Contacts of the helix formed by residues 152 - 166 (chain B) in PDB entry 2Y96
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 SER 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 2.5 32.8 + - - -
147B CYS* 4.4 0.2 - - - -
149B MET* 6.3 0.2 - - - -
150B GLY 3.9 0.4 - - - -
151B ARG* 1.3 79.3 - - - +
153B ARG* 1.3 62.7 + - - +
154B SER 3.4 0.9 - - - -
155B ALA* 3.8 1.5 - - - +
156B THR* 2.7 33.9 + - - -
184B LEU 3.6 13.2 - - - -
185B PRO* 4.0 2.2 - - - +
186B ASN* 3.1 19.4 + - - +
189B PHE* 3.3 4.0 - - - -
1202B SO4 3.0 13.6 + - - -
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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
----------------------------------------------------------
87B ALA* 3.4 30.1 - - + +
88B ALA* 3.6 12.7 - - - +
113B ALA* 2.7 38.5 + - + -
114B ASP 3.8 7.9 - - - -
115B ASP* 3.6 15.2 - - + +
121B LEU* 3.7 10.3 - - + +
147B CYS* 3.9 3.4 - - + +
148B VAL* 3.5 12.1 - - - +
152B SER* 1.3 76.5 - - - +
154B SER* 1.3 64.6 + - - +
156B THR* 3.2 11.6 + - - -
157B LEU* 3.2 12.8 + - - +
189B PHE* 3.5 29.8 - - + -
1202B SO4 2.8 45.3 + - - +
1203B SO4 3.3 40.8 + - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.6 9.6 - - - +
87B ALA* 4.1 5.4 - - - +
145B VAL* 3.8 23.5 - - - +
146B HIS* 3.7 26.5 - - - -
147B CYS* 3.0 18.0 + - - -
150B GLY* 3.3 15.2 - - - -
153B ARG* 1.3 76.4 - - - +
155B ALA* 1.3 67.9 + - - +
157B LEU* 3.0 12.6 + - - +
158B VAL* 3.1 18.0 + - - +
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Residues in contact with ALA 155 (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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64B ILE* 4.0 13.8 - - + +
150B GLY 5.0 0.7 - - - +
151B ARG* 3.3 27.1 - - - +
152B SER 3.8 3.8 - - - +
154B SER* 1.3 81.6 + - - +
156B THR* 1.3 57.6 + - - +
158B VAL* 3.3 3.5 + - - +
159B LEU* 2.9 35.8 + - + +
177B VAL* 5.1 1.5 - - + +
183B VAL* 3.6 28.9 - - + -
185B PRO* 4.7 5.8 - - + -
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.9 11.9 - - + -
125B PHE* 3.7 22.4 - - + -
152B SER 2.7 22.2 + - - -
153B ARG 3.6 4.7 - - - -
154B SER 3.2 0.4 - - - -
155B ALA* 1.3 77.0 - - - +
157B LEU* 1.3 56.5 + - - +
159B LEU* 3.5 9.8 + - - +
160B ALA* 3.0 25.8 + - - +
185B PRO* 3.3 19.4 - - - +
189B PHE* 3.5 15.1 - - + -
193B LEU* 3.7 25.2 - - + +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.4 11.9 - - + -
87B ALA* 3.9 28.5 - - + -
111B VAL* 4.7 11.4 - - + -
121B LEU* 4.0 27.4 - - + -
124B PHE* 4.2 7.6 - - + +
125B PHE* 4.0 18.3 - - + +
128B ALA* 3.9 33.1 - - + +
129B ALA* 5.4 2.4 + - - +
132B ILE* 4.2 6.8 - - + +
145B VAL* 4.8 7.2 - - + -
153B ARG 3.2 8.0 + - - +
154B SER 3.0 7.8 + - - +
156B THR* 1.3 73.8 - - - +
158B VAL* 1.3 61.9 + - - +
160B ALA* 3.4 4.4 + - - +
161B TYR* 2.9 27.9 + - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.9 25.4 - - + -
62B LEU* 3.8 21.3 - - + -
64B ILE* 3.7 17.3 - - + -
132B ILE* 4.5 4.0 - - + -
145B VAL* 3.8 29.8 - - + -
154B SER 3.1 12.2 + - - +
155B ALA 3.8 6.1 - - - +
157B LEU* 1.3 72.6 - - - +
159B LEU* 1.3 66.6 + - - +
161B TYR* 3.2 6.5 + - - +
162B LEU* 3.0 28.0 + - + +
177B VAL* 4.0 13.5 - - + -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.0 16.2 - - + -
155B ALA* 2.9 23.8 + - + +
156B THR 3.7 4.5 - - - +
157B LEU 3.3 0.2 - - - -
158B VAL* 1.3 75.7 - - - +
160B ALA* 1.3 62.9 + - - +
162B LEU* 3.1 5.6 + - - +
163B MET* 3.1 30.3 + - - +
