Contacts of the helix formed by residues 146 - 158 (chain B) in PDB entry 4Y6O
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 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ILE 3.0 23.1 + - - +
90B SER* 3.2 23.1 - - - +
91B ALA* 3.7 28.3 - - + +
145B PRO* 1.3 73.6 - - - +
147B ILE* 1.3 65.7 + - - +
148B CYS* 3.3 13.2 + - - +
149B HIS* 2.8 24.0 + - + +
150B TYR* 3.0 25.8 + - - -
325B ASP* 3.4 11.4 - - - -
349B HIS* 5.1 2.2 - - - -
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Residues in contact with ILE 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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146B THR* 1.3 72.2 - - - +
148B CYS* 1.3 51.4 + - - +
150B TYR* 3.1 3.5 + - - +
151B PHE* 2.8 32.7 + - - +
325B ASP* 3.4 33.7 + - + +
326B GLN* 5.3 1.6 - - - +
328B CYS* 4.5 4.3 - - + -
329B LEU* 3.9 35.9 - - + -
341B LEU* 3.8 26.5 - - + +
342B GLU* 6.1 3.1 - - + -
345B VAL* 4.2 28.8 - - + +
349B HIS* 5.9 0.4 - - - -
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Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.6 37.5 - - + +
146B THR* 3.1 10.0 - - - +
147B ILE* 1.3 74.5 - - - +
149B HIS* 1.3 61.5 + - - +
151B PHE* 3.1 12.1 + - - +
152B MET* 3.3 14.3 + - - +
260B MET* 3.8 28.9 - - - -
324B CYS* 4.1 15.3 - - + +
325B ASP* 3.2 12.8 + - - +
328B CYS* 3.9 18.2 - - - -
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.1 44.4 - - + +
88B SER* 3.3 16.1 + - - -
145B PRO* 3.6 16.4 - - + -
146B THR* 2.8 34.5 + - + +
148B CYS* 1.3 75.9 - - - +
150B TYR* 1.3 57.9 + - - +
152B MET* 3.2 15.3 + - + +
153B ARG* 3.1 22.5 + - - +
170B ASP* 4.6 0.4 + - - -
172B LEU* 3.3 42.7 - - + +
173B GLU* 3.7 16.7 + - + -
176B ALA* 3.9 11.6 - - + +
178B LEU* 5.3 1.2 - - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 3.4 47.3 - - + +
146B THR 3.0 22.8 + - - -
147B ILE 3.1 6.3 + - - +
149B HIS* 1.3 73.6 - - - +
151B PHE* 1.3 59.8 + - - +
153B ARG* 3.3 6.5 + - + +
154B LEU* 2.8 28.6 + - - +
175B ILE 4.4 1.4 + - - -
176B ALA* 3.7 30.6 - - + -
341B LEU* 3.7 6.2 - - + +
344B LEU* 3.6 15.1 - - + +
345B VAL* 3.7 31.0 - - + -
348B GLU* 3.3 41.4 - - + +
349B HIS* 3.7 12.2 - + - -
352B ILE* 3.5 12.3 - - - +
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Residues in contact with PHE 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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71B MET* 4.6 1.1 - - + -
147B ILE 2.8 15.6 + - - +
148B CYS 3.1 9.8 + - - +
150B TYR* 1.3 73.3 - - - +
152B MET* 1.3 57.7 + - - +
154B LEU* 3.2 6.5 + - + +
155B LEU* 2.9 48.2 + - + +
258B LEU* 3.7 30.1 - - + -
260B MET* 4.9 2.2 - - + -
328B CYS* 3.9 39.7 - - + -
331B LEU* 3.7 25.4 - - + -
332B ALA* 4.0 16.6 - - + -
335B LEU* 4.2 8.7 - - + -
337B TRP* 4.0 21.8 - + - -
341B LEU* 3.7 18.4 - - + +
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Residues in contact with MET 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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81B CYS* 3.6 27.1 - - - -
83B VAL* 3.8 10.5 - - + -
