Contacts of the helix formed by residues 126 - 147 (chain A) in PDB entry 4O91
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 THR 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.5 31.0 - - + +
125A TYR* 1.3 80.7 - - - +
127A ALA* 1.3 66.2 + - - +
128A ALA* 3.3 12.7 + - - +
129A HIS* 3.0 46.0 + - + +
130A ALA 3.1 9.7 + - - -
293A GLY 4.9 1.7 + - - -
482A VAL* 3.7 5.0 - - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 1.3 73.7 - - - +
128A ALA* 1.3 61.3 + - - +
130A ALA* 3.3 2.3 + - - +
131A MET* 3.1 28.2 + - - +
291A PHE* 3.8 22.9 - - + -
482A VAL* 3.5 31.4 - - + +
483A ASP 3.5 26.9 + - - +
484A PHE* 4.4 4.0 - - + -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.0 11.8 + - - +
127A ALA* 1.3 80.1 - - - +
129A HIS* 1.3 57.3 + - - +
131A MET 3.5 0.5 + - - -
132A SER* 2.9 30.7 + - - -
288A MET* 3.9 2.6 - - - +
291A PHE* 3.5 28.1 - - + +
292A PRO 3.4 26.0 - - - +
293A GLY 4.3 0.7 - - - -
294A ALA* 3.6 14.6 - - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 5.2 1.8 - + - -
125A TYR* 3.7 10.3 - - + -
126A THR* 3.0 45.5 + - + +
128A ALA* 1.3 75.5 - - - +
130A ALA* 1.3 66.2 + - - +
132A SER* 3.2 4.6 + - - -
133A TRP* 2.8 49.3 + + + +
168A GLY 4.8 4.0 - - - -
169A THR* 4.9 0.9 - - + -
293A GLY 4.1 9.2 + - - -
294A ALA* 3.9 17.3 - - - -
296A GLU* 2.7 33.1 + - + -
297A PRO 5.0 2.9 - - - -
298A LEU* 3.5 26.0 - - + +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 4.3 4.6 - - + -
126A THR 3.1 8.2 + - - +
127A ALA* 3.5 10.8 - - - +
129A HIS* 1.3 81.3 - - - +
131A MET* 1.3 64.1 + - + +
133A TRP* 3.2 15.1 + - - +
134A CYS* 3.2 25.1 + - - -
222A VAL* 3.8 33.8 - - + +
223A ILE* 4.7 8.5 - - + -
482A VAL* 4.3 7.2 - - + -
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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
----------------------------------------------------------
127A ALA 3.1 16.8 + - - +
128A ALA 4.0 1.6 - - - +
130A ALA* 1.3 76.6 - - + +
132A SER* 1.3 58.5 + - - +
134A CYS* 3.3 1.4 + - - -
135A LEU* 2.9 26.2 + - - +
219A LEU* 4.2 16.2 - - + -
223A ILE* 4.8 9.2 - - + -
259A ILE* 3.6 33.4 - - + -
284A MET* 3.3 39.7 - - + +
287A LEU* 3.9 17.3 - - + -
288A MET* 3.7 18.2 - - - -
291A PHE* 3.9 27.1 - - + -
484A PHE* 5.3 3.1 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 2.9 19.6 + - - -
129A HIS* 3.7 4.5 - - - -
131A MET* 1.3 79.5 - - - +
133A TRP* 1.3 57.7 + - - +
135A LEU* 3.3 5.0 + - - +
136A GLN* 2.8 51.9 + - - +
169A THR 4.3 2.9 + - - -
288A MET* 3.7 13.8 - - - -
294A ALA* 3.5 22.9 + - - +
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Residues in contact with TRP 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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112A LEU* 3.8 25.4 - - + -
115A VAL* 3.9 15.9 - - + -
116A LEU* 4.3 5.8 - - + -
125A TYR* 3.8 45.8 - + + -
129A HIS* 2.8 31.9 + - + +
130A ALA* 3.5 11.7 - - - +
132A SER* 1.3 75.9 - - - +
134A CYS* 1.3 59.4 + - - +
136A GLN* 3.2 15.6 + - - +
137A CYS* 2.9 24.5 + - - +
164A LEU* 3.6 26.0 - - + +
168A GLY 2.9 28.6 + - - -
169A THR* 4.5 4.0 - - - +
171A LEU* 3.4 25.8 - - + +
222A VAL* 4.4 8.7 - - + -
298A LEU* 4.0 13.9 - - + -
