Contacts of the helix formed by residues 131 - 149 (chain B) in PDB entry 1OLY
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 ARG 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 3.5 21.0 + - - +
160A SER* 3.7 6.5 - - - -
182A TRP* 3.1 52.3 - - + +
218A SER* 3.5 11.3 + - - +
26B GLN* 5.2 1.0 - - - +
129B ALA 4.0 1.1 + - - +
130B GLY* 1.4 71.1 - - - +
132B PHE* 1.4 65.4 + - - +
133B ASP* 2.8 35.3 + - - +
134B GLN* 3.1 32.9 + - + +
135B ILE* 3.1 17.7 + - - +
488B VIB 5.6 9.9 - - - -
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.2 21.5 - - + -
135A ILE* 3.9 25.8 - - + -
139A VAL* 4.1 12.3 - - + -
160A SER* 3.0 28.8 + - - +
162A ILE* 3.6 20.9 - - + -
186A ILE* 4.7 1.6 - - + -
236A LEU* 3.6 31.0 - - + -
238A THR* 3.6 16.6 - - + +
130B GLY 3.3 4.5 + - - -
131B ARG* 1.4 69.3 - - - +
133B ASP* 1.3 65.9 + - - +
135B ILE* 2.7 37.1 - - + +
136B MET* 3.2 36.0 + - + +
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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
----------------------------------------------------------
182A TRP* 3.6 27.3 - - + -
183A CYS 4.9 0.9 - - - +
186A ILE* 5.2 0.7 - - - -
217A THR* 3.4 26.8 - - + +
218A SER* 3.1 17.5 + - - +
238A THR* 4.0 12.1 - - + -
131B ARG* 2.8 46.5 + - - +
132B PHE* 1.3 80.3 - - - +
134B GLN* 1.3 71.9 + - - -
136B MET* 3.2 6.0 + - - +
137B ALA 2.9 22.3 + - - -
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR* 4.6 4.9 + - - -
218A SER* 2.9 29.3 + - - +
25B ASN* 5.4 8.6 + - - +
26B GLN* 6.0 2.9 - - - +
99B THR* 5.0 8.0 - - - +
127B GLY* 4.5 3.8 - - - +
129B ALA 5.5 3.1 - - - +
131B ARG* 3.4 34.9 - - + +
132B PHE 3.1 0.4 - - - -
133B ASP* 1.3 103.2 + - - +
135B ILE* 1.3 64.6 + - - +
137B ALA* 3.2 10.8 + - - +
138B SER* 3.0 25.0 + - - -
488B VIB 5.5 8.0 - - - -
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Residues in contact with ILE 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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128A LEU 5.4 1.3 - - - +
132A PHE* 3.9 23.3 - - + -
135A ILE* 3.7 24.9 - - + -
127B GLY 3.4 20.2 + - - +
128B LEU* 2.8 34.5 - - + +
129B ALA* 4.9 2.6 + - - +
130B GLY 5.4 1.3 - - - +
131B ARG 3.1 8.8 + - - +
132B PHE* 2.7 42.1 + - + +
134B GLN* 1.3 75.4 - - - +
136B MET* 1.4 78.3 + - + +
138B SER* 3.1 13.5 + - - -
139B VAL* 3.2 12.8 + - - +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 5.0 1.6 - - + -
136A MET* 4.3 24.7 - - + +
139A VAL* 5.8 0.2 - - - -
186A ILE* 3.8 43.3 - - + -
188A VAL* 4.5 9.6 - - - -
211A PHE* 4.0 10.6 - - + -
215A VAL* 5.8 0.7 - - - -
217A THR* 5.0 0.2 - - - -
132B PHE* 3.2 40.2 + - + +
133B ASP 3.5 7.0 - - - +
135B ILE* 1.4 96.4 - - + +
137B ALA* 1.3 59.8 + - - +
139B VAL* 3.1 20.0 + - + +
140B ASN* 2.9 27.1 + - - +
188B VAL* 5.9 3.4 - - + -
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Residues in contact with ALA 137 (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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215A VAL* 6.1 0.2 - - - -
217A THR* 4.0 22.4 - - - +
99B THR* 4.1 21.0 + - + +
133B ASP 2.9 14.0 + - - +
134B GLN* 3.2 18.4 + - - +
136B MET* 1.3 75.2 - - - +
138B SER* 1.3 58.4 + - - +
140B ASN* 3.0 9.4 + - - +
141B THR* 2.8 32.1 + - - -
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Residues in contact with SER 138 (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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24B LEU* 4.3 8.0 - - - +
101B PHE* 4.7 4.7 - - - +
127B GLY* 3.1 33.8 + - - -
128B LEU* 5.4 0.2 - - - -
134B GLN 3.0 10.4 + - - -
135B ILE* 3.1 9.6 + - - -
137B ALA* 1.3 78.3 - - - +
139B VAL* 1.4 62.5 + - - +
141B THR* 3.2 17.7 + - - -
142B LEU* 3.4 14.6 + - - +
155B ILE* 3.7 22.5 - - - +
162B ILE* 5.2 2.9 - - - -
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Residues in contact with VAL 139 (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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132A PHE* 4.1 27.4 - - + -
211A PHE* 4.3 10.8 - - + -
135B ILE 3.5 13.9 - - - +
136B MET* 3.1 19.6 + - + +
138B SER* 1.4 76.4 - - - +
140B ASN* 1.3 62.3 + - - +
142B LEU* 3.0 22.4 + - - +
143B PHE* 3.2 29.9 - - + -
162B ILE* 4.3 11.0 - - + -
188B VAL* 4.3 11.9 - - + -
236B LEU* 4.5 17.7 - - + -
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Residues in contact with ASN 140 (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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211A PHE* 3.7 12.5 - - + -
212A GLY* 2.9 31.3 + - - +
213A THR 5.9 0.2 - - - -
214A LEU* 5.2 2.2 - - - +
215A VAL* 3.8 30.9 + - + +
136B MET 2.9 12.9 + - - +
137B ALA* 3.4 12.6 - - - +
