Contacts of the helix formed by residues 144 - 159 (chain A) in PDB entry 3H90
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.3 22.8 + - - +
14A ILE* 4.1 3.0 - - - +
79A GLU* 2.8 18.4 + - - -
139A VAL* 4.9 1.1 - - - +
142A THR* 2.5 14.5 + - - -
143A GLN* 1.3 69.9 - - - +
145A GLN* 1.3 62.3 + - - +
146A ALA* 3.6 1.9 - - - +
147A VAL* 2.9 44.7 + - - +
148A ARG* 2.9 24.7 + - - +
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Residues in contact with GLN 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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11A ARG* 5.3 0.2 - - - +
79A GLU* 3.6 21.1 + - + +
80A SER* 3.3 17.0 + - - +
83A ALA* 3.9 5.5 - - + +
143A GLN 3.0 9.3 + - - +
144A SER* 1.3 69.8 - - - +
146A ALA* 1.3 62.6 + - - +
148A ARG* 3.6 19.0 - - - +
149A ALA* 3.2 21.3 + - - +
197A MET* 3.4 32.0 - - - +
200A GLU* 3.7 3.5 - - - +
201A ALA* 3.5 19.4 - - - +
204A SER* 2.7 28.6 + - - -
240A GLY* 5.8 6.1 - - - +
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Residues in contact with ALA 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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14A ILE* 5.2 0.2 - - + -
56A ASN* 3.9 8.8 + - - +
60A VAL* 4.0 21.3 - - + -
79A GLU* 3.2 42.3 + - + +
82A ALA* 4.7 2.0 - - + -
83A ALA* 4.8 4.5 - - - +
86A GLN* 3.7 11.4 + - - -
144A SER* 3.1 4.8 + - - +
145A GLN* 1.3 82.3 - - - +
147A VAL* 1.3 61.3 + - + +
149A ALA* 3.6 1.0 + - - +
150A ASP* 3.3 17.7 + - - +
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Residues in contact with VAL 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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14A ILE* 3.8 17.0 - - + +
17A THR* 3.6 37.0 - - + +
56A ASN* 5.0 2.2 - - - +
60A VAL* 5.3 4.0 - - + -
135A GLN* 4.3 6.9 - - + +
138A VAL* 4.7 3.1 - - + -
139A VAL* 3.6 29.4 - - + +
144A SER* 2.9 30.2 + - - +
146A ALA* 1.3 76.5 - - + +
148A ARG* 1.3 62.7 + - - +
150A ASP* 3.4 8.8 + - + +
151A MET* 2.9 30.0 + - - +
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Residues in contact with ARG 148 (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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139A VAL* 4.0 26.5 - - + -
143A GLN 5.2 5.5 + - - -
144A SER 2.9 18.3 + - - +
145A GLN* 3.6 27.1 - - - +
147A VAL* 1.3 78.9 - - - +
149A ALA* 1.3 57.3 + - - +
151A MET* 3.2 18.2 + - + +
152A LEU* 2.9 27.3 + - + +
197A MET* 3.6 24.2 - - - +
200A GLU* 2.9 41.2 + - - -
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Residues in contact with ALA 149 (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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83A ALA* 3.8 24.7 - - - +
86A GLN* 3.9 17.5 - - + +
87A SER 5.0 0.7 - - - +
90A ILE* 3.5 9.7 - - + +
145A GLN 3.2 11.2 + - - +
146A ALA 3.8 7.9 - - - +
148A ARG* 1.3 79.3 - - - +
150A ASP* 1.3 63.8 + - - +
152A LEU* 2.9 21.2 + - - +
153A HIS 3.4 4.7 + - - -
197A MET* 3.7 19.2 - - + -
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Residues in contact with ASP 150 (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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17A THR* 5.2 2.6 + - - +
18A ALA* 5.4 2.4 - - - -
21A SER* 3.5 24.8 - - - -
52A ALA* 6.0 0.2 - - - +
53A SER* 3.3 22.4 + - - -
56A ASN* 3.2 30.7 + - - +
86A GLN* 3.4 16.7 - - - +
135A GLN* 3.5 9.7 - - - +
146A ALA 3.3 4.5 + - - +
147A VAL* 3.8 9.2 - - - +
148A ARG 3.4 0.2 - - - -
149A ALA* 1.3 79.2 - - - +
151A MET* 1.3 60.8 + - - +
153A HIS* 3.8 7.0 + - - +
154A TYR* 3.1 31.9 + - - -
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Residues in contact with MET 151 (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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132A VAL* 4.1 4.7 - - + +
135A GLN* 3.2 29.8 + - + +
136A ARG* 3.6 43.1 - - + +
139A VAL* 3.8 22.0 - - + -
147A VAL 2.9 15.0 + - - +
148A ARG* 3.2 23.1 - - + +
150A ASP* 1.3 76.5 - - - +
152A LEU* 1.3 65.9 + - - +
154A TYR* 2.8 6.1 + - - +
155A GLN* 2.7 53.5 + - + +
