Contacts of the helix formed by residues 146 - 158 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ILE 3.0 23.4 + - - +
90A SER* 3.2 22.2 - - - +
91A ALA* 3.7 27.6 - - + +
145A PRO* 1.3 74.0 - - - +
147A ILE* 1.3 64.8 + - - +
148A CYS* 3.2 12.6 + - - +
149A HIS* 2.9 31.1 + - + +
150A TYR* 3.1 18.6 + - - -
325A ASP* 3.3 12.7 + - - -
349A HIS* 4.9 3.1 - - - -
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Residues in contact with ILE 147 (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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146A THR* 1.3 73.1 - - - +
148A CYS* 1.3 58.3 + - - +
150A TYR* 3.1 3.7 + - - +
151A PHE* 2.8 26.9 + - - +
325A ASP* 3.4 39.4 + - + +
326A GLN* 5.2 2.0 - - - +
328A CYS* 4.4 3.6 - - + -
329A LEU* 3.9 30.7 - - + -
341A LEU* 3.8 27.8 - - + +
342A GLU* 6.3 0.9 - - + -
345A VAL* 4.0 29.9 - - + +
349A HIS* 5.4 0.8 + - + -
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Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.5 36.6 - - + +
146A THR* 3.1 10.8 + - - +
147A ILE* 1.3 79.8 - - - +
149A HIS* 1.3 62.5 + - - +
151A PHE* 3.3 11.6 + - - +
152A MET* 3.3 14.7 + - - +
260A MET* 3.7 29.6 - - - -
324A CYS* 4.1 15.9 - - + +
325A ASP* 3.2 8.0 + - - +
328A CYS* 3.9 17.7 - - - -
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Residues in contact with HIS 149 (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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87A ILE* 3.1 45.3 - - + +
88A SER* 3.3 16.5 + - - -
145A PRO* 3.6 17.0 - - + -
146A THR* 2.9 34.9 + - + +
148A CYS* 1.3 75.9 - - - +
150A TYR* 1.3 58.9 + - - +
152A MET* 3.2 14.1 + - + +
153A ARG* 3.1 22.5 + - - +
170A ASP* 4.6 0.2 + - - -
172A LEU* 3.4 42.9 - - + +
173A GLU* 3.7 16.5 + - + -
176A ALA* 3.8 11.0 - - + +
178A LEU* 5.3 1.4 - - - +
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Residues in contact with TYR 150 (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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145A PRO* 3.3 47.8 - - + +
146A THR 3.1 20.9 + - - -
147A ILE 3.1 5.6 + - - +
149A HIS* 1.3 73.6 - - - +
151A PHE* 1.3 59.0 + - - +
153A ARG* 3.2 5.1 + - + +
154A LEU* 2.9 25.3 + - - +
175A ILE 4.6 1.6 + - - -
176A ALA* 3.8 30.2 - - + -
341A LEU* 3.7 4.0 - - + -
344A LEU* 3.5 30.3 - - + +
345A VAL* 3.7 29.2 - - + -
348A GLU* 3.4 35.8 + - + +
349A HIS* 3.8 12.9 - + - -
352A ILE* 3.6 10.2 - - - +
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Residues in contact with PHE 151 (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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71A MET* 4.5 2.9 - - + -
147A ILE 2.8 12.4 + - - +
148A CYS 3.3 10.7 + - - +
150A TYR* 1.3 76.2 - - - +
152A MET* 1.3 58.7 + - - +
154A LEU* 3.2 8.2 + - + +
155A LEU* 3.0 39.4 + - + +
258A LEU* 3.7 29.8 - - + -
260A MET* 5.1 2.2 - - + -
328A CYS* 3.9 42.4 - - + -
331A LEU* 3.7 23.1 - - + -
332A ALA* 4.1 12.1 - - + -
335A LEU* 4.1 2.9 - - + -
337A TRP* 3.9 32.5 - + - -
341A LEU* 3.6 18.1 - - + +
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Residues in contact with MET 152 (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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81A CYS* 3.6 35.2 - - - -
