Contacts of the helix formed by residues 169 - 184 (chain B) in PDB entry 4Y72
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 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A VAL* 3.9 12.4 - - + +
120A HIS* 3.8 43.6 + - + +
121A SER* 3.7 29.8 - - - -
183A THR* 4.6 12.3 - - + -
277A SER* 4.4 4.3 - - - -
278A GLY* 3.4 11.5 + - - -
279A LYS* 2.9 50.5 + - + -
167B SER* 3.1 9.8 + - - +
168B GLU* 1.3 104.1 - - + +
170B VAL* 1.3 59.0 + - - +
171B LYS 3.3 2.7 - - - -
172B ASP* 3.3 8.7 + - - +
173B ILE* 2.9 35.3 + - + +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 4.3 11.7 - - - +
167B SER* 3.5 36.1 + - - +
168B GLU 3.6 1.4 - - - -
169B TYR* 1.3 76.8 - - - +
171B LYS* 1.3 61.0 + - + +
173B ILE* 3.5 12.2 + - + +
174B TYR* 3.0 26.8 + - + +
307B ARG* 5.5 14.8 - - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLU 5.5 0.4 + - - -
169B TYR 3.3 0.4 - - - -
170B VAL* 1.3 77.3 - - + +
172B ASP* 1.3 61.0 + - - +
174B TYR* 3.1 9.9 + - + +
175B ALA* 2.8 36.8 + - - +
307B ARG* 6.3 0.7 - - - +
367B TYR* 6.0 7.2 - - - -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 3.6 34.2 + - - +
279A LYS* 3.4 33.3 + - - +
168B GLU 3.8 1.6 - - - +
169B TYR* 3.5 16.6 - - - +
171B LYS* 1.3 81.7 + - - +
173B ILE* 1.3 63.2 + - - +
175B ALA* 3.4 6.4 + - - +
176B TYR* 2.9 24.9 + - - +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A HIS 4.3 5.6 - - - +
121A SER 3.5 20.9 - - - +
123A ARG* 4.3 27.4 - - + +
153A PHE* 4.8 15.0 - - + -
167B SER* 4.5 7.9 - - - +
169B TYR* 2.9 34.1 + - + +
170B VAL* 3.7 12.8 - - + +
172B ASP* 1.3 75.9 - - - +
174B TYR* 1.3 52.5 + - - +
176B TYR* 3.2 6.6 + - + +
177B LEU* 2.8 50.1 + - + +
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.0 18.3 + - + +
171B LYS* 3.6 7.9 - - + +
173B ILE* 1.3 74.9 - - - +
175B ALA* 1.3 66.8 + - + +
177B LEU* 3.2 8.3 + - + +
178B ARG* 3.0 56.4 + - + +
304B PHE* 3.6 31.6 - + - -
307B ARG* 3.4 60.1 + - - +
341B SER* 5.4 1.2 - - - -
367B TYR 3.9 3.9 + - - -
368B LEU* 3.7 20.0 + - + +
369B SER* 4.6 5.3 - - - -
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Residues in contact with ALA 175 (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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171B LYS 2.8 19.5 + - - +
172B ASP* 3.7 7.6 - - - +
174B TYR* 1.3 76.0 - - + +
176B TYR* 1.3 59.8 + - - +
178B ARG* 3.2 10.4 + - - +
179B GLN* 3.1 22.5 + - - +
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Residues in contact with TYR 176 (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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57A GLU* 3.3 41.4 + - + +
121A SER 4.1 5.2 - - - +
122A ARG* 3.4 60.7 + - + +
153A PHE* 4.0 23.3 - + - -
172B ASP 2.9 18.6 + - - +
173B ILE* 3.3 7.2 - - - +
175B ALA* 1.3 71.9 - - - +
177B LEU* 1.3 64.3 + - + +
179B GLN* 3.4 22.0 + - - +
180B LEU* 2.9 59.8 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.8 30.7 - - + -
173B ILE* 2.8 34.9 + - + +
174B TYR* 3.2 11.6 + - + +
176B TYR* 1.3 74.1 - - + +
178B ARG* 1.3 61.9 + - - +
180B LEU* 3.3 12.5 + - + +
181B GLU* 3.0 23.6 + - - +
298B ARG* 5.3 0.7 - - + -
300B LEU* 3.5 23.7 - - + +
