Contacts of the helix formed by residues 158 - 165 (chain B) in PDB entry 5HJS
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 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B SER 4.7 6.8 + - - +
147B GLU* 4.0 14.6 - - + +
148B SER* 4.5 6.1 - - - -
157B TYR* 1.3 71.9 - - - +
159B ARG* 1.3 63.6 + - - +
160B GLU* 3.0 24.6 + - - +
161B ASP* 3.1 32.6 + - - +
162B PHE* 3.2 15.8 + - - -
176B PHE* 3.6 9.4 - - - -
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Residues in contact with ARG 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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142B TYR* 5.4 2.6 + - - -
147B GLU* 2.8 36.9 + - - +
158B ASN* 1.3 75.1 - - - +
160B GLU* 1.4 60.0 + - - +
162B PHE* 3.4 4.2 + - - +
163B ALA* 3.2 20.8 + - - +
172B ILE* 3.8 21.1 - - + +
173B ASN* 3.9 21.7 + - - +
176B PHE* 3.5 58.5 + - + +
177B GLU* 4.7 3.4 + - - +
180B ARG* 6.1 1.6 - - - +
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Residues in contact with GLU 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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158B ASN* 3.0 15.5 + - - +
159B ARG* 1.4 74.6 - - - +
161B ASP* 1.3 62.3 + - - +
163B ALA* 3.2 9.7 + - + +
164B LYS* 3.0 55.0 + - + +
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Residues in contact with ASP 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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74B TRP* 3.4 26.8 + - + -
93B PHE* 4.4 1.3 - - - -
156B SER 3.9 2.9 - - - +
157B TYR* 3.4 35.1 - - + -
158B ASN* 3.1 36.3 + - - +
160B GLU* 1.3 74.6 - - - +
162B PHE* 1.4 65.5 + - - +
164B LYS* 3.4 18.6 + - - +
165B ALA* 3.1 17.8 + - - +
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Residues in contact with PHE 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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93B PHE* 3.8 25.1 - + - -
138B THR* 5.0 1.6 - - + -
149B ILE* 3.8 20.2 - - + -
151B PHE* 3.9 21.3 - + - -
157B TYR* 3.8 22.4 - - + -
158B ASN 3.2 20.9 + - - -
159B ARG 3.6 9.2 - - - +
160B GLU 3.2 0.2 - - - -
161B ASP* 1.4 74.6 - - - +
163B ALA* 1.3 61.2 + - - +
165B ALA* 3.1 13.5 + - - +
167B LEU* 3.3 39.3 + - + +
172B ILE* 3.9 17.9 - - + -
175B ILE* 4.2 23.1 - - + -
176B PHE* 3.6 24.7 - + - -
301B 668 5.6 5.8 - - + -
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Residues in contact with ALA 163 (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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159B ARG 3.2 13.2 + - - +
160B GLU* 3.4 13.5 - - + +
162B PHE* 1.3 77.0 - - - +
164B LYS* 1.3 55.8 + - + +
166B GLY* 3.0 20.3 + - - -
167B LEU 3.7 15.3 + - - +
169B VAL* 5.5 5.6 - - + -
172B ILE* 3.6 10.7 - - + +
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Residues in contact with LYS 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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74B TRP* 4.4 2.2 - - + -
86B ARG* 4.6 12.5 - - - +
89B ARG* 3.3 53.4 + - - +
160B GLU* 3.0 42.7 + - + +
161B ASP* 3.6 24.7 + - - +
162B PHE 3.3 0.2 - - - -
163B ALA* 1.3 74.8 - - + +
165B ALA* 1.3 58.1 + - - +
166B GLY 3.2 1.6 + - - -
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Residues in contact with ALA 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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74B TRP* 4.2 2.2 - - + -
86B ARG 5.5 0.4 - - - -
89B ARG* 4.0 14.6 - - - +
90B PHE* 3.3 30.2 - - - -
93B PHE* 3.6 42.4 - - + -
161B ASP 3.1 9.6 + - - +
162B PHE 3.1 11.9 + - - +
164B LYS* 1.3 75.1 - - - +
166B GLY* 1.3 57.0 + - - +
167B LEU* 3.6 6.1 + - + +
301B 668 4.4 2.1 - - - +
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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