Contacts of the helix formed by residues 83 - 91 (chain L) in PDB entry 1NSK
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 VAL 83 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L GLU* 3.5 2.1 + - + -
6L ARG 3.3 23.6 - - - +
7L THR* 4.0 11.1 - - + +
28L PHE* 5.5 1.8 - - + -
33L PHE* 3.7 34.3 - - + -
78L TRP* 3.3 31.2 - - + +
79L GLU 4.1 0.2 - - - -
80L GLY 2.8 33.1 + - - +
81L LEU 3.3 1.4 - - - -
82L ASN* 1.3 72.5 - - - +
84L VAL* 1.3 54.0 + - - +
86L THR* 3.9 5.4 - - - -
87L GLY* 2.6 34.2 + - - -
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Residues in contact with VAL 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L GLU* 3.0 19.6 + - - +
6L ARG 3.6 17.9 - - - +
7L THR* 3.6 20.6 - - - +
82L ASN 3.1 0.2 + - - -
83L VAL* 1.3 79.0 - - - +
85L LYS* 1.3 61.7 + - - +
88L ARG* 3.0 31.0 + - - +
120L SER 3.6 15.5 - - - +
121L ASP 4.0 3.1 - - - +
122L SER* 3.6 29.4 - - - +
123L VAL* 4.0 13.5 - - + +
126L ALA* 4.1 9.4 - - + -
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Residues in contact with LYS 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ASN* 3.1 35.1 + - - +
84L VAL* 1.3 82.6 - - - +
86L THR* 1.3 66.4 + - + +
88L ARG* 3.3 6.2 + - - +
89L VAL* 3.2 29.4 + - + +
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Residues in contact with THR 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L LYS* 5.0 11.0 - - - +
33L PHE* 2.9 31.3 - - + -
81L LEU 4.8 2.2 - - - +
82L ASN* 3.0 27.1 + - + +
83L VAL 3.8 0.2 + - - -
85L LYS* 1.3 78.0 - - + +
87L GLY* 1.3 60.7 + - - +
89L VAL* 3.0 13.0 + - + +
90L MET* 2.8 33.7 + - - +
96O PRO 5.7 1.3 - - - +
97O ALA* 5.0 20.9 - - + +
110O ILE* 6.0 2.5 - - + -
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Residues in contact with GLY 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L THR* 5.6 0.2 - - - -
9L ILE* 5.2 5.8 - - - -
28L PHE* 4.2 20.9 - - - -
33L PHE* 4.8 1.3 - - - -
83L VAL 2.6 26.3 + - - -
84L VAL 4.1 0.4 - - - -
86L THR* 1.3 73.1 + - - +
88L ARG* 1.3 56.2 + - - +
90L MET* 3.2 8.2 + - - +
91L LEU* 3.0 36.9 + - - +
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Residues in contact with ARG 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L VAL* 3.0 24.0 + - - +
85L LYS* 3.6 6.3 - - - +
86L THR 3.2 0.4 - - - -
87L GLY* 1.3 74.3 - - - +
89L VAL* 1.3 59.9 + - + +
91L LEU* 2.9 13.8 + - - +
92L GLY 2.8 30.9 + - - +
94L THR* 3.9 20.7 + - - +
105L ARG* 5.7 4.4 - - - +
118L HIS* 5.8 0.4 + - - -
119L GLY* 3.5 22.5 + - - +
120L SER 2.9 24.4 + - - +
121L ASP* 3.7 31.2 + - - +
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Residues in contact with VAL 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L LYS* 3.2 22.4 - - + +
86L THR* 3.0 13.3 + - + +
88L ARG* 1.3 76.9 - - + +
90L MET* 1.3 61.9 + - + +
92L GLY* 3.2 10.9 + - - +
103L THR* 3.3 15.0 - - + +
99O SER 5.5 2.2 - - - +
100O LYS* 5.2 8.3 - - + -
101O PRO* 3.5 26.6 - - + +
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Residues in contact with MET 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ARG* 3.6 39.6 + - + +
28L PHE* 3.9 30.5 - - + -
31L LYS* 4.0 14.6 - - + -
33L PHE* 3.5 31.9 - - - -
86L THR* 2.8 16.3 + - - +
87L GLY* 3.3 8.3 - - - +
89L VAL* 1.3 77.7 - - - +
91L LEU* 1.3 58.9 + - - +
103L THR* 3.5 4.7 - - - -
104L ILE* 3.0 30.3 + - + +
101O PRO* 4.0 16.4 - - + -
106O GLY 5.1 7.9 - - - +
107O ASP 6.0 0.2 - - - +
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Residues in contact with LEU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ILE* 4.5 3.4 - - + -
28L PHE* 3.5 26.7 - - + -
87L GLY 3.0 23.2 + - - +
88L ARG* 2.9 16.9 + - + +
90L MET* 1.3 79.6 - - - +
92L GLY* 1.3 57.8 + - - +
103L THR* 3.8 1.2 - - - -
104L ILE* 4.1 5.4 - - + -
105L ARG* 3.0 52.3 + - - +
117L ILE* 3.7 32.3 - - + -
118L HIS* 3.8 7.2 - - - +
119L GLY* 3.4 37.0 - - - +
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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