Contacts of the helix formed by residues 95 - 105 (chain C) in PDB entry 3LNJ
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 GLU 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B DAR 4.2 2.5 - - - -
91C PHE* 3.8 8.1 - - + +
92C SER* 2.9 44.0 + - - +
94C LYS* 1.3 77.0 - - - +
96C HIS* 1.3 63.5 + - - +
97C ARG 3.4 3.1 - - - -
98C LYS* 3.5 34.4 + - + +
99C ILE* 3.2 24.5 + - + +
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Residues in contact with HIS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 5.1 4.6 + - + +
100A TYR* 5.2 0.2 - - + -
11B DLE 3.9 6.3 - - - +
12B DAR 2.9 28.5 + - + +
93C VAL 3.2 19.1 + - - -
94C LYS 3.5 7.5 + - - -
95C GLU* 1.3 68.6 - - - +
97C ARG* 1.3 66.0 + - - +
99C ILE* 3.0 7.3 + - - -
100C TYR* 3.0 41.4 + - + -
8D DGL 2.7 34.3 + - - +
11D DLE 3.8 32.4 + - + +
12D DAR 3.5 33.0 + - + +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET* 4.0 13.7 - - + -
51A LYS* 3.5 65.8 - - - +
54A LEU* 3.8 7.4 - - + -
100A TYR* 3.3 22.8 - - + +
9B DLY 4.5 0.8 + - - -
10B DLE 2.9 47.0 + - - +
11B DLE 3.7 3.4 + - - -
12B DAR 3.8 10.4 + - - +
95C GLU 3.4 0.4 - - - -
96C HIS* 1.3 77.2 - - - +
98C LYS* 1.3 63.0 + - - +
100C TYR* 3.4 1.9 + - - +
101C THR* 2.7 29.8 + - - +
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL* 3.8 29.0 - - - +
90C SER 4.7 6.1 + - - -
91C PHE* 4.7 3.4 - - + -
95C GLU* 3.5 40.3 + - + +
96C HIS 3.3 0.4 - - - -
97C ARG* 1.3 79.8 - - - +
99C ILE* 1.3 58.6 + - + +
101C THR* 3.7 5.5 - - - -
102C MET* 2.7 56.0 + - + +
44E GLN* 5.3 9.1 + - - -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 4.7 0.9 - - + -
57C LEU* 4.6 11.2 - - + -
86C PHE* 4.7 4.0 - - + -
91C PHE* 4.0 26.0 - - + -
92C SER 3.8 15.9 - - - +
93C VAL* 3.8 21.3 - - + +
95C GLU 3.2 17.8 + - - +
96C HIS 3.0 6.7 + - - +
98C LYS* 1.3 78.1 - - + +
100C TYR* 1.3 58.1 + - - +
102C MET* 3.3 9.2 + - + +
103C ILE* 2.8 54.3 + - + +
7D DLE 5.5 4.3 - - + -
11D DLE 4.0 28.7 - - + -
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 5.3 0.2 - - + -
97A ARG* 3.2 28.9 - - + +
100A TYR* 3.1 62.1 - + + -
104A TYR* 2.4 29.9 + + + +
50C MET* 3.5 32.3 - - + -
54C LEU* 3.6 5.8 - - + +
96C HIS* 3.0 30.0 + - + +
97C ARG 4.0 2.5 - - - +
99C ILE* 1.3 75.9 - - - +
101C THR* 1.3 56.7 + - - +
103C ILE* 3.2 2.8 + - - -
104C TYR* 2.8 16.6 + - - +
10D DLE 3.5 0.2 + - - -
11D DLE 2.6 55.1 + - + -
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 4.0 33.4 - - + +
28A VAL* 4.7 9.4 - - + -
50A MET* 3.3 38.2 - - + +
100A TYR* 5.6 0.2 - - - -
104A TYR* 5.5 0.9 - - - -
97C ARG* 2.7 24.2 + - - +
98C LYS* 3.7 7.0 - - - -
100C TYR* 1.3 78.5 - - - +
102C MET* 1.3 65.8 + - - +
103C ILE 3.2 0.5 + - - -
104C TYR* 3.3 11.1 + - + +
105C ARG* 3.2 17.4 + - - +
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Residues in contact with MET 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 5.6 3.1 - - - +
86C PHE* 3.3 66.8 - - + +
88C VAL* 3.8 26.2 - - + -
91C PHE* 4.1 12.6 - - + -
98C LYS* 2.7 44.7 + - + +
99C ILE* 3.7 17.9 - - + +
101C THR* 1.3 74.6 - - - +
103C ILE* 1.3 60.8 + - - +
105C ARG* 3.3 16.2 - - - +
106C ASN* 2.9 26.2 + - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.0 5.8 - - - +
34C LEU* 4.8 7.2 - - + -
50C MET* 4.1 15.9 - - + -
53C VAL* 4.5 13.7 - - + -
54C LEU* 3.8 22.0 - - + -
57C LEU* 4.0 11.2 - - + -
86C PHE* 4.1 19.5 - - + -
99C ILE* 2.8 40.3 + - + +
100C TYR* 3.6 4.5 - - - +
101C THR 3.1 0.2 - - - -
102C MET* 1.3 76.3 - - - +
104C TYR* 1.3 65.8 + - - +
106C ASN* 3.0 17.7 + - - +
107C LEU* 3.4 32.0 - - + +
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 6.3 1.6 - - + -
28A VAL* 4.5 21.5 - - + -
104A TYR* 3.4 55.7 + + + -
107A LEU* 3.5 29.0 + - + +
108A VAL 2.3 39.7 + - - -
100C TYR 2.8 14.3 + - - +
101C THR* 3.3 8.0 + - + +
103C ILE* 1.3 71.2 - - - +
105C ARG* 1.3 70.5 + - + +
107C LEU* 3.0 30.7 + - + +
108C VAL* 6.4 2.0 - - - -
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.5 37.1 + - + +
31C LYS* 2.9 28.1 + - - +
84C ASP 5.4 1.4 + - - -
85C LEU 3.9 16.9 + - - -
86C PHE 4.3 15.0 + - - -
87C GLY* 4.9 4.2 - - - +
101C THR 3.2 15.5 - - - +
102C MET* 3.3 22.2 - - - +
104C TYR* 1.3 82.5 - - + +
106C ASN* 1.3 59.7 + - - +
107C LEU 3.4 1.1 - - - -
59E GLN* 6.2 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