Contacts of the helix formed by residues 166 - 180 (chain B) in PDB entry 2Y1X
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 ASP 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B ASN 3.7 7.4 + - - +
163B MET 3.0 16.4 + - - +
164B MET 3.9 0.2 - - - -
165B GLN* 1.3 73.1 - - - +
167B TYR* 1.3 59.9 + - - +
168B VAL* 3.3 9.9 + - - +
169B ARG* 3.0 23.7 + - + +
170B THR* 2.9 29.3 + - - -
413B LEU 4.7 0.7 - - - +
414B THR* 3.3 13.4 - - - -
415B HIS* 2.6 52.2 + - + +
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Residues in contact with TYR 167 (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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164B MET 4.8 2.2 - - - -
165B GLN 2.8 11.7 + - - +
166B ASP* 1.3 68.7 + - - +
168B VAL* 1.3 70.4 + - + +
170B THR* 4.5 1.1 - - - +
171B GLY* 2.8 35.5 + - - +
175B ARG* 6.3 0.7 - - - -
320D HIS* 3.7 31.6 - + - -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 3.3 6.0 - - - +
167B TYR* 1.3 86.2 - - + +
169B ARG* 1.3 62.2 + - - +
172B THR* 2.5 37.5 + - - +
175B ARG* 6.2 0.2 - - - +
405B LEU* 3.8 18.4 - - + -
406B SER 4.8 4.9 - - - +
412B PRO* 4.4 27.4 - - + +
413B LEU 4.1 18.6 - - - +
414B THR* 4.3 10.8 - - + -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B MET* 2.9 33.6 + - - +
164B MET* 3.8 4.0 - - - +
166B ASP* 3.0 23.6 + - - +
168B VAL* 1.3 79.3 - - - +
170B THR* 1.3 85.4 + - - +
172B THR* 3.8 0.9 - - - -
173B TYR* 3.0 30.5 + - + -
198B ILE* 4.4 6.3 - - - +
199B LEU* 5.3 3.8 - - - +
258B GLU* 2.8 37.7 + - + +
405B LEU* 4.0 16.2 - - + -
414B THR* 5.4 0.6 - - - +
415B HIS* 3.5 13.0 - - - -
416B TRP* 3.4 34.1 - - + -
1001B SAH 2.9 43.8 + - - +
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Residues in contact with THR 170 (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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163B MET 3.3 0.7 + - - -
164B MET* 2.7 28.2 + - - +
166B ASP 2.9 10.6 + - - -
167B TYR* 4.5 0.4 - - - -
169B ARG* 1.3 99.4 + - - +
171B GLY* 1.3 59.0 + - - +
173B TYR* 3.3 5.4 + - - +
174B GLN* 3.0 24.6 + - - +
198B ILE* 4.3 11.0 - - + -
199B LEU* 6.0 0.4 - - + -
202B PHE* 3.6 30.1 - - + -
319D PHE* 4.6 2.2 - - + -
320D HIS* 3.8 22.9 - - + +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 2.8 31.0 + - - -
170B THR* 1.3 71.8 - - - +
172B THR* 1.3 64.7 + - - +
174B GLN* 3.4 5.0 + - - +
175B ARG* 3.1 31.7 + - - +
320D HIS* 3.9 17.6 - - - -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 2.5 35.0 + - - +
169B ARG 3.8 2.5 - - - -
171B GLY* 1.3 75.0 - - - +
173B TYR* 1.3 59.5 + - - +
175B ARG* 3.2 22.8 + - - +
176B ALA* 2.8 28.9 + - - +
396B PHE* 4.7 4.5 - - + -
403B VAL* 3.8 16.8 - - + +
404B TRP 3.6 25.0 + - - +
405B LEU* 3.9 19.1 - - + +
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ARG* 3.0 26.1 + - + +
170B THR* 3.6 8.7 - - - +
172B THR* 1.3 77.1 - - - +
174B GLN* 1.3 61.5 + - - +
176B ALA* 3.3 5.3 + - - +
177B ILE* 3.0 38.5 + - + +
199B LEU* 3.6 39.5 - - + -
202B PHE* 4.3 1.1 - - + -
256B ILE* 5.7 1.8 - - + -
257B SER 2.7 29.7 + - - -
258B GLU* 3.2 30.6 - - + +
260B MET* 3.5 13.6 - - + +
287B PHE* 4.7 2.5 - - + -
288B PRO* 3.9 4.9 - - - +