83A VAL* 3.8 9.9 - - + -
87A ILE* 3.8 29.2 - - + -
148A CYS 3.3 8.5 + - - +
149A HIS* 3.2 20.5 + - - +
151A PHE* 1.3 74.9 - - + +
153A ARG* 1.3 58.9 + - - +
155A LEU* 3.2 11.9 + - + +
156A LYS* 3.0 26.9 + - - +
161A LEU* 4.1 4.5 - - + +
164A CYS* 3.6 26.2 - - - -
173A GLU* 4.2 11.4 - - + -
178A LEU* 3.8 18.0 - - + +
260A MET* 3.9 13.2 - - + -
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Residues in contact with ARG 153 (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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149A HIS 3.1 12.0 + - - +
150A TYR* 3.2 13.4 + - + +
152A MET* 1.3 76.6 - - - +
154A LEU* 1.3 55.5 + - - +
156A LYS* 3.3 7.7 + - - +
157A ASP* 2.9 54.0 + - - +
175A ILE 5.5 0.2 + - - -
176A ALA 2.9 33.8 + - - +
177A GLY* 3.7 24.0 + - - -
178A LEU* 3.9 9.9 - - + +
344A LEU* 3.9 26.4 - - + +
348A GLU* 4.6 20.8 + - - +
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Residues in contact with LEU 154 (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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150A TYR 2.9 15.3 + - - +
151A PHE* 3.2 11.2 + - + +
153A ARG* 1.3 73.9 - - - +
155A LEU* 1.3 65.0 + - - +
157A ASP* 3.3 9.1 + - + +
158A LYS* 3.0 38.8 + - - +
337A TRP* 4.0 29.4 - - + -
340A GLU* 3.6 33.4 - - + +
341A LEU* 3.8 36.3 - - + +
344A LEU* 3.7 20.9 - - + -
347A ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 155 (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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71A MET* 4.0 26.7 - - + -
79A VAL* 4.4 13.5 - - + -
81A CYS* 3.6 31.2 - - - -
151A PHE* 3.0 35.2 + - + +
152A MET* 3.2 9.4 + - - +
154A LEU* 1.3 75.4 - - - +
156A LYS* 1.3 62.2 + - - +
158A LYS* 3.4 2.4 + - - -
159A GLY 3.3 3.5 + - - -
160A LEU* 2.9 43.6 + - + +
161A LEU* 3.9 15.7 - - + +
258A LEU* 4.2 4.9 - - + -
337A TRP* 4.0 16.8 - - + -
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Residues in contact with LYS 156 (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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152A MET 3.0 13.1 + - - +
153A ARG* 3.4 11.9 - - - +
154A LEU 3.3 0.2 - - - -
155A LEU* 1.3 75.0 - - - +
157A ASP* 1.3 71.1 + - - +
159A GLY* 3.0 20.3 + - - -
161A LEU* 3.7 15.8 + - + +
177A GLY 3.5 24.7 - - - +
178A LEU* 4.0 13.5 - - + -
179A GLU* 2.8 26.5 + - - -
182A ASP* 2.7 39.6 + - - +
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Residues in contact with ASP 157 (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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153A ARG* 2.9 54.0 + - - +
154A LEU* 3.3 11.3 + - + +
156A LYS* 1.3 88.3 - - - +
158A LYS* 1.3 60.4 + - + +
159A GLY 3.3 1.1 + - - -
340A GLU* 6.0 1.1 - - - +
344A LEU* 5.4 2.6 - - - +
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Residues in contact with LYS 158 (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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154A LEU* 3.0 27.3 + - + +
155A LEU 3.4 3.8 + - - +
156A LYS 3.2 0.2 - - - -
157A ASP* 1.3 78.5 - - + +
159A GLY* 1.3 60.9 + - - +
160A LEU* 3.3 17.9 + - + +
337A TRP* 3.5 52.9 - - + +
340A GLU* 2.8 41.2 + - - +
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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