Contacts of the helix formed by residues 139 - 152 (chain B) in PDB entry 4OE5
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 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET* 2.8 43.8 + - + +
135B LEU* 4.0 4.3 - - - -
138B PRO* 1.3 86.5 - - + +
140B ARG* 1.3 65.9 + - - +
141B ALA 3.4 2.2 - - - -
142B GLU* 2.8 34.3 + - - +
143B ILE* 3.0 24.1 + - - +
244B ALA 5.3 0.2 + - - -
247B ARG* 5.1 4.2 - - - +
248B ILE* 3.6 38.1 - - + +
251B GLU* 2.9 41.2 + - - -
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 2.9 20.8 + - - +
36B PRO 3.1 20.0 + - - -
38B LEU* 3.5 26.0 - - - +
40B PHE* 5.0 1.1 - - - -
46B GLU* 5.5 2.2 - - - -
135B LEU 3.1 18.8 + - - +
136B SER* 2.8 29.0 + - - +
137B GLY 3.3 13.9 + - - +
138B PRO 3.5 0.2 - - - -
139B ARG* 1.3 74.0 - - - +
141B ALA* 1.3 68.3 + - - +
143B ILE* 3.1 7.7 - - + +
144B LEU* 2.9 43.3 + - + +
159B GLU* 2.4 42.5 + - - +
162B ALA* 5.4 1.6 - - + -
163B ALA* 3.9 11.9 - - - +
167B ILE* 4.2 6.3 - - + +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU 5.4 0.4 - - - +
49B ALA* 3.4 41.5 - - + +
50B LEU* 3.9 6.9 - - + +
53B ALA* 3.4 10.0 - - + +
137B GLY 4.8 1.0 + - - -
138B PRO 5.2 3.1 + - - +
139B ARG 3.4 0.2 - - - -
140B ARG* 1.3 77.6 - - - +
142B GLU* 1.3 57.8 + - - +
144B LEU* 3.7 9.5 - - - +
145B ALA* 2.9 32.6 + - - +
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Residues in contact with GLU 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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53B ALA* 4.1 8.4 - - - +
138B PRO 5.5 0.8 + - - +
139B ARG* 2.8 51.3 + - - +
140B ARG 3.2 0.8 - - - -
141B ALA* 1.3 78.5 - - - +
143B ILE* 1.3 63.6 + - - +
145B ALA* 3.9 1.1 - - - +
146B LYS* 2.7 67.9 + - + +
244B ALA* 3.5 16.7 - - - +
248B ILE* 5.0 3.6 - - - -
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Residues in contact with ILE 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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135B LEU* 3.9 20.9 - - + +
139B ARG 3.0 15.0 + - - +
140B ARG* 3.1 18.2 - - + +
142B GLU* 1.3 77.4 - - - +
144B LEU* 1.3 70.1 + - + +
146B LYS* 3.4 1.0 + - + -
147B THR* 3.0 29.9 + - + +
162B ALA* 4.4 16.6 - - + -
166B LEU* 4.0 18.4 - - + -
167B ILE* 6.2 0.2 - - + -
215B ILE* 4.2 3.8 - - + -
241B ALA* 3.8 37.0 - - + +
244B ALA* 4.2 9.4 - - + -
245B VAL* 3.9 13.9 - - + -
248B ILE* 5.7 1.3 - - + -
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Residues in contact with LEU 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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40B PHE* 3.4 34.5 - - + -
50B LEU* 3.9 13.9 - - + -
140B ARG* 2.9 34.3 + - + +
141B ALA* 3.7 7.4 - - - +
143B ILE* 1.3 76.7 - - - +
145B ALA* 1.3 57.9 + - - +
147B THR* 3.0 8.9 + - - -
148B MET* 2.8 33.6 + - - +
155B VAL* 5.8 0.9 - - + +
158B ALA* 3.3 37.7 - - + +
159B GLU* 3.5 17.7 - - + +
162B ALA* 3.6 17.3 - - + -
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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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50B LEU* 3.9 2.6 - - + +
53B ALA* 3.6 27.1 - - + -
54B LEU* 3.8 20.0 - - + -
57B LEU* 3.5 16.2 - - + -
141B ALA 2.9 18.6 + - - +
142B GLU* 3.9 2.7 - - - +
144B LEU* 1.3 76.8 - - - +
146B LYS* 1.3 57.6 + - - +
148B MET* 3.7 0.4 - - - +
149B VAL* 2.8 35.7 + - - +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.7 28.3 - - + -
