Contacts of the helix formed by residues 130 - 147 (chain A) in PDB entry 3IH9
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLU 3.8 1.0 + - - -
129A ALA* 1.3 75.9 - - - +
131A ARG* 1.3 65.8 + - - +
132A LYS* 3.4 9.6 + - - +
133A GLU* 2.9 46.3 + - - +
134A ARG* 3.1 15.2 + - - +
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Residues in contact with ARG 131 (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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121A HIS* 5.2 1.8 - - - -
130A SER* 1.3 74.4 - - - +
132A LYS* 1.3 65.5 + - - +
134A ARG* 3.3 8.8 + - - +
135A LEU* 3.3 22.2 + - + +
157A TYR* 5.1 2.8 + - - -
185A GLU* 3.0 32.3 + - - -
186A GLU* 3.7 53.4 + - + +
189A ALA* 3.9 19.3 - - - +
190A GLY* 5.8 6.8 - - - +
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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
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130A SER* 3.2 7.7 + - - +
131A ARG* 1.3 84.3 - - + +
133A GLU* 1.3 63.8 + - + +
135A LEU* 3.5 7.3 + - + +
136A ASP* 2.8 59.1 + - - +
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Residues in contact with GLU 133 (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 VAL* 3.6 20.2 - - + +
128A GLU 4.1 4.3 - - - +
129A ALA* 3.6 10.0 - - + -
130A SER* 2.9 40.3 + - - +
132A LYS* 1.3 78.8 - - + +
134A ARG* 1.3 59.1 + - - +
136A ASP* 3.5 7.3 + - - +
137A ARG* 2.9 29.1 + - - +
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Residues in contact with ARG 134 (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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121A HIS* 3.7 33.0 - - + -
122A GLN* 3.0 39.5 + - - +
124A LEU* 3.4 21.2 - - + +
125A VAL* 3.5 19.5 - - - +
126A GLY 3.1 27.3 + - - -
127A PRO* 4.0 8.7 + - - +
129A ALA* 3.3 30.9 + - + +
130A SER 3.1 12.0 + - - +
131A ARG* 3.3 8.5 + - - +
133A GLU* 1.3 72.9 - - - +
135A LEU* 1.3 61.6 + - - +
137A ARG* 3.2 1.8 + - - +
138A ALA 2.9 22.7 + - - -
182A ASP* 3.5 15.0 + - - -
186A GLU* 4.5 4.9 + - - -
187A ILE* 4.7 5.7 - - - +
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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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121A HIS* 4.3 7.3 - - + +
131A ARG* 3.3 11.9 + - + +
132A LYS* 3.8 10.5 - - + +
134A ARG* 1.3 75.9 - - - +
136A ASP* 1.3 68.0 + - - +
138A ALA* 2.9 10.2 + - + +
139A VAL* 2.8 47.6 + - + +
152A VAL* 4.5 4.5 - - + -
154A TRP* 4.1 20.2 - - + -
190A GLY* 4.7 8.5 - - - +
193A ALA* 3.8 32.3 - - + -
194A GLN* 4.5 8.3 - - - +
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Residues in contact with ASP 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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132A LYS* 2.8 54.8 + - - +
133A GLU* 3.7 7.3 - - - +
135A LEU* 1.3 83.2 - - - +
137A ARG* 1.3 52.8 + - - +
139A VAL* 3.7 6.9 - - - +
140A GLU* 2.7 36.8 + - - +
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Residues in contact with ARG 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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73A ALA* 3.7 22.4 + - + +
76A VAL* 4.3 13.3 - - - +
77A ASP* 2.9 33.6 + - - +
124A LEU* 3.6 27.8 - - + +
125A VAL* 3.5 13.7 - - + -
133A GLU 2.9 18.5 + - - +
134A ARG* 3.5 6.1 - - - +
135A LEU 3.1 0.2 - - - -
136A ASP* 1.3 74.1 - - - +
138A ALA* 1.3 65.2 + - - +
140A GLU* 3.2 29.0 + - - +
141A ILE* 3.0 47.2 + - - +
144A LEU* 5.0 4.0 - - - +
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Residues in contact with ALA 138 (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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70A THR* 3.8 24.2 - - + -
121A HIS* 4.6 1.8 - - - +
124A LEU* 3.9 7.8 - - + +
134A ARG 2.9 12.6 + - - +
135A LEU* 2.9 14.3 + - + +
137A ARG* 1.3 76.5 - - - +
139A VAL* 1.3 62.5 + - + +
141A ILE* 3.0 26.7 - - - +
142A MET* 3.3 13.8 + - - +
194A GLN* 4.3 18.6 - - + +
197A VAL* 5.9 0.4 - - + -