170B LEU* 4.9 2.0 - - + -
173B ALA* 3.4 41.7 - - + +
174B ILE* 3.6 12.3 - - + +
177B VAL* 3.9 16.2 - - + -
183B VAL* 5.4 1.3 - - + -
185B PRO* 4.0 18.6 - - + -
193B LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 160 (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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125B PHE* 3.7 42.4 - - + +
156B THR 3.0 18.1 + - - +
157B LEU* 3.7 5.2 - - - +
159B LEU* 1.3 74.0 - - - +
161B TYR* 1.3 64.5 + - - +
163B MET* 3.2 3.0 + - - +
164B ILE* 3.0 30.8 + - + +
193B LEU* 4.0 4.6 - - + +
196B LEU* 4.0 15.9 - - + -
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Residues in contact with TYR 161 (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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59B TRP* 4.5 2.7 - - - -
62B LEU* 4.0 14.1 - - + -
129B ALA* 3.5 28.8 - - + +
132B ILE* 3.7 32.8 - - + -
133B ASP* 3.6 30.8 + - + -
136B LEU* 3.5 18.9 - - + +
157B LEU 2.9 15.1 + - - +
158B VAL* 3.4 7.2 - - - +
160B ALA* 1.3 76.3 - - - +
162B LEU* 1.3 88.1 + - + +
165B HIS* 3.0 43.7 + + + +
166B LYS* 3.4 27.1 - - + -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 3.8 33.9 - - + -
62B LEU* 5.1 0.2 - - + -
158B VAL* 3.0 19.6 + - + +
159B LEU 3.1 6.3 + - - +
161B TYR* 1.3 101.0 - - + +
163B MET* 1.3 56.8 + - - +
166B LYS* 3.0 39.8 + - + +
168B MET* 3.5 19.5 + - + +
173B ALA* 4.2 10.1 - - + +
176B GLN* 3.8 31.0 - - + -
177B VAL* 4.0 21.3 - - + -
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Residues in contact with MET 163 (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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159B LEU 3.1 23.7 + - - +
160B ALA 3.6 5.6 - - - +
162B LEU* 1.3 78.2 - - - +
164B ILE* 1.3 62.3 + - - +
167B ASP* 4.0 5.7 + - - -
168B MET 3.3 31.0 + - - +
169B THR 4.1 9.2 - - - -
170B LEU* 3.7 24.7 - - + -
173B ALA* 4.1 6.1 - - + -
193B LEU* 3.6 31.6 - - - +
196B LEU* 3.9 13.7 - - + -
197B ASP* 3.6 34.1 - - + +
200B LEU* 3.4 19.9 - - + +
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Residues in contact with ILE 164 (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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125B PHE* 4.0 25.1 - - + +
126B TYR* 3.7 55.9 - - + +
129B ALA* 4.1 4.3 - - + -
160B ALA 3.0 23.3 + - - +
163B MET* 1.3 76.6 - - - +
165B HIS* 1.3 87.4 + - + +
167B ASP* 4.8 1.4 + - - -
196B LEU* 4.2 12.6 - - + -
200B LEU* 4.2 10.9 - - + +
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Residues in contact with HIS 165 (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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126B TYR* 5.2 1.6 + - - -
129B ALA* 3.6 39.9 + - + +
130B ALA* 4.1 6.6 + - + +
133B ASP* 3.9 26.4 + - + +
161B TYR* 3.0 35.2 + + + +
164B ILE* 1.3 98.0 + - + +
166B LYS* 1.3 69.7 + - + +
167B ASP 3.5 2.5 - - - -
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Residues in contact with LYS 166 (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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59B TRP* 3.7 36.2 - - + +
133B ASP* 4.8 7.2 + - - -
136B LEU* 6.4 0.2 - - - -
161B TYR* 3.4 26.9 - - + -
162B LEU* 3.0 30.5 + - + +
165B HIS* 1.3 84.4 + - - +
167B ASP* 1.3 70.6 + - - +
168B MET* 3.1 18.3 + - + +
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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