* 3.3 6.6 + - - +
143A CYS* 3.0 43.8 + - - -
201A GOL 2.8 43.9 + - - -
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN 2.9 16.8 + - - +
137A GLU* 3.7 10.4 - - - +
139A HIS* 1.3 79.6 + - - +
141A PHE* 1.3 59.0 + - - +
143A CYS* 3.4 7.3 + - - +
144A SER* 3.0 27.2 + - - -
74B GLU* 5.6 2.1 - - + +
75B GLY* 4.0 29.6 - - - +
76B PHE 4.3 7.8 + - - +
77B LYS* 3.9 23.3 + - - +
94B TRP* 5.2 2.0 - - - +
202B MG 3.6 20.7 - - - -
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.6 25.6 - - + -
74A GLU 3.2 23.1 - - - -
75A GLY* 3.5 24.7 - - - -
76A PHE* 3.8 23.3 - + + -
95A LEU* 3.5 17.5 - - + -
137A GLU 3.0 18.2 + - - +
138A GLY 3.2 3.1 + - - +
140A GLN* 1.3 75.5 - - - +
142A LEU* 1.3 67.9 + - + +
144A SER* 2.9 17.6 + - - -
145A ILE* 3.1 37.5 + - + +
75B GLY 3.6 13.0 + - - +
78B ARG* 6.1 0.2 - - - +
141B PHE* 3.6 31.6 - + - -
144B SER* 4.3 1.6 - - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.6 50.3 - - + -
13A ARG* 4.3 8.2 + - - +
24A ILE* 4.0 26.5 - - + -
26A PHE* 4.9 2.5 - - + -
73A ILE* 4.2 15.7 - - + -
95A LEU* 3.7 23.1 - - + -
138A GLY 3.0 21.0 + - - +
139A HIS* 3.3 8.3 + - - +
141A PHE* 1.3 76.1 - - + +
143A CYS* 1.3 63.8 + - - +
145A ILE* 3.4 6.4 + - + +
146A GLU* 3.1 33.7 + - - +
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Residues in contact with CYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.6 8.1 - - - -
139A HIS* 3.0 47.2 + - - +
140A GLN* 3.7 7.2 - - + +
142A LEU* 1.3 77.4 - - - +
144A SER* 1.3 61.6 + - - +
146A GLU* 3.4 13.6 + - - +
147A ALA* 3.0 23.7 + - - +
201A GOL 6.4 0.2 - - - -
74B GLU* 5.2 0.4 - - - -
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLN 3.0 6.8 + - - -
141A PHE* 2.9 15.4 + - - -
143A CYS* 1.3 76.1 - - - +
145A ILE* 1.3 60.3 + - - +
147A ALA* 3.3 3.5 + - - +
148A LEU* 3.0 34.8 + - - +
74B GLU* 3.7 28.8 + - - +
75B GLY* 3.5 33.9 - - - -
141B PHE* 4.1 11.5 - - - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 5.3 7.2 - - + -
74A GLU 5.4 0.7 - - - +
141A PHE* 3.1 50.6 + - + +
142A LEU* 3.7 9.6 - - + +
144A SER* 1.3 83.8 + - - +
146A GLU* 1.3 68.1 + - + +
148A LEU* 3.1 13.0 + - + +
149A GLU* 2.9 48.5 + - - +
141B PHE* 4.9 5.4 - - + -
144B SER* 4.9 5.2 - - - +
145B ILE* 5.4 2.5 - - + -
148B LEU* 3.8 25.8 - - + -
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 2.7 41.9 + - - +
24A ILE* 4.0 11.0 - - - +
142A LEU 3.1 24.7 + - - +
143A CYS* 3.7 11.6 - - - +
145A ILE* 1.3 80.0 - - + +
147A ALA* 1.3 58.1 + - - +
149A GLU* 3.4 12.8 + - - +
150A HIS* 2.8 30.9 + - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A CYS 3.0 13.9 + - - +
144A SER 3.6 7.9 - - - +
145A ILE 3.2 0.2 - - - -
146A GLU* 1.3 77.7 - - - +
148A LEU* 1.3 64.1 - - + +
150A HIS* 3.3 24.0 + - - +
74B GLU* 4.0 16.6 - - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER* 3.0 23.3 + - - +
145A ILE* 3.1 11.2 + - + +
147A ALA* 1.3 77.2 - - + +
149A GLU* 1.3 62.8 + - - +
150A HIS 4.4 2.8 - - - -
141B PHE* 6.3 0.4 - - + -
145B ILE* 4.0 42.2 - - + +
148B LEU* 4.9 16.8 - - + -
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 2.9 40.2 + - + +
146A GLU* 3.9 11.6 - - - +
148A LEU* 1.3 73.8 - - - +
150A HIS* 1.3 65.8 + - - +
148B LEU* 3.9 25.3 - - + +
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU 2.8 19.2 + - - +
147A ALA* 3.3 19.3 + - - +
148A LEU 4.4 2.5 - - - -
149A GLU* 1.3 82.2 - - - +
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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) + - + + + + + -
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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