Contacts of the helix formed by residues 155 - 166 (chain B) in PDB entry 2YG9
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 GLY 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B VAL* 3.5 11.4 - - - -
153B GLY 3.9 1.0 - - - -
154B ILE* 1.3 76.6 - - - +
156B ARG* 1.3 65.4 + - - -
157B TRP 3.4 2.5 - - - -
158B THR 3.5 0.7 + - - -
159B ALA* 3.1 22.7 + - - +
1227B CL 3.3 20.3 - - - +
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Residues in contact with ARG 156 (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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142B GLU* 2.9 41.0 + - - -
145B ILE* 3.7 19.8 - - + +
149B VAL* 3.5 15.1 - - + +
155B GLY* 1.3 72.1 - - - -
157B TRP* 1.3 52.8 + - - +
159B ALA* 3.1 4.5 + - - +
160B GLU* 2.8 68.3 + - + +
175B SER* 5.5 6.5 - - - -
176B GLY* 6.2 1.6 - - - +
1227B CL 4.1 0.6 - - - +
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Residues in contact with TRP 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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72B GLN* 4.3 13.0 - - + -
156B ARG* 1.3 78.2 - - - +
158B THR* 1.3 89.7 + - - +
160B GLU* 3.1 11.6 + - - +
161B MET* 2.9 54.9 + - + +
174B SER* 3.4 18.8 - - - +
176B GLY* 4.1 9.9 - - - +
177B ASP* 2.9 44.0 + - - +
1227B CL 3.8 11.6 - - + +
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Residues in contact with THR 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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65B LEU* 4.8 9.6 - - + -
68B SER* 4.4 13.5 - - - +
69B VAL* 5.2 2.5 - - + -
72B GLN* 3.2 29.9 + - - +
153B GLY 4.6 3.6 + - - -
154B ILE* 4.0 26.5 - - + -
155B GLY 3.9 4.9 + - - -
157B TRP* 1.3 89.8 - - - +
159B ALA* 1.3 61.9 + - - +
161B MET* 3.5 3.8 + - + +
162B PHE* 3.1 22.4 + - + +
1227B CL 3.1 19.7 - - - +
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Residues in contact with ALA 159 (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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65B LEU* 6.2 0.2 - - - -
145B ILE* 3.9 35.0 - - + +
148B LEU* 4.0 24.0 - - + +
149B VAL* 4.6 0.9 - - + -
154B ILE* 4.3 2.4 - - + +
155B GLY 3.1 14.9 + - - +
156B ARG 3.1 7.8 + - - +
158B THR* 1.3 76.1 - - - +
160B GLU* 1.3 59.0 + - - +
162B PHE* 3.4 9.3 + - - +
163B LEU* 3.0 30.0 + - - +
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Residues in contact with GLU 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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145B ILE* 3.9 18.5 - - + +
156B ARG* 2.8 59.7 + - + +
157B TRP* 3.6 6.2 - - - +
159B ALA* 1.3 70.8 - - - +
161B MET* 1.3 67.8 + - - +
163B LEU* 3.2 8.7 + - - +
164B LEU* 3.0 24.4 + - - +
172B VAL* 3.8 19.6 - - + +
173B PHE 4.3 5.7 - - - +
174B SER* 2.7 44.8 + - - +
175B SER* 4.3 3.5 + - - -
176B GLY* 4.8 2.6 + - - -
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Residues in contact with MET 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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157B TRP* 2.9 57.0 + - + +
158B THR* 3.7 6.3 - - + +
160B GLU* 1.3 79.4 - - - +
162B PHE* 1.3 57.6 + - - +
164B LEU* 4.5 5.8 - - + -
165B PHE* 2.8 52.0 + - + +
172B VAL* 5.6 0.2 - - + -
174B SER* 3.4 36.3 - - - +
212B TRP* 3.7 36.8 - - + -
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Residues in contact with PHE 162 (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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61B PRO* 3.4 43.5 - - + -
64B ARG 4.3 1.8 - - - -
65B LEU* 3.8 33.0 - - + -
68B SER* 5.8 4.9 - - - +
133B PHE* 5.5 1.3 - + - -
136B LEU* 4.2 11.7 - - + -
144B VAL* 4.8 1.6 - - + -
148B LEU* 3.5 26.7 - - + -
158B THR 3.1 13.4 + - - +
159B ALA* 3.4 11.0 - - - +
161B MET* 1.3 75.2 - - - +
163B LEU* 1.3 62.4 + - - +
166B ALA* 2.8 52.1 + - + +
167B LEU* 3.0 31.5 + - + -
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Residues in contact with LEU 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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141B ASP* 3.6 25.1 - - + +
144B VAL* 3.9 18.4 - - + -
145B ILE* 3.6 32.5 - - + -
159B ALA 3.0 14.4 + - - +
160B GLU* 3.2 9.8 + - - +
162B PHE* 1.3 76.1 - - - +
164B LEU* 1.3 59.6 + - - +
167B LEU* 3.4 19.9 - - + +
168B ALA 3.2 6.9 + - - -
169B ARG* 2.9 61.0 + - + +
172B VAL* 3.9 15.7 - - + -
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Residues in contact with LEU 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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55B LEU* 3.8 7.1 - - + +
160B GLU 3.0 15.8 + - - +
161B MET* 4.0 7.2 - - + +
163B LEU* 1.3 76.2 - - - +
165B PHE* 1.3 89.1 + - + +
168B ALA* 3.2 24.1 - - - -
169B ARG 4.0 8.4 - - - +
172B VAL* 3.7 31.4 - - + +
174B SER* 6.0 0.7 - - - +
205B SER* 3.7 23.3 - - - +
208B SER* 4.1 3.8 - - - -
209B ARG* 4.0 19.1 - - + -
212B TRP* 3.9 26.7 - - + -
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Residues in contact with PHE 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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55B LEU* 3.8 32.9 - - + +
56B ALA 4.9 3.1 - - - +
64B ARG* 3.2 17.6 + - - +
161B MET* 2.8 46.7 + - + +
162B PHE* 5.3 0.2 - - - -
164B LEU* 1.3 88.0 - - + +
166B ALA* 1.3 58.4 + - - +
168B ALA 4.2 1.5 + - - -
209B ARG* 4.6 9.6 - - + -
212B TRP* 3.6 36.3 - + - -
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Residues in contact with ALA 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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56B ALA 3.9 2.6 - - - +
57B PRO* 3.6 1.7 - - - +
58B THR* 2.7 45.1 + - + +
64B ARG* 3.6 21.2 + - + +
162B PHE* 2.8 53.1 + - + +
165B PHE* 1.3 74.5 - - - +
167B LEU* 1.3 55.1 + - - +
168B ALA 3.4 0.7 - - - -
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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