Contacts of the helix formed by residues 139 - 152 (chain B) in PDB entry 4OE4
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 TYR 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 2.8 26.3 + - + +
135B ILE* 3.7 9.6 - - + -
138B LYS* 1.3 105.4 - - + +
140B ARG* 1.3 65.4 + - - +
141B TYR 3.3 2.7 - - - -
142B ASP* 3.4 23.6 + - + +
143B MET* 2.9 24.1 + - - +
245B LEU* 4.6 9.9 - - + -
249B VAL* 3.5 33.2 - - + -
252B GLU* 2.3 42.9 + - - -
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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
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135B ILE 3.1 16.8 + - - +
136B SER* 2.8 37.6 + - - +
137B THR* 2.9 16.0 + - - +
138B LYS 3.5 0.4 - - - -
139B TYR* 1.3 76.7 - - - +
141B TYR* 1.3 85.0 + - + +
143B MET* 3.8 1.7 - - - +
144B LEU* 2.9 45.4 + - + +
159B GLU* 2.7 35.3 + - - +
163B ILE* 3.8 27.6 - - + +
164B THR* 5.8 0.6 + - - -
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 3.4 33.1 - - + +
46B LEU* 3.6 36.2 - - + +
47B LEU* 3.7 22.4 - - + +
50B SER* 3.2 26.0 - - - +
137B THR 5.2 3.8 - - - -
138B LYS 5.3 2.7 + - - -
139B TYR 3.3 0.4 - - - -
140B ARG* 1.3 99.4 - - + +
142B ASP* 1.3 60.7 + - - +
144B LEU* 3.6 15.2 - - + +
145B ALA 2.8 25.3 + - - -
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Residues in contact with ASP 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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50B SER* 2.9 20.9 + - - -
53B LYS* 5.8 1.4 - - - +
54B PHE* 3.7 21.8 - - + -
138B LYS 5.9 0.2 - - - -
139B TYR* 3.4 27.8 + - + +
141B TYR* 1.3 76.0 - - - +
143B MET* 1.3 58.1 + - - +
146B ALA* 2.9 30.5 + - - +
245B LEU* 4.0 20.0 - - + -
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 4.1 26.2 - - + -
139B TYR 2.9 17.7 + - - +
140B ARG 3.8 2.9 - - - +
142B ASP* 1.3 73.0 - - - +
144B LEU* 1.3 66.6 + - - +
146B ALA* 3.5 0.5 + - - +
147B THR* 3.1 40.8 + - - -
162B CYS* 3.5 31.4 - - + +
163B ILE* 4.4 1.1 - - + -
166B LEU* 4.7 1.6 - - + -
214B THR* 4.0 11.9 - - + -
242B SER* 3.6 28.0 - - - +
245B LEU* 4.0 19.7 - - + +
246B LEU* 3.7 25.4 - - + +
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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
----------------------------------------------------------
47B LEU* 3.8 20.4 - - + -
140B ARG* 2.9 46.9 + - + +
141B TYR* 3.6 13.0 - - + +
143B MET* 1.3 77.4 - - - +
145B ALA* 1.3 57.9 + - - +
147B THR* 3.7 1.4 - - - -
148B MET* 2.9 37.9 + - - +
155B VAL* 4.4 14.8 - - + +
158B ALA* 3.8 8.5 - - + -
159B GLU* 3.6 42.4 - - + +
162B CYS* 4.0 3.4 - - - -
163B ILE* 3.8 13.7 - - + -
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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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47B LEU* 4.3 1.5 - - + +
50B SER* 3.7 10.1 - - - +
51B LEU* 3.7 46.7 - - + +
54B PHE* 3.9 5.8 - - + -
141B TYR 2.8 21.0 + - - +
142B ASP 3.8 2.9 - - - +
144B LEU* 1.3 72.7 - - - +
146B ALA* 1.3 57.7 + - - +
148B MET* 3.6 1.1 - - - +
149B LEU* 2.8 39.5 + - + +
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Residues in contact with ALA 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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54B PHE* 4.5 3.7 - - + -
142B ASP 2.9 18.6 + - - +
