Contacts of the helix formed by residues 187 - 199 (chain B) in PDB entry 2HKU
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LEU* 5.5 0.7 - - - -
177B LYS* 4.2 25.7 - - - +
188B LEU* 1.3 67.7 + - - +
189B GLU* 3.6 9.4 + - - +
190B GLU* 3.5 36.4 + - - +
191B ALA* 3.1 25.9 + - - +
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Residues in contact with LEU 188 (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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98B VAL* 5.8 0.4 - - + -
99B GLY* 4.1 30.7 - - - +
102B LEU* 4.9 21.3 - - + +
103B GLY* 6.1 2.0 - - - +
177B LYS* 6.5 1.1 - - + -
187B SER* 1.3 78.1 + - - +
189B GLU* 1.3 60.5 + - - +
191B ALA* 3.1 7.1 + - - +
192B VAL* 2.8 40.8 + - + +
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Residues in contact with GLU 189 (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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187B SER* 3.3 8.9 + - - +
188B LEU* 1.3 79.7 - - - +
190B GLU* 1.3 56.3 + - - +
192B VAL* 4.0 4.0 - - - +
193B ALA* 3.0 29.1 + - - +
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Residues in contact with GLU 190 (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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160A ASP* 4.7 8.3 - - - +
161A VAL* 4.1 22.1 - - + +
164A LYS* 2.5 40.2 + - + +
173B LEU* 5.6 2.0 - - + -
187B SER* 3.5 28.8 + - - +
189B GLU* 1.3 78.7 - - - +
191B ALA* 1.3 57.0 + - - +
193B ALA* 3.4 6.5 + - - +
194B VAL* 3.0 35.7 + - + +
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Residues in contact with ALA 191 (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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98B VAL* 4.1 3.8 - - + -
102B LEU* 3.1 36.8 - - + -
173B LEU* 4.0 23.2 - - + +
177B LYS* 4.8 0.9 - - - -
187B SER 3.1 13.1 + - - +
188B LEU* 3.1 5.4 + - - +
190B GLU* 1.3 77.7 - - - +
192B VAL* 1.3 65.0 + - - +
194B VAL* 3.2 13.9 + - - +
195B ILE* 3.2 19.3 + - - +
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Residues in contact with VAL 192 (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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94B THR* 4.1 7.9 - - + +
95B GLU* 3.8 35.0 - - + +
98B VAL* 3.8 25.8 - - + -
99B GLY 5.2 0.4 - - - +
188B LEU* 2.8 24.6 + - + +
189B GLU* 4.1 5.4 - - - +
191B ALA* 1.3 75.2 - - - +
193B ALA* 1.3 57.0 + - - +
195B ILE* 3.0 10.0 + - - +
196B PHE* 2.8 61.7 + - + -
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Residues in contact with ALA 193 (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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157A ALA* 4.8 7.3 - - + +
161A VAL* 4.0 21.4 - - + +
189B GLU 3.0 19.1 + - - +
190B GLU* 3.7 7.2 - - - +
191B ALA 3.3 0.4 - - - -
192B VAL* 1.3 76.8 - - - +
194B VAL* 1.3 55.6 + - - +
196B PHE* 3.8 11.2 - - + +
197B ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 194 (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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161A VAL* 4.3 10.8 - - + +
164A LYS* 4.5 7.0 - - + -
165A ALA* 3.7 34.8 - - + +
168A SER* 4.0 9.9 - - - +
169B ALA* 4.1 12.8 - - + -
173B LEU* 4.3 20.0 - - + -
190B GLU* 3.0 24.3 + - + +
191B ALA 3.2 8.7 + - - +
193B ALA* 1.3 73.2 - - - +
195B ILE* 1.3 66.4 + - - +
197B ALA* 3.4 2.0 + - - +
198B ASN* 3.0 43.1 + - - +
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Residues in contact with ILE 195 (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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94B THR* 4.1 20.2 - - + -
98B VAL* 3.9 17.5 - - + -
166B PHE* 4.1 30.7 - - + -
169B ALA* 3.7 29.4 - - + -
170B ILE* 4.3 11.9 - - + -
173B LEU* 4.9 2.2 - - + -
191B ALA 3.2 15.7 - - - +
192B VAL* 3.0 8.1 + - - +
194B VAL* 1.3 76.4 - - + +
196B PHE* 1.3 67.8 + - + +
198B ASN* 4.8 0.7 - - - -
199B LEU* 3.1 50.9 + - + +
201B ILE* 5.4 2.0 - - + -
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Residues in contact with PHE 196 (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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90B VAL* 5.1 1.8 - - + -
91B GLY* 3.8 25.8 - - - -
94B THR* 3.7 25.6 - - + -
95B GLU* 5.0 5.8 - - - -
192B VAL* 2.8 45.2 + - + +
193B ALA* 3.8 9.4 - - + +
195B ILE* 1.3 77.0 - - - +
197B ALA* 1.3 55.6 + - - +
199B LEU 3.7 0.3 + - - -
200B GLN* 3.1 20.4 + - - -
201B ILE* 3.1 32.4 + - + +
206B ARG* 3.8 58.5 + - + +
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Residues in contact with ALA 197 (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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156A ARG* 3.5 45.0 + - + +
157A ALA* 4.7 8.1 - - + -
161A VAL* 5.3 1.1 - - + -
162A GLU* 4.2 9.9 - - - +
165A ALA* 5.0 4.3 - - + -
193B ALA 3.0 21.4 + - - +
194B VAL* 3.8 5.4 - - - +
195B ILE 3.3 0.2 - - - -
196B PHE* 1.3 68.2 - - - +
198B ASN* 1.3 67.4 + - - +
199B LEU 3.1 2.2 - - - -
200B GLN* 3.0 23.0 + - - +
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Residues in contact with ASN 198 (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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156A ARG* 4.2 3.6 + - - -
165A ALA* 3.5 27.4 + - - +
169A ALA* 4.8 1.4 - - - +
197A ALA 3.7 2.9 - - - +
198A ASN* 3.5 57.5 + - - +
162B GLU* 4.1 5.7 - - - +
165B ALA* 4.9 3.4 + - + +
169B ALA* 4.3 13.1 - - + +
194B VAL* 3.0 37.9 + - - +
195B ILE* 4.8 0.7 - - - -
197B ALA* 1.3 76.6 - - - +
199B LEU* 1.3 70.5 + - + +
200B GLN* 3.1 13.5 + - - +
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Residues in contact with LEU 199 (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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144B LEU* 4.0 26.0 - - + -
153B TRP* 3.4 14.6 - - - -
155B LEU* 4.2 8.7 - - + -
156B ARG* 4.3 2.6 - - - +
162B GLU* 3.7 30.5 - - - +
165B ALA* 4.8 9.9 - - + -
166B PHE* 4.9 13.9 - - + +
195B ILE* 3.1 44.2 + - + +
198B ASN* 1.3 89.3 - - + +
200B GLN* 1.3 76.9 + - - +
201B ILE* 3.2 27.9 + - + -
214B PG4 6.1 0.2 - - - +
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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