Contacts of the helix formed by residues 172 - 185 (chain B) in PDB entry 2YWB
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 LYS 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B GLY 5.5 1.3 + - - +
116B LEU* 3.1 49.0 + - + +
117B GLU 3.8 6.9 + - - -
119B GLU 2.8 29.3 + - - +
120B VAL* 4.6 11.7 - - + -
121B GLN 5.1 1.0 + - - +
170B THR* 3.3 4.3 - - + +
171B PRO* 1.3 78.0 - - + +
173B GLY* 1.3 62.4 + - - +
174B MET 3.3 2.0 - - - -
175B GLN* 3.3 12.3 + - + +
176B ILE* 3.1 23.6 + - - +
253D GLU* 6.1 1.6 - - - +
407D ASP* 3.0 35.7 + - - -
411D SER* 3.8 15.0 - - - +
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Residues in contact with GLY 173 (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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165B PRO* 3.1 28.7 - - - +
170B THR* 2.7 31.1 + - - +
171B PRO 3.1 0.8 - - - -
172B LYS* 1.3 71.8 - - - +
174B MET* 1.3 56.8 + - - +
176B ILE* 3.0 7.7 + - - +
177B LEU* 2.9 31.6 + - - +
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Residues in contact with MET 174 (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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18B ARG* 3.4 58.1 - - + +
21B GLU* 3.7 20.0 - - + +
22B LEU* 3.5 32.9 - - + +
165B PRO 3.9 2.3 + - - +
170B THR 4.6 0.4 + - - -
171B PRO 4.4 7.3 + - - +
172B LYS 3.3 0.4 - - - -
173B GLY* 1.3 75.0 - - - +
175B GLN* 1.3 57.5 + - - +
177B LEU* 3.5 7.1 + - - +
178B GLU* 2.8 29.3 + - - +
373D ASP* 5.3 4.9 - - + -
374D THR* 3.8 16.6 - - + -
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Residues in contact with GLN 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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114B ARG 4.2 4.4 - - - +
116B LEU* 3.6 20.6 - - + -
172B LYS* 3.3 16.4 + - + +
173B GLY 3.2 0.6 - - - -
174B MET* 1.3 75.6 - - - +
176B ILE* 1.3 56.3 + - - +
178B GLU* 3.2 14.0 + - - +
179B ASN* 2.7 60.1 + - - +
182B GLU* 5.0 1.2 - - - +
253D GLU* 3.4 54.6 + - - +
374D THR* 4.1 23.8 + - + +
375D LEU* 5.2 3.4 - - - +
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Residues in contact with ILE 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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75B LEU* 5.5 2.9 - - + -
112B LEU* 4.0 35.4 - - + +
113B PHE* 3.9 10.3 - - + -
116B LEU* 3.4 33.0 - - + -
120B VAL* 5.1 5.4 - - + -
161B VAL* 5.3 3.4 - - + -
163B PHE* 3.8 29.2 - - + -
165B PRO* 4.2 13.9 - - + -
170B THR* 4.9 3.6 - - + -
172B LYS 3.1 11.2 + - - +
173B GLY* 3.0 14.6 + - - +
175B GLN* 1.3 73.0 - - - +
177B LEU* 1.3 63.1 + - + +
179B ASN* 2.9 5.7 + - - +
180B PHE* 2.8 26.3 + - - +
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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
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15B ILE* 5.5 3.8 - - + +
18B ARG* 4.0 27.6 - - + -
19B LEU* 5.2 5.4 - - + +
22B LEU* 3.7 16.6 - - + -
47B ILE* 4.3 17.0 - - + -
75B LEU* 3.7 26.9 - - + -
77B ILE* 4.9 3.6 - - + -
165B PRO* 4.0 33.0 - - + +
166B GLU* 4.3 6.1 - - + -
173B GLY 2.9 20.3 + - - +
174B MET* 3.9 5.8 - - - +
176B ILE* 1.3 75.7 - - + +
178B GLU* 1.3 63.3 + - - +
180B PHE* 3.2 8.0 + - + +
181B LEU* 2.9 27.7 + - - +
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Residues in contact with GLU 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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22B LEU* 3.8 14.6 - - + +
174B MET 2.8 19.8 + - - +
175B GLN* 3.3 21.8 - - - +
177B LEU* 1.3 76.3 - - - +
179B ASN* 1.3 63.4 + - - +
181B LEU* 3.2 3.3 + - - +
182B GLU* 2.5 48.5 + - - +
188B ARG* 2.8 41.3 + - - -
257D ALA* 4.4 5.0 - - + +