143B MET* 3.8 3.8 - - - +
145B ALA* 1.3 78.0 - - - +
147B THR* 1.3 56.9 + - - +
150B GLY* 2.9 27.0 + - - -
151B GLN* 4.1 2.6 - - - +
241B LEU* 3.8 34.6 - - + +
242B SER* 3.9 17.1 + - - -
245B LEU* 3.9 16.4 - - + -
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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
----------------------------------------------------------
143B MET* 3.1 18.9 + - - -
144B LEU 3.8 2.5 - - - -
146B ALA* 1.3 72.5 - - - +
148B MET* 1.3 61.6 + - - +
151B GLN* 2.9 42.2 + - - +
152B GLY 3.7 0.7 + - - -
153B LYS* 3.8 26.8 + - + -
158B ALA* 4.0 11.2 - - + -
161B ASP* 3.9 8.1 - - - +
162B CYS* 3.3 15.4 - - - +
214B THR* 3.0 25.7 + - - +
242B SER* 3.6 6.3 - - - -
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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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47B LEU* 4.2 18.6 - - + -
51B LEU* 3.8 30.7 - - + -
83B ASN* 5.0 0.9 - - - +
144B LEU* 2.9 27.4 + - - +
145B ALA* 3.6 3.6 - - - +
147B THR* 1.3 77.1 - - - +
149B LEU* 1.3 59.0 + - + +
152B GLY* 3.0 24.4 + - - -
153B LYS* 3.2 30.8 + - - +
154B ASN* 3.7 3.8 - - - +
155B VAL* 3.8 30.1 - - + +
158B ALA* 3.5 16.8 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.7 35.4 - - + +
54B PHE* 3.7 30.3 - - + -
55B LYS* 3.9 22.9 - - + -
83B ASN* 3.2 42.7 - - - +
84B PRO* 3.2 8.5 - - - +
91B LEU* 3.3 24.5 - - + +
145B ALA* 2.8 25.5 + - + +
146B ALA* 4.4 2.2 - - - +
148B MET* 1.3 75.7 - - + +
150B GLY* 1.3 61.3 + - - +
241B LEU* 5.1 1.1 - - + -
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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* 3.6 18.0 + - - +
82B THR 4.3 1.6 - - - +
84B PRO* 3.5 14.3 - - - +
91B LEU* 3.5 15.2 - - - +
146B ALA 2.9 17.0 + - - -
149B LEU* 1.3 80.2 - - - +
151B GLN* 1.3 63.1 + - - +
238B THR* 3.4 13.2 - - - +
241B LEU* 5.2 1.6 - - - -
403B ILE* 3.8 3.6 - - - +
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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* 5.5 0.2 + - - -
84B PRO* 3.9 5.0 - - - +
146B ALA 4.1 1.4 - - - +
147B THR* 2.9 26.9 + - + +
150B GLY* 1.3 76.1 - - - +
152B GLY* 1.3 64.0 + - - +
153B LYS* 3.5 9.9 - - + -
211B PHE 2.8 29.8 + - - +
212B ASN 4.2 3.6 + - - -
213B PHE 4.1 0.2 - - - -
214B THR* 3.2 28.5 + - - +
238B THR 3.6 17.5 - - - +
239B ALA* 3.9 10.7 - - + +
242B SER* 2.7 31.8 + - - -
346B PHE* 3.4 22.5 - - + -
349B GLN* 4.9 1.7 + - - -
401B PRO 5.3 0.9 - - - +
402B VAL 6.0 0.2 - - - -
403B ILE* 4.0 14.3 - - + +
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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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83B ASN* 5.3 1.8 - - - -
84B PRO* 3.6 18.6 - - - +
85B ALA* 5.6 1.3 - - - -
148B MET 3.0 11.0 + - - -
149B LEU 4.7 0.2 - - - -
150B GLY 3.5 2.0 - - - -
151B GLN* 1.3 79.3 - - - +
153B LYS* 1.3 60.4 + - - +
154B ASN 4.3 0.2 + - - -
157B GLN* 4.3 1.0 - - - +
346B PHE* 3.5 14.4 - - - -
347B GLN* 4.1 3.8 + - - -
400B GLY* 5.1 0.9 - - - -
401B PRO* 3.8 28.6 - - - +
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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
------------------------------------------------------------
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