139B VAL* 1.3 73.5 - - - +
141B THR* 1.3 67.2 + - - +
143B PHE* 2.9 16.9 + - - +
144B GLN* 3.1 31.5 + - - +
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Residues in contact with THR 141 (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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99B THR* 3.9 6.8 + - - -
101B PHE* 3.0 48.1 - - + -
102B THR* 3.2 26.2 + - + +
105B LEU* 3.4 18.8 - - + -
137B ALA 2.8 17.4 + - - -
138B SER 3.5 3.4 - - - -
139B VAL 3.2 0.4 - - - -
140B ASN* 1.3 75.5 - - - +
142B LEU* 1.4 53.0 + - - +
144B GLN* 3.0 11.5 + - - -
145B ALA* 2.7 33.1 + - - +
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Residues in contact with LEU 142 (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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101B PHE* 5.0 3.8 - - + -
138B SER 3.7 8.5 - - - +
139B VAL* 3.0 11.7 + - - +
141B THR* 1.4 78.4 - - + +
143B PHE* 1.3 64.0 + - + +
145B ALA* 3.4 15.4 + - + +
146B THR* 3.8 10.0 + - - +
153B ILE* 4.0 35.9 - - + +
155B ILE* 3.8 17.0 - - + -
162B ILE* 3.6 36.8 - - + +
163B TYR* 4.6 0.2 - - - -
164B LEU* 3.9 26.7 - - + +
236B LEU* 3.9 20.2 - - + -
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Residues in contact with PHE 143 (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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211A PHE* 3.9 32.1 - + + -
212A GLY* 3.6 19.1 - - - -
139B VAL* 3.2 36.6 - - + -
140B ASN* 2.9 14.8 + - - +
142B LEU* 1.3 77.0 - - + +
144B GLN* 1.3 58.0 + - - +
146B THR* 2.9 26.3 + - - +
147B HIS* 4.3 3.2 + - - -
164B LEU* 3.8 30.5 - - + -
166B GLN* 5.7 0.2 - - - -
188B VAL* 3.6 26.9 - - + -
189B GLY* 5.0 1.3 - - - -
234B PRO* 3.9 27.1 - - + -
236B LEU* 6.0 0.7 - - + -
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Residues in contact with GLN 144 (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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212A GLY* 4.4 17.0 + - - +
213A THR 5.6 2.8 + - - -
98B HIS* 3.8 24.7 + - - -
102B THR* 2.9 40.2 + - + +
140B ASN* 3.6 28.5 + - - +
141B THR* 3.0 10.3 + - - +
143B PHE* 1.3 71.7 - - - +
145B ALA* 1.3 65.9 + - - +
146B THR 3.0 2.7 - - - -
147B HIS* 2.8 28.1 + - + +
148B ILE* 3.4 12.4 + - + +
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Residues in contact with ALA 145 (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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105B LEU* 4.1 6.1 - - + -
141B THR 2.7 19.5 + - - +
142B LEU* 3.5 12.3 - - + +
143B PHE 3.3 0.6 - - - -
144B GLN* 1.3 72.2 - - - +
146B THR* 1.3 62.8 + - + +
148B ILE* 2.9 24.0 + - + -
149B THR* 2.9 17.9 + - - +
153B ILE* 3.3 34.1 - - + -
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Residues in contact with THR 146 (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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142B LEU 3.8 9.0 - - - +
143B PHE 2.9 21.2 + - - +
145B ALA* 1.3 78.7 - - - +
147B HIS* 1.3 73.7 + - - +
149B THR 3.7 12.1 + - - +
150B PRO* 5.4 0.5 - - - +
164B LEU* 4.8 0.4 - - + -
166B GLN* 3.1 42.5 + - + +
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Residues in contact with HIS 147 (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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212A GLY* 5.6 7.0 + - - -
143B PHE 4.3 4.8 + - - -
144B GLN* 2.8 17.9 + - + +
146B THR* 1.3 96.6 + - - +
148B ILE* 1.4 63.3 + - + +
149B THR* 4.8 0.2 - - - -
150B PRO* 5.9 0.2 - - - +
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Residues in contact with ILE 148 (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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102B THR* 3.7 38.8 - - + +
105B LEU* 3.8 35.2 - - + +
106B LYS* 3.9 21.5 - - + +
109B GLN* 3.6 20.1 + - + +
141B THR 5.4 0.2 - - - +
144B GLN* 3.7 10.5 - - + +
145B ALA* 2.9 23.0 + - - +
147B HIS* 1.4 81.2 - - + +
149B THR* 1.3 61.2 + - + +
150B PRO* 4.5 1.3 - - - +
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Residues in contact with THR 149 (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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105B LEU* 5.7 2.7 - - + +
109B GLN* 2.6 28.3 + - - -
122B ILE* 4.1 12.3 - - + +
145B ALA 2.9 18.6 + - - +
146B THR* 3.7 10.3 - - - +
147B HIS 3.6 0.4 - - - -
148B ILE* 1.3 80.9 - - + +
150B PRO* 1.3 71.6 - - - +
151B PHE* 2.9 35.7 - - - +
153B ILE* 4.1 17.0 - - + -
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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
------------------------------------------------------------
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