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Residues in contact with CYS 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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130A ALA 3.2 13.5 + - - +
131A MET 3.8 6.3 - - - +
133A TRP* 1.3 75.9 - - - +
135A LEU* 1.3 63.7 - - - +
137A CYS* 3.4 4.4 + - - -
138A SER* 3.0 10.6 + - - -
215A TRP* 2.8 47.0 + - + +
218A ILE* 4.4 10.1 - - - -
219A LEU* 3.6 33.2 - - + -
222A VAL* 3.7 20.2 - - - -
284A MET* 3.9 6.7 - - + -
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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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131A MET 2.9 17.8 + - - +
132A SER* 3.6 7.2 - - - +
134A CYS* 1.3 77.1 - - - +
136A GLN* 1.3 60.7 + - + +
138A SER* 2.7 24.6 + - - +
139A GLN* 2.9 38.8 + - + +
281A VAL* 3.7 11.9 - - - +
284A MET* 3.7 20.5 - - + +
285A THR* 3.6 26.9 - - + +
288A MET* 3.6 28.5 - - + -
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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
----------------------------------------------------------
88A ASN* 3.2 35.6 + - - +
132A SER* 2.8 42.4 + - - +
133A TRP* 3.6 10.2 - - - +
135A LEU* 1.3 81.1 - - + +
137A CYS* 1.3 60.3 + - - +
139A GLN* 3.6 14.3 + - - +
140A GLY* 3.3 15.8 + - - -
169A THR 2.9 18.9 + - - -
170A VAL* 3.2 11.9 - - - +
171A LEU* 2.8 36.0 + - + +
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Residues in contact with CYS 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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133A TRP 2.9 16.6 + - - +
134A CYS* 3.7 8.3 - - - +
135A LEU 3.1 0.2 - - - -
136A GLN* 1.3 75.2 - - - +
138A SER* 1.3 65.4 + - - +
140A GLY 3.2 1.9 + - - -
141A VAL* 3.0 31.9 + - - +
157A LEU* 4.0 28.3 - - - -
162A LEU* 4.1 21.3 - - + -
171A LEU* 4.0 15.7 - - + +
173A ILE* 3.6 5.4 - - - +
215A TRP* 4.1 15.9 - - + -
218A ILE* 4.9 5.4 - - + -
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Residues in contact with SER 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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134A CYS 3.0 13.7 + - - -
135A LEU* 2.7 23.2 + - - +
137A CYS* 1.3 75.0 - - - +
139A GLN* 1.3 57.0 + - - +
141A VAL* 4.0 0.3 - - - +
142A ALA* 2.8 33.1 + - - +
215A TRP* 3.8 5.9 - - - +
277A MET* 3.8 17.4 - - - +
280A ILE* 3.6 28.8 + - - +
281A VAL* 3.4 23.5 + - - +
284A MET* 4.7 0.2 - - - +
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Residues in contact with GLN 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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86A HIS* 3.6 18.2 + - + +
88A ASN* 3.2 20.9 - - - +
135A LEU* 2.9 43.7 + - - +
136A GLN* 3.7 16.9 - - - +
138A SER* 1.3 77.3 + - - +
140A GLY* 1.3 60.1 + - - +
142A ALA* 3.7 2.1 + - - +
143A TYR* 3.2 15.6 + - - +
281A VAL* 3.8 23.4 - - + +
285A THR* 4.4 6.7 + - - -
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Residues in contact with GLY 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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86A HIS* 4.0 13.7 - - - -
88A ASN* 4.3 1.3 - - - -
89A ILE* 3.5 18.8 - - - +
136A GLN 3.3 6.6 + - - -
137A CYS 3.2 6.4 + - - -
139A GLN* 1.3 77.5 - - - +
141A VAL* 1.3 66.0 + - - +
143A TYR* 3.3 5.6 + - - +
144A LEU* 3.1 18.0 + - - +