62B GLU* 4.1 14.5 + - - -
142B GLU* 2.7 50.9 + - + +
143B ILE* 3.9 3.6 - - - +
145B ALA* 1.3 77.3 - - + +
147B THR* 1.3 58.5 + - - +
150B GLY* 2.9 27.8 + - - +
151B GLN* 4.4 0.7 - - - +
240B LEU* 3.9 34.0 + - + +
241B ALA* 4.1 15.4 - - - +
244B ALA* 3.7 24.3 - - + +
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Residues in contact with THR 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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143B ILE* 3.0 20.8 + - + +
144B LEU* 3.0 15.4 + - - +
146B LYS* 1.3 74.8 - - - +
148B MET* 1.3 65.2 + - - +
151B GLN* 3.0 39.2 + - - +
152B GLY 3.4 2.3 + - - -
153B LYS* 3.4 27.6 + - - +
158B ALA* 3.4 17.7 + - - +
215B ILE* 4.0 14.4 - - + -
241B ALA* 3.6 20.0 - - + -
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Residues in contact with MET 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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50B LEU* 4.1 20.0 - - - -
54B LEU* 4.1 19.3 - - + -
85B PHE* 3.4 7.8 - - - -
144B LEU* 2.8 21.8 + - - +
145B ALA 3.7 3.6 - - - +
147B THR* 1.3 76.2 - - - +
149B VAL* 1.3 58.6 + - - +
152B GLY* 2.8 30.1 + - - -
153B LYS 3.2 20.0 + - - +
154B THR 4.0 0.4 - - - +
155B VAL* 3.6 29.2 - - - +
158B ALA* 3.8 14.6 - - + -
380B PRO* 3.5 33.2 - - + +
381B ALA* 4.2 1.8 - - + +
384B PHE* 4.1 13.9 - - + -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.8 23.8 - - + +
57B LEU* 4.0 24.9 - - + -
58B LYS* 6.4 0.2 - - - -
83B SER* 2.9 32.0 + - - +
84B PRO* 3.5 3.5 - - - +
85B PHE* 3.9 15.4 - - + -
89B HIS* 3.9 18.4 - - + +
91B VAL* 3.8 22.9 - - + -
145B ALA 2.8 22.4 + - - +
146B LYS* 5.0 0.2 - - - -
148B MET* 1.3 73.0 - - - +
150B GLY* 1.3 59.9 + - - +
240B LEU* 5.2 1.3 - - + -
381B ALA* 4.8 4.9 - - + -
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Residues in contact with GLY 150 (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 GLN* 2.9 31.2 + - - +
82B VAL 3.8 5.2 - - - +
84B PRO* 3.5 12.6 - - - +
91B VAL* 4.2 13.9 - - - -
146B LYS* 2.9 18.8 + - - +
149B VAL* 1.3 78.6 - - - +
151B GLN* 1.3 60.1 + - - +
237B THR 3.4 4.9 - - - +
240B LEU* 4.7 2.9 - - - +
392B ILE* 4.5 0.9 - - - +
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Residues in contact with GLN 151 (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 GLN* 4.4 0.7 + - - +
84B PRO* 3.6 12.0 - - - +
146B LYS 4.4 0.7 - - - +
147B THR* 3.0 24.1 + - - +
150B GLY* 1.3 76.2 - - - +
152B GLY* 1.3 63.4 + - - +
153B LYS* 3.4 17.6 - - + +
213B THR 3.4 22.7 + - - +
214B ALA* 4.3 4.4 - - - +
215B ILE* 4.2 4.4 - - - +
237B THR 3.3 21.1 - - - +
238B ALA* 3.5 24.1 - - + +
241B ALA* 3.4 28.2 + - - +
343B TYR* 3.1 27.1 + - - +
346B GLN* 4.9 1.2 + - - -
390B ALA 4.9 2.3 - - - +
392B ILE* 3.8 15.1 - - + +
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Residues in contact with GLY 152 (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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84B PRO* 3.7 10.8 - - - +
85B PHE* 4.1 18.2 - - - -
148B MET 2.8 14.2 + - - -
151B GLN* 1.3 78.3 - - - +
153B LYS* 1.3 64.7 + - - +
154B THR* 3.7 1.0 + - - +
343B TYR* 4.1 9.0 - - - -
380B PRO* 4.4 0.9 - - - -
389B SER* 3.4 26.7 + - - -
390B ALA 4.7 3.6 - - - +
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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