87B ILE* 3.9 27.8 - - + -
148B CYS 3.3 7.8 + - - +
149B HIS* 3.2 18.9 + - + +
151B PHE* 1.3 74.1 - - - +
153B ARG* 1.3 58.4 + - - +
155B LEU* 3.3 11.9 + - + +
156B LYS* 3.0 26.2 + - - +
161B LEU* 3.9 5.4 - - + +
164B CYS* 3.6 33.2 - - - -
173B GLU* 4.1 12.1 - - + -
178B LEU* 3.8 17.2 - - + +
260B MET* 3.8 14.4 - - + -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 3.3 38.4 + - - +
203A GLU 5.3 0.2 - - - +
223A ASP* 4.9 3.0 + - - -
149B HIS 3.1 12.9 + - - +
150B TYR* 3.4 12.3 - - + +
152B MET* 1.3 74.6 - - - +
154B LEU* 1.3 58.2 + - - +
156B LYS* 3.2 6.7 + - - +
157B ASP* 2.8 53.2 + - - +
176B ALA 2.9 32.5 + - - +
177B GLY* 3.9 19.3 - - - -
178B LEU* 3.9 10.4 - - + +
344B LEU* 3.8 28.3 - - + +
347B ARG* 5.8 1.8 - - - +
348B GLU* 2.8 32.7 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 4.1 11.9 - - - +
150B TYR 2.8 17.6 + - - +
151B PHE* 3.4 12.1 - - + +
153B ARG* 1.3 73.3 - - - +
155B LEU* 1.3 56.7 + - - +
157B ASP* 3.1 6.2 + - + +
158B LYS* 2.8 55.6 + - + +
337B TRP* 3.7 44.4 - - + +
340B GLU* 4.4 13.2 - - + +
341B LEU* 4.1 26.5 - - + +
344B LEU* 4.3 13.9 - - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.9 21.1 - - + -
79B VAL* 4.3 13.2 - - + -
81B CYS* 3.8 29.8 - - - -
151B PHE* 2.9 37.7 + - + +
152B MET* 3.5 8.5 - - - +
154B LEU* 1.3 74.4 - - - +
156B LYS* 1.3 60.7 + - - +
158B LYS* 3.3 5.7 + - - -
159B GLY 3.2 3.6 + - - -
160B LEU* 2.9 38.5 + - + +
161B LEU* 3.9 15.0 - - + +
258B LEU* 4.2 5.2 - - + -
337B TRP* 3.8 27.8 - - + -
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 4.9 10.3 - - - -
204A TYR* 6.0 3.4 - - - -
205A PRO* 4.2 4.9 - - - +
222A GLU* 4.7 10.1 + - - -
152B MET 3.0 12.4 + - - +
153B ARG* 3.3 10.3 - - - +
155B LEU* 1.3 73.7 - - - +
157B ASP* 1.3 72.1 + - - +
159B GLY* 2.9 21.3 + - - -
161B LEU* 3.7 17.8 - - + +
177B GLY 3.5 22.7 - - - +
178B LEU* 4.1 12.1 - - + -
179B GLU* 4.3 13.8 - - - +
181B GLU* 5.2 2.8 + - - -
182B ASP* 2.8 37.0 + - - +
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Residues in contact with ASP 157 (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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202A HIS* 3.2 19.5 + - - -
203A GLU* 3.7 48.0 + - - +
204A TYR* 3.9 3.1 - - - -
205A PRO* 3.2 26.9 - - - +
153B ARG* 2.8 50.5 + - - +
154B LEU* 3.7 7.9 - - + +
156B LYS* 1.3 82.8 - - - +
158B LYS* 1.3 59.0 + - - +
159B GLY 3.3 0.7 - - - -
344B LEU* 5.0 5.4 - - - +
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Residues in contact with LYS 158 (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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192A THR* 4.7 10.8 - - + +
203A GLU* 2.8 27.2 + - - +
205A PRO* 3.7 9.7 - - - +
154B LEU* 2.8 33.1 + - + +
155B LEU 3.3 4.0 + - - +
156B LYS 3.2 0.2 - - - -
157B ASP* 1.3 75.8 - - - +
159B GLY* 1.3 60.9 + - - +
160B LEU* 3.3 12.9 + - + +
337B TRP* 3.6 47.2 - - + +
340B GLU* 2.8 31.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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