173A ILE* 3.8 17.0 - - - -
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Residues in contact with VAL 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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137A CYS* 3.0 21.0 + - - +
138A SER 4.0 0.7 - - - +
140A GLY* 1.3 72.6 - - - +
142A ALA* 1.3 61.2 + - - +
144A LEU* 3.0 13.3 + - + +
145A HIS* 2.8 58.5 + - + +
154A HIS* 5.5 1.1 - - + -
157A LEU* 3.6 26.2 - - + -
173A ILE* 3.7 13.2 - - + -
211A ASP* 3.9 11.4 - - + +
277A MET* 3.7 22.7 - - + -
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Residues in contact with ALA 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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138A SER 2.8 19.8 + - - +
139A GLN 4.0 3.6 - - - +
141A VAL* 1.3 76.2 - - - +
143A TYR* 1.3 61.6 + - - +
145A HIS* 3.3 5.2 + - - +
146A SER* 3.1 26.2 + - - -
277A MET* 3.8 21.5 - - + +
278A GLU* 3.8 25.6 - - + +
281A VAL* 3.9 14.1 - - + -
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Residues in contact with TYR 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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83A ARG 3.5 11.6 + - - -
84A VAL* 4.0 10.1 - - + -
85A ASN* 3.0 45.9 + - - +
86A HIS* 3.6 32.5 - + + -
89A ILE* 3.8 15.7 - - + -
139A GLN 3.2 8.0 + - - +
140A GLY 3.4 8.7 - - - +
142A ALA* 1.3 76.1 - - - +
144A LEU* 1.3 67.0 + - + +
146A SER* 2.8 24.6 + - - -
147A MET* 3.2 32.6 - - + +
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Residues in contact with LEU 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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84A VAL* 4.0 18.6 - - + -
89A ILE* 3.8 15.9 - - + -
140A GLY 3.1 14.7 + - - +
141A VAL* 3.0 15.9 + - + +
143A TYR* 1.3 80.0 - - + +
145A HIS* 1.3 62.3 + - + +
146A SER 3.3 0.7 + - - -
147A MET* 3.6 16.1 + - - +
152A LEU* 2.9 48.8 + - + +
154A HIS* 4.5 22.9 - - + +
173A ILE* 5.0 4.3 - - + -
601A NG2 3.7 39.9 - - - -
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Residues in contact with HIS 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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141A VAL* 2.8 34.3 + - + +
142A ALA* 3.7 8.3 - - - +
143A TYR 3.2 0.4 - - - -
144A LEU* 1.3 76.3 - - + +
146A SER* 1.3 57.9 + - - +
147A MET 3.5 0.4 - - - -
151A ALA* 3.2 20.3 - - - +
152A LEU 3.4 17.7 - - - -
153A ILE* 4.5 0.8 - - + -
208A GLU* 3.2 55.2 - - + +
211A ASP* 2.9 24.4 + - + -
212A VAL* 5.1 1.6 - - + -
277A MET* 3.8 21.9 + - + +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 3.1 12.6 + - - -
143A TYR* 2.8 23.8 + - - -
145A HIS* 1.3 75.6 - - - +
147A MET* 1.3 68.1 + - - +
148A GLN* 3.5 19.6 + - - +
278A GLU* 4.6 10.5 + - - -
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Residues in contact with MET 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.5 62.6 - - + +
84A VAL* 3.8 16.6 - - + -
143A TYR* 3.2 30.5 + - + +
144A LEU* 3.6 15.0 - - - +
145A HIS 3.5 1.6 - - - -
146A SER* 1.3 80.6 - - - +
148A GLN* 1.3 67.1 + - - +
149A PRO 4.1 0.2 - - - -
150A LYS 3.3 21.2 - - - +
151A ALA* 3.5 4.3 + - - +
152A LEU* 3.7 27.1 - - + +
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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