Contacts of the helix formed by residues 117 - 138 (chain B) in PDB entry 3A7H
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO 4.3 0.2 + - - -
116B LEU* 1.3 76.4 - - - +
118B GLU* 1.3 63.0 + - - +
119B THR* 3.0 13.4 + - - -
120B GLN* 2.7 57.2 + - - +
121B ILE* 3.0 21.1 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.9 11.1 - - - -
117B ASP* 1.3 74.9 - - - +
119B THR* 1.3 56.2 + - - +
121B ILE* 4.1 9.9 - - + -
122B ALA* 2.9 31.9 + - - +
242B ASN 4.6 0.2 - - - +
243B TYR* 3.2 18.6 - - + +
244B SER* 2.6 51.6 + - - -
247B LEU* 4.0 17.9 - - + +
273B PHE* 3.4 19.0 - - + -
277B ASN* 3.9 14.3 + - - +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.0 12.5 + - - -
118B GLU* 1.3 78.1 - - - +
120B GLN* 1.3 57.4 + - + +
122B ALA 3.5 0.2 + - - -
123B THR* 2.6 39.4 + - - +
277B ASN* 3.1 22.8 + - - +
279B LYS* 3.1 46.4 - - + +
283B TYR* 6.1 1.8 - - + -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO 4.6 1.0 - - - +
116B LEU* 3.4 18.9 - - + +
117B ASP* 2.7 49.1 + - - +
119B THR* 1.3 72.3 - - + +
121B ILE* 1.3 65.1 + - - +
123B THR* 3.3 2.2 + - - -
124B ILE* 3.0 31.1 + - - +
283B TYR 5.3 5.1 + - - +
284B LEU* 4.4 15.3 - - + -
286B GLU* 5.4 5.3 - - - +
287B LEU* 3.7 43.3 - - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.7 27.6 - - + +
117B ASP 3.0 26.5 + - - +
118B GLU* 3.7 11.9 - - + +
120B GLN* 1.3 74.8 - - - +
122B ALA* 1.3 57.7 + - - +
124B ILE* 3.3 2.5 + - - +
125B LEU* 2.9 54.8 + - + +
209B ALA 4.9 3.8 - - - +
212B LEU* 3.8 20.9 - - + +
213B ALA* 3.7 30.1 - - + -
243B TYR* 5.2 2.7 - - + -
247B LEU* 4.4 14.4 - - + -
273B PHE* 4.0 12.1 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU 2.9 19.9 + - - +
119B THR 3.9 0.2 - - - +
121B ILE* 1.3 76.8 - - - +
123B THR* 1.3 57.9 + - - +
126B ARG* 2.8 31.9 + - - +
273B PHE* 3.6 24.9 - - + +
274B ILE* 3.4 8.1 - - + +
277B ASN* 3.5 10.3 - - + -
278B ALA* 3.5 28.4 - - + +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 2.6 23.0 + - - +
120B GLN* 3.7 4.9 - - - -
122B ALA* 1.3 78.6 - - - +
124B ILE* 1.3 61.8 + - - +
126B ARG* 3.4 7.3 + - - +
127B GLU* 3.2 23.6 + - - +
278B ALA* 4.2 7.0 - - - -
279B LYS* 3.0 41.4 + - - +
280B LYS 4.2 2.2 - - - +
281B THR* 4.1 12.6 - - + -
284B LEU* 3.9 30.7 - - + -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 4.6 11.0 - - + +
110B LEU* 5.1 7.6 - - + -
116B LEU* 3.7 26.7 - - + -
120B GLN 3.0 19.9 + - - +
121B ILE 3.8 3.1 - - - +
123B THR* 1.3 73.7 - - - +
125B LEU* 1.3 68.4 + - - +
127B GLU* 3.2 5.0 + - - +
128B ILE* 3.0 41.2 + - + +
150B VAL* 4.3 12.8 - - + -
152B LEU* 5.0 3.8 - - + -
158B VAL* 4.5 12.1 - - + -
212B LEU* 4.1 14.8 - - + -
284B LEU* 4.1 19.3 - - + -
287B LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 2.9 38.5 + - + +
122B ALA 3.9 2.5 - - - +
124B ILE* 1.3 78.6 - - - +
126B ARG* 1.3 62.8 + - - +
128B ILE* 3.2 8.8 + - + +
129B LEU* 2.9 27.9 + - + +
205B LEU* 3.8 27.1 - - + +
208B THR* 4.8 0.9 - - + -
209B ALA* 3.9 30.7 - - + +
212B LEU* 3.8 19.7 - - + -
247B LEU* 4.9 0.7 - - + -
250B PHE* 4.0 18.2 - - + -
273B PHE* 4.1 12.6 - - + -
274B ILE* 4.0 9.4 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 2.8 19.1 + - - +
123B THR* 3.6 10.5 - - - +
124B ILE 3.2 0.2 - - - -
125B LEU* 1.3 77.7 - - - +
127B GLU* 1.3 77.5 + - - +
129B LEU* 3.2 8.7 + - - +
130B LYS* 3.0 41.4 + - - +
269B LEU* 3.5 20.0 - - + +
274B ILE* 3.8 29.1 - - + +
278B ALA* 3.6 23.5 + - + +
279B LYS 2.7 32.1 + - - +
280B LYS* 4.5 1.6 - - - +
281B THR* 4.3 8.1 - - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.4 31.1 - - + +
123B THR 3.2 12.1 + - - +
124B ILE 3.2 5.4 + - - +
126B ARG* 1.3 92.8 + - - +
128B ILE* 1.3 64.6 + - - +
130B LYS* 2.6 37.3 + - - +
131B GLY* 3.1 16.5 + - - -
157B GLU* 5.8 0.3 - - - -
158B VAL* 3.4 37.1 + - + +
160B LEU* 5.6 0.3 - - - +