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Residues in contact with LEU 152 (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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87A SER* 6.0 0.2 - - - -
90A ILE* 4.1 13.7 - - + -
148A ARG* 2.9 13.0 + - + +
149A ALA* 2.9 12.7 + - - +
151A MET* 1.3 73.5 - - - +
153A HIS* 1.3 64.4 + - - +
155A GLN* 3.1 27.2 + - + +
156A SER* 3.1 18.9 + - - -
189A TYR* 5.8 0.9 - - + -
190A ILE* 4.0 19.5 - - + +
193A SER* 3.7 24.0 - - - +
194A ALA* 3.4 42.2 - - + +
197A MET* 4.2 15.0 - - + -
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Residues in contact with HIS 153 (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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4A ZN 2.4 35.0 - - - -
45A ASP* 3.8 8.1 - - - -
48A VAL* 6.4 0.9 - - + -
49A ASP* 2.8 19.7 + - - -
53A SER* 5.9 0.4 - - - -
86A GLN* 5.5 1.3 - - - +
90A ILE* 3.7 30.8 - - + +
93A SER* 5.9 5.4 + - - -
149A ALA 3.4 3.8 + - - -
150A ASP* 4.0 10.5 - - - +
151A MET 3.1 0.8 - - - -
152A LEU* 1.3 79.2 - - - +
154A TYR* 1.3 68.3 + + - +
156A SER* 2.9 26.1 + - - -
157A ASP* 2.9 26.4 + - - +
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Residues in contact with TYR 154 (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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21A SER* 3.0 18.7 + - - -
24A LEU* 3.9 15.9 - - + +
49A ASP* 3.3 24.8 - - - +
53A SER* 2.8 21.8 + - - -
128A THR* 3.6 13.8 - - + +
131A LEU* 3.7 25.8 - - + -
132A VAL* 3.6 19.7 - - + -
135A GLN* 3.5 15.0 - - - +
150A ASP* 3.1 43.3 - - - -
151A MET 2.8 9.8 + - - +
153A HIS* 1.3 78.9 - + - +
155A GLN* 1.3 51.5 + - - +
157A ASP* 3.0 15.7 + - - +
158A VAL* 2.7 34.1 + - - +
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Residues in contact with GLN 155 (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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132A VAL* 3.8 20.4 - - + +
136A ARG* 3.9 24.8 + - - +
151A MET* 2.7 39.6 + - + +
152A LEU* 3.2 46.3 - - + +
154A TYR* 1.3 73.8 - - - +
156A SER* 1.3 56.0 + - - +
158A VAL* 3.6 9.7 + - + +
159A MET* 3.2 31.6 + - + +
189A TYR* 5.8 1.1 + - - -
190A ILE* 4.8 5.2 - - + -
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Residues in contact with SER 156 (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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90A ILE* 5.2 1.7 - - - +
152A LEU 3.1 5.7 + - - -
153A HIS* 2.9 17.9 + - - -
155A GLN* 1.3 73.5 - - - +
157A ASP* 1.3 65.9 + - - +
158A VAL 3.2 0.2 - - - -
159A MET* 3.1 30.8 + - - +
186A ILE* 4.6 4.8 - - - +
190A ILE* 3.2 40.9 - - - +
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Residues in contact with ASP 157 (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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4A ZN 2.0 37.7 - - - -
27A LYS* 5.8 4.4 + - - +
45A ASP* 3.9 6.9 - - - +
49A ASP* 3.1 6.9 - - - +
124A ALA 6.0 0.3 - - - -
125A LEU* 5.5 1.0 - - - +
128A THR* 4.0 17.1 + - + +
153A HIS* 2.9 26.7 + - - -
154A TYR* 3.0 14.3 + - - +
156A SER* 1.3 75.9 - - - +
158A VAL* 1.3 64.2 + - - +
159A MET 3.4 0.5 + - - -
160A MET* 3.4 31.1 + - - +
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Residues in contact with VAL 158 (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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125A LEU* 4.3 12.5 - - + +
128A THR* 3.7 24.9 - - + -
129A ILE* 3.8 42.0 - - + +
132A VAL* 4.0 13.2 - - + -
154A TYR 2.7 15.6 + - - +
155A GLN* 3.8 11.0 - - + +
156A SER 3.2 0.4 - - - -
157A ASP* 1.3 68.4 - - - +
159A MET* 1.3 58.4 + - - +
160A MET* 2.7 24.1 + - - +
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Residues in contact with MET 159 (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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155A GLN* 3.2 25.1 + - + +
156A SER* 3.1 20.8 + - - +
157A ASP 3.9 0.7 - - - -
158A VAL* 1.3 78.3 - - - +
160A MET* 1.3 59.8 + - - +
161A ASN* 4.3 3.1 + - - -
186A ILE* 3.5 54.2 - - + +
189A TYR* 4.1 31.9 - - + -
190A ILE* 4.8 2.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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