Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 2HNK
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 ASN 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.6 24.3 - - + +
156B ASP* 2.6 29.6 + - - +
157B LYS 3.1 0.8 - - - -
158B GLU* 1.3 91.7 + - - +
160B TYR* 1.3 55.5 + - - +
161B PRO* 3.1 4.0 - - - -
162B ASN* 2.7 45.4 + - + +
163B TYR* 2.9 30.1 + - + -
3006B PEG 4.7 3.8 - - - +
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Residues in contact with TYR 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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153B LEU* 3.5 45.9 + - + +
154B ASP* 3.7 0.7 - - - -
155B ALA 4.1 9.0 - - - -
156B ASP 3.8 3.8 - - - -
157B LYS* 3.1 57.0 + - + +
159B ASN* 1.3 76.7 - - - +
161B PRO* 1.4 67.1 - - + +
163B TYR* 3.3 7.5 + + - +
164B TYR 3.1 18.5 + - - -
179B ALA* 4.8 5.6 - - + -
180B ASP 2.6 29.9 + - - -
181B ASN 4.7 1.3 - - - -
182B VAL* 4.8 2.9 - - + -
200B GLY 4.1 1.8 - - - +
201B ILE* 4.2 19.5 - - + -
204B PHE* 3.5 41.2 - + + -
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Residues in contact with PRO 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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158B GLU 3.7 13.2 - - - +
159B ASN 3.2 3.4 - - - -
160B TYR* 1.4 89.0 - - + +
162B ASN* 1.3 64.1 + - - +
163B TYR 3.5 0.2 - - - -
164B TYR* 3.9 3.8 - - + +
165B PRO* 3.1 21.8 - - - +
200B GLY* 3.3 27.8 - - - +
203B LYS* 3.9 18.6 - - + -
204B PHE* 4.2 4.9 - - + +
207B LEU* 3.7 29.8 - - + +
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Residues in contact with ASN 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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122B LEU* 3.9 18.1 - - + +
158B GLU 4.4 4.2 + - - -
159B ASN* 2.7 39.7 + - - +
161B PRO* 1.3 78.3 - - - +
163B TYR* 1.3 62.4 + - - +
164B TYR 3.3 0.4 - - - -
165B PRO* 3.5 14.2 - - - +
166B LEU* 3.5 16.1 - - - +
3006B PEG 3.6 40.8 + - - +
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.0 9.9 - - + -
121B ALA* 3.8 19.5 - - + +
122B LEU* 3.7 33.3 + - + +
125B LEU* 4.0 16.6 - - + -
153B LEU* 3.8 18.6 - - + -
155B ALA* 4.1 8.4 - - + +
156B ASP* 2.6 35.8 + - - -
159B ASN* 2.9 35.7 + - + -
160B TYR 3.3 6.3 + - - +
162B ASN* 1.3 76.3 - - - +
164B TYR* 1.3 55.3 + - - +
166B LEU* 2.8 8.9 + - - +
167B ILE* 2.8 50.7 + - + +
2002B SAH 3.3 19.4 + - - -
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Residues in contact with TYR 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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160B TYR 3.1 15.6 + - - +
161B PRO* 3.9 4.9 - - + +
163B TYR* 1.3 75.5 - - - +
165B PRO* 1.4 77.3 - - + +
167B ILE* 3.2 10.6 + - + +
168B LEU* 3.0 45.5 + - + +
177B LEU* 4.2 8.5 - - + -
204B PHE* 3.8 25.6 - + + -
207B LEU* 4.3 27.6 - - + -
208B VAL* 3.6 19.7 - - + -
211B ASP* 2.6 39.9 + - - +
214B VAL* 3.3 19.4 - - - +
228B VAL* 4.4 8.5 - - + -
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Residues in contact with PRO 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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161B PRO 3.1 22.7 - - - +
162B ASN* 3.5 15.0 - - - +
164B TYR* 1.4 97.2 - - + +
166B LEU* 1.3 58.5 + - + +
168B LEU* 3.3 6.7 + - + +
169B LYS* 3.0 31.4 + - - +
207B LEU* 5.6 0.9 - - + -
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Residues in contact with LEU 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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122B LEU* 3.6 36.8 - - + +
125B LEU* 4.3 19.1 - - + -
126B GLN* 3.3 31.2 - - + +
129B ILE* 3.8 20.6 - - + -
162B ASN 3.5 20.2 - - - +
163B TYR* 2.8 7.7 + - - +
165B PRO* 1.3 75.9 - - + +
167B ILE* 1.3 66.4 + - - +
169B LYS* 3.3 6.0 + - + +
170B LEU* 3.0 28.9 + - - +
3006B PEG 4.5 11.2 - - - +
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Residues in contact with ILE 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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67B ILE* 4.0 14.8 - - + -
125B LEU* 4.9 1.8 - - + +
151B PHE* 3.6 42.5 - - + -
153B LEU* 3.9 13.7 - - + -
163B TYR* 2.8 39.5 + - + +
164B TYR* 3.4 10.3 - - - +
166B LEU* 1.3 71.8 - - - +
168B LEU* 1.3 60.2 + - + +
170B LEU 3.2 1.0 + - - -
171B LEU* 2.9 41.8 + - + +
177B LEU* 3.7 37.2 - - + -
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Residues in contact with LEU 168 (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 TYR* 3.0 49.9 + - + +
165B PRO* 3.7 7.0 - - + +
167B ILE* 1.3 76.9 - - + +
169B LYS* 1.3 60.7 + - - +
170B LEU 3.5 0.2 + - - -
171B LEU* 3.5 17.0 - - + +
177B LEU* 5.5 0.7 - - + -
211B ASP* 3.3 25.8 - - - +
213B LEU* 4.6 16.4 - - + -
214B VAL* 3.9 18.6 - - + -
228B VAL* 5.2 2.7 - - + -
230B LYS* 2.6 46.7 + - + +
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Residues in contact with LYS 169 (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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129B ILE* 3.9 30.1 - - + -
145B PRO* 3.4 32.7 - - + +
146B SER* 2.9 21.8 + - - -
165B PRO 3.0 14.7 + - - +
166B LEU* 3.3 10.5 + - + +
168B LEU* 1.3 78.3 - - - +
170B LEU* 1.3 58.1 + - - +
171B LEU 3.8 1.6 - - - +
230B LYS* 4.4 1.5 + - - +
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Residues in contact with LEU 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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65B ILE* 4.6 2.5 - - + -
125B LEU* 3.8 46.9 - - + +
128B LEU* 4.2 22.7 - - + -
129B ILE* 3.6 20.4 - - + -
144B GLY 3.3 24.0 - - - +
146B SER 3.9 1.8 - - - +
147B SER* 2.7 36.0 + - - +
148B ILE* 3.0 13.4 + - + -
151B PHE* 3.6 20.9 - - + -
166B LEU 3.0 16.0 + - - +
169B LYS* 1.3 74.3 - - - +
171B LEU* 1.3 62.3 + - - +
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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