Contacts of the helix formed by residues 153 - 160 (chain B) in PDB entry 5HNK
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 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 4.6 1.1 - - - +
29B ASN* 4.4 2.5 - - - +
82B TYR* 5.0 7.3 + - - -
83B LYS* 5.2 2.8 - - - +
128B GLU* 5.1 1.8 + - - -
130B ASP* 2.6 33.2 + - - +
151B SER* 3.3 14.8 + - - +
152B THR* 1.3 77.4 + - - +
154B GLY* 1.3 67.4 + - - +
155B ASP* 3.2 33.2 + - - +
156B TRP* 3.3 27.7 + - + +
166B ARG* 3.6 9.3 + - - -
201B ASP* 6.0 0.2 - - - -
204B ASP* 4.3 15.8 + - - -
6Y C 3.4 55.8 + - - +
7Y G 4.6 1.1 - - - +
101Y MG 4.5 1.2 - - - -
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Residues in contact with GLY 154 (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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152B THR 3.3 3.6 + - - -
153B LYS* 1.3 70.8 - - - +
155B ASP* 1.3 55.6 + - - +
156B TRP 3.2 0.4 - - - -
157B ASP* 3.0 30.0 + - - +
166B ARG* 3.9 15.3 - - - -
184B HIS* 3.8 10.3 - - - -
192B PHE* 3.5 12.2 - - - -
196B LYS* 5.5 1.3 - - - -
7Y G 2.9 23.2 + - - -
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.9 5.5 - - - +
153B LYS* 3.2 43.8 + - - +
154B GLY* 1.3 72.2 - - - +
156B TRP* 1.3 55.9 + - - +
157B ASP 3.1 5.4 - - - -
158B THR* 2.7 36.3 + - + +
192B PHE* 3.9 13.0 - - + -
196B LYS* 4.2 31.4 + - + +
201B ASP* 4.3 5.4 - - - +
204B ASP* 4.7 2.9 - - - +
260B VAL* 5.7 5.2 - - + +
262B LEU* 4.0 6.9 - - + +
7Y G 4.6 1.2 + - - -
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Residues in contact with TRP 156 (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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24B ILE* 4.3 11.4 - - + -
26B ASP* 3.6 36.2 + - + -
66B LEU* 4.5 6.3 - - + -
129B ALA* 4.0 12.6 - - + -
130B ASP* 3.1 32.0 + - - +
133B ALA* 3.6 31.2 - - + -
149B LEU* 3.8 40.0 - - + +
151B SER* 3.7 21.1 - - - -
153B LYS* 3.3 25.3 + - + +
154B GLY 3.2 0.2 - - - -
155B ASP* 1.3 86.0 - - - +
157B ASP* 1.3 57.2 + - - +
158B THR* 3.1 4.3 - - - -
159B LEU* 3.0 33.0 + - + +
160B LEU 4.2 0.5 + - - -
166B ARG* 3.9 10.5 - - - -
262B LEU* 4.6 7.6 - - + -
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Residues in contact with ASP 157 (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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154B GLY 3.0 15.3 + - - +
156B TRP* 1.3 71.9 - - - +
158B THR* 1.3 58.0 + - - +
159B LEU 3.0 6.1 + - - -
160B LEU* 3.3 43.6 + - + +
166B ARG* 2.6 40.9 + - - +
175B TYR* 3.8 9.7 - - - +
180B MET* 3.5 15.9 - - + +
183B HIS* 5.0 0.3 + - - -
184B HIS* 2.6 33.6 + - + +
189B VAL* 3.8 2.1 - - - +
192B PHE* 4.0 7.4 - - + -
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Residues in contact with THR 158 (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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155B ASP* 2.7 26.1 + - + +
157B ASP* 1.3 76.7 - - - +
159B LEU* 1.3 58.9 + - - +
160B LEU 3.5 0.4 - - - -
189B VAL* 3.3 28.1 - - - +
192B PHE* 3.6 22.8 - - + -
193B ILE* 3.7 22.9 - - + +
260B VAL 4.5 9.2 - - - +
262B LEU* 3.5 22.3 - - - +
263B PRO* 3.4 23.5 - - - +
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Residues in contact with LEU 159 (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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130B ASP 4.9 0.2 - - - +
133B ALA* 4.3 12.1 - - + +
134B ALA* 3.6 46.9 - - + +
137B VAL* 4.6 13.0 - - + +
138B LYS* 6.0 1.8 - - - -
149B LEU* 4.1 19.7 - - + -
156B TRP* 3.0 21.8 + - + +
158B THR* 1.3 91.4 - - - +
160B LEU* 1.3 65.1 + - - +
161B THR* 3.8 6.8 - - - +
164B VAL* 3.3 20.8 - - + +
262B LEU* 4.5 10.8 - - + -
263B PRO* 4.1 16.8 - - + -
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Residues in contact with LEU 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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149B LEU* 4.7 4.0 - - + -
156B TRP 4.4 3.4 - - - +
157B ASP* 3.3 49.5 + - + +
158B THR 3.5 0.6 - - - +
159B LEU* 1.3 80.7 - - - +
161B THR* 1.3 65.4 + - - +
164B VAL 3.5 16.8 - - - +
165B SER* 3.9 19.1 - - - -
166B ARG* 4.1 2.9 - - + +
175B TYR* 3.7 11.4 - - + +
176B HIS 3.5 30.7 - - - +
177B LEU* 4.0 17.7 - - + +
180B MET* 4.2 10.5 - - + -
183B HIS* 6.1 0.7 - - - +
189B VAL* 3.9 15.8 - - - +
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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