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Residues in contact with VAL 139 (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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135A LEU* 2.8 42.1 + - + +
136A ASP* 3.8 6.5 - - - +
138A ALA* 1.3 72.0 - - - +
140A GLU* 1.3 59.6 + - - +
142A MET* 3.6 3.9 + - - +
143A SER* 2.7 39.0 + - - +
149A ARG* 5.9 5.2 - - - +
150A LEU* 3.7 27.5 - - + +
152A VAL* 4.0 18.6 - - + -
197A VAL* 4.1 16.8 - - + -
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Residues in contact with GLU 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 ASP 2.7 23.4 + - - +
137A ARG* 3.2 33.9 + - - +
139A VAL* 1.3 74.4 - - - +
141A ILE* 1.3 65.0 + - - +
143A SER* 2.9 7.8 + - - -
144A LEU* 2.8 43.6 + - + +
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Residues in contact with ILE 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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69A PHE* 3.6 38.1 - - + +
70A THR* 4.5 2.0 - - + +
72A ALA* 5.0 0.9 - - + -
73A ALA* 3.9 19.7 - - + +
137A ARG* 3.0 35.2 + - - +
138A ALA* 3.0 20.0 - - - +
140A GLU* 1.3 76.0 - - - +
142A MET* 1.3 68.3 + - + +
144A LEU* 3.4 10.9 + - + +
145A LEU* 3.4 39.9 + - + +
224A MET 5.0 3.4 - - - +
225A LEU* 4.1 25.6 - - + -
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Residues in contact with MET 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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62A ILE* 3.1 48.7 - - + -
66A SER* 3.8 21.1 - - - +
69A PHE* 3.8 20.2 - - + -
70A THR* 5.7 2.0 - - + -
138A ALA 3.3 15.4 + - - +
139A VAL* 4.0 4.3 - - - +
140A GLU 3.2 0.6 - - - -
141A ILE* 1.3 82.8 - - + +
143A SER* 1.3 57.0 + - - +
145A LEU* 3.6 0.8 + - - -
146A ALA* 3.0 29.6 + - - +
150A LEU* 3.9 7.6 - - + -
194A GLN* 4.5 4.9 - - - +
197A VAL* 3.8 28.0 - - + -
199A VAL* 4.2 3.4 - - + -
207A MET* 3.7 23.8 - - + +
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Residues in contact with SER 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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139A VAL* 2.7 26.5 + - - +
140A GLU* 2.9 8.2 + - - -
142A MET* 1.3 76.9 - - - +
144A LEU* 1.3 59.8 + - - +
146A ALA* 4.3 0.2 - - - -
147A GLY* 2.9 23.7 + - - -
148A ARG 3.2 24.5 + - - -
149A ARG* 3.9 10.1 + - - +
150A LEU* 3.0 30.3 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 5.0 5.6 - - - +
140A GLU* 2.8 41.7 + - + +
141A ILE* 3.4 13.7 + - + +
143A SER* 1.3 78.5 - - - +
145A LEU* 1.3 62.8 + - + +
147A GLY* 3.8 5.9 + - - -
217A HIS* 3.7 7.6 - - - -
224A MET* 3.1 39.3 - - + +
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Residues in contact with LEU 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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69A PHE* 3.4 36.8 - - + -
72A ALA* 6.1 0.2 - - + -
141A ILE* 3.4 26.1 + - + +
142A MET* 4.2 1.1 - - - +
143A SER 3.2 0.4 - - - -
144A LEU* 1.3 75.7 - - + +
146A ALA* 1.3 60.8 + - - +
147A GLY 3.1 1.6 - - - -
206A VAL* 3.2 11.4 - - - +
207A MET* 3.9 17.0 - - + +
210A CYS* 3.7 25.5 - - + -
211A LEU* 4.7 1.8 - - + -
217A HIS* 2.9 21.8 + - - -
224A MET* 3.4 33.7 - - + +
225A LEU* 4.5 22.4 - - + -
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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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142A MET 3.0 19.8 + - - +
143A SER* 3.9 3.8 - - - +
145A LEU* 1.3 78.9 - - - +
147A GLY* 1.3 60.7 + - - +
148A ARG* 3.4 7.9 + - - +
150A LEU* 4.1 14.6 - - + -
203A ASP* 4.2 22.6 - - + +
206A VAL* 4.0 14.9 - - - +
207A MET* 3.6 22.8 - - + +
217A HIS* 4.5 0.5 + - - -
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Residues in contact with GLY 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 SER 2.9 8.3 + - - -
144A LEU* 3.8 8.3 + - - -
145A LEU 3.1 3.2 - - - -
146A ALA* 1.3 79.2 - - - +
148A ARG* 1.3 60.5 + - - +
217A HIS* 4.2 10.8 - - - -
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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