303B HIS* 3.7 32.5 - - + +
304B PHE* 3.7 24.0 - - + -
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Residues in contact with ARG 178 (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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174B TYR* 3.0 57.2 + - + +
175B ALA* 3.4 11.2 - - - +
176B TYR 3.2 0.4 - - - -
177B LEU* 1.3 75.2 - - - +
179B GLN* 1.3 64.7 + - - +
181B GLU* 3.2 34.4 + - - +
182B GLU* 3.4 8.6 + - - +
304B PHE* 4.2 6.3 - - + -
341B SER* 3.1 26.5 + - - -
368B LEU 4.6 0.6 + - - -
369B SER* 4.0 21.9 + - - -
370B TYR* 3.3 20.6 + - - -
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Residues in contact with GLN 179 (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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122A ARG* 4.6 11.1 + - - +
175B ALA 3.1 9.6 + - - +
176B TYR* 3.6 29.6 - - - +
178B ARG* 1.3 80.5 - - - +
180B LEU* 1.3 62.3 + - + +
182B GLU* 3.1 25.1 + - - +
183B GLU* 3.2 33.4 + - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 4.8 11.0 - - + +
176B TYR* 2.9 57.0 + - + +
177B LEU* 3.5 15.9 - - + +
178B ARG 3.3 0.2 - - - -
179B GLN* 1.3 76.8 - - + +
181B GLU* 1.3 59.0 + - - +
183B GLU* 3.4 21.6 + - + +
184B GLN* 3.0 59.4 + - - +
297B GLY* 4.9 1.1 - - - -
298B ARG* 3.9 26.7 - - + +
300B LEU* 4.1 6.5 - - + -
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Residues in contact with GLU 181 (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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177B LEU 3.0 7.6 + - - +
178B ARG* 3.2 32.9 + - - +
179B GLN 3.2 0.8 - - - -
180B LEU* 1.3 73.6 - - - +
182B GLU* 1.3 66.9 + - + +
184B GLN* 3.5 3.5 + - - +
185B ALA* 3.4 20.4 + - - +
300B LEU* 3.6 20.9 - - + -
304B PHE* 3.3 11.8 - - + -
339B PRO* 3.7 17.7 - - + +
340B PRO* 3.4 16.3 - - + +
341B SER* 2.6 51.0 + - - -
370B TYR* 4.2 0.3 + - - -
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Residues in contact with GLU 182 (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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178B ARG 3.4 9.3 + - - +
179B GLN* 3.1 16.1 + - - +
181B GLU* 1.3 79.2 - - + +
183B GLU* 1.3 68.3 + - + +
185B ALA* 3.0 23.3 + - - +
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Residues in contact with GLU 183 (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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179B GLN* 3.2 37.3 + - + +
180B LEU* 3.8 24.1 - - + +
182B GLU* 1.3 80.0 - - + +
184B GLN* 1.3 60.7 + - + +
185B ALA 3.3 3.3 + - - +
231B ARG* 5.2 2.1 - - - -
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Residues in contact with GLN 184 (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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180B LEU* 3.0 46.5 + - - +
181B GLU* 3.5 6.3 + - - +
182B GLU 3.1 0.2 - - - -
183B GLU* 1.3 78.9 - - + +
185B ALA* 1.3 64.7 + - - +
186B VAL* 3.7 5.5 + - - +
227B SER* 4.7 8.7 + - - +
231B ARG* 3.7 44.9 + - - +
296B LEU 4.5 1.3 - - - -
297B GLY* 3.4 11.4 - - - -
298B ARG 2.9 37.4 - - - +
300B LEU* 3.8 9.9 - - + +
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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