Contacts of the helix formed by residues 162 - 169 (chain J) in PDB entry 5NSS
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 ARG 162 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114J MET* 3.5 23.5 - - + +
117J GLN* 3.6 6.1 - - + +
118J GLU* 3.5 38.6 - - + +
156J VAL* 3.8 8.3 - - - +
161J PHE* 1.3 75.6 - - - +
163J ALA* 1.3 64.1 + - - +
164J ASP* 3.2 5.8 + - + +
165J LEU* 3.3 16.6 + - - +
166J LEU 4.0 0.2 + - - -
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Residues in contact with ALA 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J VAL* 4.3 15.8 + - + +
161J PHE 3.9 1.6 + - - -
162J ARG* 1.3 71.7 - - - +
164J ASP* 1.3 60.7 + - - +
165J LEU 3.2 0.2 - - - -
166J LEU* 3.5 3.5 + - - +
167J ASP* 2.9 32.9 + - + +
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Residues in contact with ASP 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ARG* 5.3 10.3 - - + -
118J GLU* 4.6 14.1 - - + +
121J LEU* 3.4 16.9 - - + +
122J ARG* 4.7 9.0 - - + +
162J ARG* 3.2 2.7 - - + +
163J ALA* 1.3 78.6 - - - +
165J LEU* 1.3 55.2 + - - +
167J ASP* 3.8 5.4 - - - +
168J ARG* 2.7 39.8 + - + +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J GLN* 3.7 27.3 + - + +
121J LEU* 3.6 10.6 - - + +
152J LEU* 5.4 10.0 - - + +
156J VAL* 6.2 0.2 - - + -
161J PHE* 5.6 2.9 - - + -
162J ARG 3.3 11.7 + - - +
163J ALA 3.2 0.8 - - - -
164J ASP* 1.3 78.1 - - - +
166J LEU* 1.3 60.3 + - - +
169J LEU* 3.3 26.4 + - + +
170J ALA* 3.3 8.0 + - - +
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Residues in contact with LEU 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J LEU* 4.5 4.7 - - + +
153J PRO* 4.1 33.9 - - + -
156J VAL* 4.2 13.2 - - + -
162J ARG 4.0 1.8 + - - -
163J ALA* 3.5 5.2 + - - +
164J ASP 3.5 0.2 - - - -
165J LEU* 1.3 80.0 - - - +
167J ASP* 1.3 58.7 + - - +
168J ARG 3.4 0.2 - - - -
170J ALA* 3.3 28.2 - - + +
171J PHE* 4.4 0.9 + - - -
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Residues in contact with ASP 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G GLY* 6.3 2.5 - - - -
227G ARG* 4.8 3.6 - - - +
228G GLU* 4.9 12.3 - - + +
231G ASN* 4.2 13.9 - - - +
163J ALA* 2.9 20.8 + - + +
164J ASP* 4.5 3.8 - - - +
166J LEU* 1.3 76.7 - - - +
168J ARG* 1.3 59.1 + - - +
171J PHE* 4.9 6.0 - - - +
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Residues in contact with ARG 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ARG* 5.9 5.8 - - + +
231G ASN* 4.7 10.8 - - + +
31J PRO* 4.6 4.9 - - - +
121J LEU* 4.4 19.3 - - + +
125J GLU* 4.4 12.3 - - + -
164J ASP* 2.7 24.0 + - + +
166J LEU 3.4 0.6 - - - -
167J ASP* 1.3 79.4 - - - +
169J LEU* 1.3 64.0 + - + +
170J ALA 3.2 1.6 + - - -
171J PHE* 3.5 17.2 + - - +
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Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J PRO* 3.7 34.6 - - + +
32J VAL 4.8 0.2 - - - -
33J LEU* 3.8 16.5 + - + +
121J LEU* 5.8 4.5 - - + -
144J LEU* 4.7 11.7 - - + +
146J CYS* 6.5 0.4 - - + -
165J LEU* 3.3 13.2 + - + +
168J ARG* 1.3 79.6 - - + +
170J ALA* 1.3 58.8 + - - +
171J PHE 3.3 0.6 + - - -
172J ASP 4.0 0.2 - - - +
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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