Contacts of the helix formed by residues 153 - 160 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.3 24.7 - - - +
29A ASN* 3.6 25.5 - - - +
32A PHE* 5.8 3.8 - - - -
68A ASP* 4.9 8.5 - - - -
130A ASP* 4.6 9.2 - - - +
151A SER* 3.2 10.3 + - - +
152A THR* 1.3 75.2 - - - +
154A GLY* 1.3 64.1 + - - +
155A ASP* 4.3 11.4 - - + +
156A TRP* 3.1 36.5 + - + +
166A ARG* 3.6 9.8 + - - -
1X A 4.4 0.8 - - - -
2X A 2.6 43.4 + - - +
3X A 3.9 0.7 - - - +
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Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR 3.4 3.6 + - - -
153A LYS* 1.3 68.1 - - - +
155A ASP* 1.3 56.8 + - - +
157A ASP* 2.9 30.0 + - - +
166A ARG* 3.9 14.8 - - - -
184A HIS* 4.3 10.5 - - - -
192A PHE* 3.7 13.0 - - - -
3X A 2.8 23.9 + - - -
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 4.3 18.8 - - - +
153A LYS* 4.3 10.6 - - + +
154A GLY* 1.3 75.0 - - - +
156A TRP* 1.3 61.7 + - + +
158A THR* 2.9 30.8 + - - +
192A PHE* 4.8 2.0 - - - -
196A LYS* 2.7 39.0 + - - +
201A ASP* 4.4 6.5 - - - +
204A ASP* 4.1 15.6 - - - +
262A LEU* 4.6 5.1 - - + +
3X A 4.4 2.3 + - - -
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Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.4 6.5 - - + -
25A VAL 4.6 0.2 - - - -
26A ASP* 3.4 52.6 + - + -
66A LEU* 4.4 7.0 - - + -
129A ALA* 3.9 5.8 - - + -
130A ASP* 3.1 53.8 + - + -
133A ALA* 3.8 25.1 - - + -
149A LEU* 3.8 38.3 - - + +
151A SER* 3.8 14.1 - - - -
153A LYS* 3.1 26.8 + - + +
154A GLY 3.1 1.8 + - - -
155A ASP* 1.3 79.3 - - + +
157A ASP* 1.3 57.4 + - - +
158A THR* 3.1 3.4 - - - -
159A LEU* 3.1 34.5 + - + +
160A LEU* 4.2 0.7 + - - +
166A ARG* 3.9 11.9 - - - -
262A LEU* 5.3 1.6 - - + -
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 2.9 11.9 + - - +
156A TRP* 1.3 74.0 - - - +
158A THR* 1.3 58.1 + - - +
159A LEU 3.1 5.9 + - - -
160A LEU* 3.4 43.0 + - + +
166A ARG* 2.6 45.3 + - - +
175A TYR* 3.7 9.4 - - - +
180A MET* 3.7 5.4 - - + +
183A HIS* 5.6 0.2 - - - -
184A HIS* 2.5 34.0 + - + +
189A VAL* 3.6 11.6 - - - +
192A PHE* 4.0 6.7 - - + -
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ASP 2.9 19.1 + - - +
156A TRP 3.1 0.2 - - - -
157A ASP* 1.3 75.4 - - - +
159A LEU* 1.3 62.4 + - - +
160A LEU 3.5 0.4 - - - +
189A VAL* 3.2 24.3 - - - +
192A PHE* 3.6 25.2 - - + -
193A ILE* 3.9 21.8 - - + -
196A LYS* 4.1 12.1 - - + -
260A VAL 4.0 14.1 - - - +
262A LEU* 3.5 22.7 - - + +
263A PRO* 3.6 17.4 - - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 4.1 4.9 - - - +
133A ALA* 4.0 15.7 - - + +
134A ALA* 3.6 45.8 - - + +
137A VAL* 4.8 9.3 - - + +
149A LEU* 3.9 21.1 - - + -
156A TRP* 3.3 21.8 - - + +
157A ASP 3.1 1.2 - - - -
158A THR* 1.3 82.1 - - - +
160A LEU* 1.3 64.3 + - - +
161A THR* 3.6 9.4 + - - +
164A VAL* 3.6 15.6 - - + +
262A LEU* 3.7 26.0 - - + -
263A PRO* 4.4 8.7 - - + -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 4.7 4.3 - - + -
156A TRP 4.5 2.9 - - - +
157A ASP* 3.4 52.5 + - + +
158A THR 3.5 0.7 - - - +
159A LEU* 1.3 80.8 - - - +
161A THR* 1.3 66.7 + - - +
164A VAL* 3.5 18.6 - - - +
165A SER* 3.9 18.8 - - - -
166A ARG* 4.1 3.6 - - + +
175A TYR* 4.0 9.6 - - + +
176A HIS 3.9 26.9 - - - +
177A LEU* 4.1 6.5 - - + +
180A MET* 4.2 12.6 - - - -
183A HIS* 6.2 0.9 - - + -
184A HIS* 5.8 0.2 - - + -
189A VAL* 3.3 24.0 - - + +
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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
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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