281B THR* 3.5 28.9 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 5.9 0.7 - - + -
124B ILE* 3.0 32.1 + - + +
125B LEU* 3.2 14.6 + - + +
127B GLU* 1.3 75.0 - - - +
129B LEU* 1.3 51.4 + - - +
131B GLY* 2.9 5.2 + - - -
132B LEU* 2.8 41.7 + - + +
145B ILE* 4.6 9.6 - - + -
150B VAL* 3.7 36.1 - - + -
158B VAL* 4.4 2.9 - - + -
160B LEU* 3.8 22.7 - - + +
205B LEU* 3.6 20.4 - - + -
208B THR* 4.4 19.3 - - + -
212B LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU 2.9 17.0 + - - +
126B ARG 3.3 7.9 - - - +
127B GLU 3.2 0.2 - - - -
128B ILE* 1.3 78.2 - - - +
130B LYS* 1.3 54.8 + - - +
132B LEU* 4.3 7.0 - - + +
133B ASP* 2.8 31.1 + - - +
202B ILE* 5.4 0.2 - - + -
205B LEU* 3.5 27.1 - - + -
250B PHE* 4.0 16.4 - - + -
265B ALA* 3.7 22.4 - - + +
268B LEU* 3.5 47.1 - - + +
269B LEU* 3.6 17.0 - - + +
274B ILE* 4.2 11.7 - - + -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.7 45.4 + - + +
126B ARG* 3.0 35.7 + - - +
127B GLU* 2.6 39.4 + - - +
129B LEU* 1.3 75.6 - - - +
131B GLY* 1.3 57.4 + - - +
133B ASP* 3.5 6.5 + - - +
134B TYR* 3.0 26.2 + - - +
269B LEU* 4.2 16.2 - - + -
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.5 22.1 - - - +
82B VAL* 5.0 1.3 - - - -
127B GLU 3.1 7.4 + - - -
128B ILE 2.9 7.5 + - - -
130B LYS* 1.3 76.1 - - - +
132B LEU* 1.3 58.8 + - - +
134B TYR* 3.3 5.2 + - - +
135B LEU* 2.9 33.1 + - - +
160B LEU* 3.6 17.3 - - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 2.8 28.7 + - + +
129B LEU* 3.3 8.9 + - + +
131B GLY* 1.3 71.3 - - - +
133B ASP* 1.3 61.4 + - - +
135B LEU* 4.4 7.2 - - + +
136B HIS* 2.8 47.3 + - + +
145B ILE* 3.7 26.7 - - + -
160B LEU* 4.1 7.0 - - + -
201B ASP* 3.9 42.4 - - + +
202B ILE* 4.7 6.3 - - + -
205B LEU* 4.3 19.3 - - + -
265B ALA* 3.8 10.1 - - + -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU 2.8 17.5 + - - +
130B LYS* 3.6 8.0 - - - +
132B LEU* 1.3 77.9 - - - +
134B TYR* 1.3 63.9 + - - +
136B HIS* 3.9 4.0 - - - +
137B SER* 3.0 27.8 + - - -
264B THR* 5.9 0.3 - - - -
265B ALA* 3.6 12.2 - - + +
266B LYS* 2.7 52.8 + - - +
269B LEU* 4.6 7.9 - - + +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLN 3.8 6.1 + - - -
77B CYS* 3.4 30.2 - - + -
78B ASP* 2.9 37.6 + - - +
79B SER* 3.6 30.3 - - - +
81B TYR* 5.2 1.3 - - + -
82B VAL* 4.1 11.2 - - + -
130B LYS 3.0 15.5 + - - +
131B GLY* 3.5 7.2 - - - +
132B LEU 3.3 0.2 - - - -
133B ASP* 1.3 77.1 + - - +
135B LEU* 1.3 68.1 + - + +
137B SER* 2.6 26.5 + - - -
138B GLU* 3.3 38.1 + - + +
140B LYS* 5.4 0.4 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B CYS* 3.7 29.8 - - - -
82B VAL* 4.3 2.9 - - + -
131B GLY 2.9 16.0 + - - +
132B LEU* 3.7 7.6 - - + +
134B TYR* 1.3 85.5 - - + +
136B HIS* 1.3 61.5 + - + +
138B GLU* 3.0 15.4 + - - +
140B LYS* 2.8 47.1 + - + +
141B ILE 5.3 0.4 - - - -
142B HIS* 4.0 19.5 - - + +
160B LEU* 3.8 20.4 - - + -
163B PHE* 3.6 34.5 - - + -
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 2.8 35.8 + - + +
133B ASP* 4.1 3.8 - - - +
135B LEU* 1.3 76.7 - - + +
137B SER* 1.3 56.3 + - - +
138B GLU 3.1 0.4 - - - -
139B LYS* 3.2 23.8 + - - +
140B LYS 3.4 20.6 - - - +
198B SER* 3.4 44.0 + - - +
201B ASP* 2.9 32.9 + - + +
202B ILE* 3.9 20.7 - - + +
264B THR* 6.0 0.6 - - - -
265B ALA* 4.5 6.8 + - + +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASP* 3.0 20.2 + - - -
134B TYR* 2.6 25.3 + - - -
136B HIS* 1.3 75.6 - - - +
138B GLU* 1.3 66.0 + - - +
139B LYS* 3.4 6.0 + - - +
266B LYS* 5.6 5.2 - - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN 4.8 2.9 - - - +
134B TYR* 3.4 46.1 + - + +
135B LEU* 3.0 10.8 + - - +
137B SER* 1.3 86.5 + - - +
139B LYS* 1.3 68.5 + - - +
140B LYS* 3.3 30.6 + - + +
168B GLN* 4.7 2.1 - - - +
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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