396B PHE* 3.6 28.8 - + - -
405B LEU* 3.7 24.0 - - + -
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR 3.0 11.7 + - - +
171B GLY* 3.8 5.5 + - - +
173B TYR* 1.3 77.4 - - - +
175B ARG* 1.3 58.1 + - - +
177B ILE* 3.2 1.6 + - - +
178B LEU* 2.8 50.3 + - + +
202B PHE* 3.5 34.8 - - + -
205B GLN* 3.1 12.1 - - - +
320D HIS* 3.0 51.7 + - - +
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Residues in contact with ARG 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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167B TYR* 6.3 0.8 - - - -
168B VAL* 6.2 0.2 - - - +
171B GLY 3.1 14.7 + - - +
172B THR* 3.4 34.4 + - - +
174B GLN* 1.3 76.0 - - - +
176B ALA* 1.3 60.4 + - - +
178B LEU* 4.5 4.3 - - - +
179B GLN* 2.9 71.0 + - - +
403B VAL* 4.0 22.3 - - + +
404B TRP 5.3 1.0 + - - -
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Residues in contact with ALA 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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172B THR 2.8 17.6 + - - +
173B TYR* 3.6 4.7 - - - +
175B ARG* 1.3 76.6 - - - +
177B ILE* 1.3 62.1 + - + +
180B ASN* 3.1 27.9 + - - -
287B PHE* 3.5 7.0 - - + -
396B PHE* 3.7 42.0 - - + -
403B VAL* 4.0 21.9 - - + +
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Residues in contact with ILE 177 (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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173B TYR* 3.0 33.0 + - + +
174B GLN 3.7 2.9 - - - +
176B ALA* 1.3 78.8 - - + +
178B LEU* 1.3 63.7 + - - +
180B ASN 3.4 20.1 + - - +
181B HIS* 3.5 2.1 + - - -
184B PHE* 3.7 35.6 - - + -
199B LEU* 4.2 10.3 - - + +
202B PHE* 3.7 48.0 - - + +
203B ALA* 4.0 2.7 - - - +
206B ALA* 3.9 5.0 - - + +
256B ILE* 4.5 16.2 - - + -
287B PHE* 4.3 8.5 - - + -
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Residues in contact with LEU 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 GLN* 2.8 45.9 + - + +
175B ARG* 4.3 3.4 - - - +
177B ILE* 1.3 73.5 - - + +
179B GLN* 1.3 63.6 + - + +
181B HIS* 3.4 25.1 - - - +
202B PHE 3.9 4.7 - - - +
205B GLN* 3.8 31.2 - - + +
206B ALA* 3.8 24.9 - - + +
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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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175B ARG* 2.9 49.7 + - + +
176B ALA* 4.7 1.1 - - - +
178B LEU* 1.3 80.1 - - + +
180B ASN* 1.3 60.9 + - - +
181B HIS* 3.4 4.5 - - - -
400B ILE* 3.6 28.9 - - - +
401B MET* 3.2 38.6 - - + +
403B VAL* 4.4 3.5 - - + +
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Residues in contact with ASN 180 (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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176B ALA* 3.1 27.0 + - - +
177B ILE 3.4 6.9 + - - +
178B LEU 3.3 0.4 - - - -
179B GLN* 1.3 77.9 - - - +
181B HIS* 1.3 56.4 + - - +
182B THR 3.1 4.0 - - - +
183B ASP* 2.8 35.6 + - + +
184B PHE* 3.4 6.6 - - - -
287B PHE* 3.7 13.8 - - + -
396B PHE 4.6 2.0 + - - -
398B GLY* 3.4 14.1 - - - +
400B ILE* 3.0 16.9 + - - +
401B MET* 2.9 49.6 + - - +
403B VAL* 4.8 2.0 - - - +
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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