Contacts of the helix formed by residues 158 - 165 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A SER 4.9 4.2 + - - +
147A GLU 4.0 14.4 - - - +
148A SER* 4.3 7.0 - - - -
157A TYR* 1.3 72.3 - - - +
159A ARG* 1.3 66.3 + - - +
160A GLU* 3.2 13.4 + - - +
161A ASP* 3.0 49.8 + - - +
162A PHE* 3.2 15.1 + - - -
176A PHE* 3.6 9.9 - - - -
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Residues in contact with ARG 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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142A TYR* 5.2 2.8 + - - -
147A GLU* 3.0 38.5 + - - +
158A ASN* 1.3 75.4 - - - +
160A GLU* 1.4 60.8 + - - +
162A PHE* 3.6 0.9 + - - -
163A ALA* 3.4 19.2 + - - +
172A ILE* 3.7 23.8 - - + +
173A ASN* 4.0 20.1 + - - +
176A PHE* 3.4 61.0 + - + +
177A GLU* 4.5 9.9 + - - +
180A ARG* 6.0 3.0 - - - +
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Residues in contact with GLU 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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158A ASN* 3.2 15.5 + - - +
159A ARG* 1.4 75.7 - - - +
161A ASP* 1.4 60.4 + - - +
163A ALA* 3.3 9.4 + - + +
164A LYS* 3.0 55.0 + - + +
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Residues in contact with ASP 161 (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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74A TRP* 3.3 24.0 + - + -
93A PHE* 4.6 0.7 - - - -
156A SER 3.9 3.3 - - - +
157A TYR* 3.4 35.2 - - + -
158A ASN* 3.0 40.9 + - - +
160A GLU* 1.4 76.5 - - - +
162A PHE* 1.4 57.9 + - - +
164A LYS* 3.4 23.7 + - - +
165A ALA* 3.1 22.6 + - - +
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Residues in contact with PHE 162 (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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93A PHE* 3.7 32.1 - + - -
138A THR* 5.0 1.6 - - + -
149A ILE* 3.9 20.0 - - + -
151A PHE* 3.9 21.3 - + - -
157A TYR* 3.9 17.7 - - + -
158A ASN 3.2 20.8 + - - -
159A ARG 3.7 9.4 - - - +
160A GLU 3.3 0.2 - - - -
161A ASP* 1.4 72.3 - - - +
163A ALA* 1.4 64.5 - - - +
165A ALA 3.3 6.1 + - - -
167A LEU* 3.2 46.9 + - + +
172A ILE* 3.9 16.8 - - + -
175A ILE* 4.2 22.9 - - + -
176A PHE* 3.8 25.4 - + - -
301A 668 5.4 5.8 - - + -
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Residues in contact with ALA 163 (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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159A ARG 3.4 11.3 + - - +
160A GLU* 3.3 15.6 + - + +
162A PHE* 1.4 77.0 - - - +
164A LYS* 1.4 62.9 + - + +
166A GLY* 3.2 14.2 + - - -
167A LEU 3.7 9.0 + - - +
169A VAL* 5.2 8.5 - - + -
172A ILE* 3.5 16.3 - - + +
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Residues in contact with LYS 164 (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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74A TRP* 4.9 2.7 - - + -
86A ARG* 4.4 9.9 - - - +
89A ARG* 3.2 51.6 + - - +
160A GLU* 3.0 43.8 + - + +
161A ASP* 3.5 25.5 + - - +
162A PHE 3.3 0.2 - - - -
163A ALA* 1.4 75.9 - - + +
165A ALA* 1.4 56.5 + - - +
166A GLY 3.2 4.3 + - - -
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Residues in contact with ALA 165 (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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74A TRP* 4.0 2.9 - - + -
86A ARG 5.1 0.7 - - - -
89A ARG* 3.9 16.8 - - - +
90A PHE* 3.4 29.4 - - - +
93A PHE* 3.7 39.5 - - + -
161A ASP 3.1 15.7 + - - +
162A PHE 3.6 7.0 - - - +
163A ALA 3.2 1.0 - - - -
164A LYS* 1.4 74.6 - - - +
166A GLY* 1.3 56.8 + - - +
167A LEU* 3.5 6.9 + - + +
301A 668 4.8 1.7 - - - +
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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