Contacts of the helix formed by residues 82 - 93 (chain P) in PDB entry 1NJI
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 SER 82 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659A A 3.4 29.4 - - - -
660A A 3.0 26.3 + - - -
63P LYS* 4.0 1.4 - - - +
64P VAL 3.0 11.6 + - - -
65P LEU* 4.1 6.5 - - - -
66P GLY 3.5 0.2 + - - -
81P PHE* 1.3 79.7 - - - +
83P GLY* 1.3 64.0 + - - +
84P THR 3.6 2.1 + - - -
85P ALA* 3.0 25.0 + - - +
86P GLU* 3.1 16.8 + - - +
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Residues in contact with GLY 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A A 2.9 17.4 + - - -
81P PHE 3.8 0.4 + - - -
82P SER* 1.3 72.4 - - - +
84P THR* 1.3 60.6 + - - +
86P GLU* 3.7 7.1 + - - +
87P THR* 3.0 27.4 + - - -
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Residues in contact with THR 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A A 4.8 0.8 + - - -
660A A 3.3 25.6 + - - +
66P GLY* 4.1 5.8 - - - +
82P SER* 3.2 1.2 + - - -
83P GLY* 1.3 73.4 - - - +
85P ALA* 1.3 69.1 + - - +
87P THR* 3.0 7.6 + - - -
88P LYS* 2.9 50.7 + - + +
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Residues in contact with ALA 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 4.7 6.5 - - + -
64P VAL* 3.6 28.7 - - + +
65P LEU 3.8 3.4 - - - -
66P GLY* 3.7 18.6 - - - +
81P PHE* 4.1 4.7 - - + -
82P SER* 3.0 24.1 + - - +
84P THR* 1.3 78.7 - - - +
86P GLU* 1.3 64.6 + - - +
87P THR 2.9 1.6 + - - -
88P LYS* 3.0 1.6 + - - +
89P ILE* 2.9 28.7 + - - +
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Residues in contact with GLU 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P PHE* 4.0 26.0 - - + +
82P SER 3.1 13.1 + - - +
83P GLY* 4.1 6.6 - - - +
85P ALA* 1.3 79.5 - - - +
87P THR* 1.3 59.9 + - - +
89P ILE* 4.1 1.1 - - - -
90P ASP* 3.1 37.1 + - - +
95P ALA* 3.9 25.6 - - + +
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Residues in contact with THR 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P GLY 3.0 14.8 + - - -
84P THR* 3.0 11.3 + - - -
85P ALA 3.0 1.0 - - - -
86P GLU* 1.3 78.9 - - - +
88P LYS* 1.3 64.4 + - + +
90P ASP* 3.5 4.1 + - - +
91P GLN* 2.9 43.4 + - + +
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Residues in contact with LYS 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M GLU 5.3 1.6 + - - -
72M ASN* 4.4 13.7 + - - -
75M LEU* 4.5 17.3 - - + +
45P LEU* 3.3 31.2 - - + -
66P GLY 2.9 22.6 + - - +
68P GLY 3.2 19.4 + - - +
69P VAL* 5.6 1.7 - - - +
70P LEU* 5.0 5.3 - - + +
84P THR* 2.9 30.0 + - + +
85P ALA 3.7 2.0 - - - +
87P THR* 1.3 79.3 - - + +
89P ILE* 1.3 62.1 + - - +
91P GLN* 3.2 33.1 + - - +
92P VAL* 3.8 9.8 + - - +
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Residues in contact with ILE 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 3.6 30.7 - - + -
48P ILE* 4.8 0.7 - - + -
64P VAL* 4.1 15.9 - - + -
70P LEU* 3.7 21.8 - - + -
74P VAL 4.8 1.3 - - - +
76P VAL* 4.5 16.8 - - + -
81P PHE* 4.2 18.4 - - + -
85P ALA 2.9 18.2 + - - +
86P GLU 4.3 2.7 - - - +
88P LYS* 1.3 76.6 - - - +
90P ASP* 1.3 53.3 + - - +
91P GLN 3.0 0.9 + - - -
92P VAL* 3.1 2.8 + - - +
93P GLY* 2.6 33.5 + - - -
94P GLU 3.6 33.0 - - - +
95P ALA* 3.6 6.7 - - + +
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Residues in contact with ASP 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P GLU* 3.1 34.2 + - - +
87P THR* 4.1 4.0 - - - +
88P LYS 3.4 0.2 - - - -
89P ILE* 1.3 75.0 - - - +
91P GLN* 1.3 60.3 + - - +
92P VAL 3.3 0.2 - - - -
93P GLY 3.5 13.5 + - - +
94P GLU* 3.5 6.1 - - - +
95P ALA* 2.7 35.0 + - - +
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Residues in contact with GLN 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU* 5.8 6.3 - - - +
87P THR* 2.9 38.5 + - + +
88P LYS* 3.4 23.1 - - - +
89P ILE 3.0 1.0 + - - -
90P ASP* 1.3 78.0 - - - +
92P VAL* 1.3 66.6 + - + +
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Residues in contact with VAL 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P LEU* 3.5 37.2 - - + +
71P GLN* 3.7 16.3 - - + +
72P LYS 3.6 14.6 - - - +
73P ASP* 3.0 28.9 - - - +
88P LYS 4.0 7.4 - - - +
89P ILE 3.6 6.7 - - - +
91P GLN* 1.3 91.5 - - + +
93P GLY* 1.3 56.6 + - - +
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Residues in contact with GLY 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P LEU* 6.1 0.2 - - - -
73P ASP* 3.5 13.7 - - - -
74P VAL* 3.5 13.9 - - - -
89P ILE* 2.6 20.6 + - - +
90P ASP* 3.5 14.4 - - - +
91P GLN 3.8 0.2 - - - -
92P VAL* 1.3 79.0 - - - +
94P GLU* 1.3 62.6 + - - +
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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