261D LEU* 6.0 0.2 - - - +
372D PRO* 3.5 22.7 - - + +
374D THR* 4.3 10.8 - - + +
375D LEU* 6.4 0.4 - - + -
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Residues in contact with ASN 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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111B PRO 3.5 18.2 - - - +
112B LEU* 3.2 15.5 + - - +
113B PHE* 3.7 2.0 - - - +
114B ARG* 2.9 48.0 + - - +
116B LEU* 4.0 6.3 - - - +
175B GLN* 2.7 38.3 + - - +
176B ILE 3.3 6.7 - - - +
178B GLU* 1.3 74.0 - - - +
180B PHE* 1.3 57.7 + - - +
182B GLU* 3.1 16.4 + - - +
183B LEU* 2.8 36.9 + - + +
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Residues in contact with PHE 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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2B VAL* 5.6 0.4 - - + -
45B ALA* 4.0 21.3 - - + -
46B LEU 3.9 6.1 - - - -
47B ILE* 4.2 11.9 - - + -
73B PRO* 3.9 14.6 - - + -
74B LEU* 3.5 46.0 - - - -
75B LEU* 3.6 27.8 - - + -
112B LEU* 4.0 13.3 - - + +
157B ARG 4.6 0.7 - - - -
159B TYR* 4.2 22.9 - + - -
176B ILE 2.8 12.2 + - - +
177B LEU* 3.4 11.7 - - + +
179B ASN* 1.3 77.2 - - - +
181B LEU* 1.3 69.9 + - + +
183B LEU* 3.2 8.3 + - + +
184B ALA* 2.9 30.8 + - + +
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Residues in contact with LEU 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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2B VAL* 4.0 9.9 - - + -
19B LEU* 3.8 20.9 - - + -
22B LEU* 3.7 37.2 - - + -
24B ALA* 4.0 18.4 - - + -
177B LEU 2.9 16.9 + - - +
178B GLU* 3.6 7.0 - - - +
180B PHE* 1.3 87.9 - - + +
182B GLU* 1.3 58.0 + - - +
184B ALA 3.4 0.3 + - - -
185B GLY 3.0 23.4 + - - -
186B VAL* 3.0 37.4 + - + +
188B ARG* 3.7 22.0 - - - +
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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
----------------------------------------------------------
114B ARG* 4.7 8.5 - - - -
175B GLN* 5.0 0.9 - - - +
178B GLU* 2.5 46.2 + - - +
179B ASN* 3.5 17.1 - - - +
181B LEU* 1.3 77.4 - - - +
183B LEU* 1.3 65.2 + - + +
185B GLY* 3.2 12.2 + - - -
188B ARG* 3.9 3.8 - - - +
253D GLU 4.7 1.8 - - - +
256D GLY* 3.5 25.9 - - - +
257D ALA* 3.2 17.3 + - - +
260D ALA* 3.7 23.9 - - + +
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Residues in contact with LEU 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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111B PRO* 3.0 38.6 - - + +
112B LEU* 3.9 15.5 - - + +
114B ARG* 6.4 2.0 - - - -
156B GLY 5.1 4.3 - - - +
159B TYR* 3.3 42.4 - - + +
179B ASN* 2.8 26.6 + - - +
180B PHE* 3.4 12.6 - - + +
182B GLU* 1.3 80.0 - - + +
184B ALA* 1.3 58.4 + - + +
185B GLY* 3.1 5.2 + - - -
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Residues in contact with ALA 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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44B GLN* 4.3 6.1 - - - +
45B ALA* 4.2 6.5 - - + -
73B PRO* 3.4 41.7 - - + +
157B ARG* 6.1 0.9 - - - +
180B PHE* 2.9 21.6 + - + +
181B LEU* 4.7 0.2 - - - -
183B LEU* 1.3 75.6 - - - +
185B GLY* 1.3 62.4 + - - +
186B VAL* 3.3 18.0 + - + -
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Residues in contact with GLY 185 (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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44B GLN* 3.4 11.2 + - - -
181B LEU 3.0 6.8 + - - -
182B GLU* 3.2 8.4 + - - -
183B LEU 3.1 6.6 + - - -
184B ALA* 1.3 78.3 - - - +
186B VAL* 1.3 65.2 + - - +
187B LYS* 3.3 6.9 + - - +
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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