Contacts of the helix formed by residues 82 - 100 (chain C) in PDB entry 3MTS
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 CYS 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ARG* 4.0 24.0 - - - +
45C VAL* 3.8 34.3 - - + -
48C LEU* 4.9 2.0 - - - -
80C LEU* 3.5 18.3 - - - -
81C LYS* 1.3 72.3 - - - +
83C VAL* 1.3 58.5 + - - +
84C ARG 3.3 3.3 + - - -
85C ILE* 3.4 17.8 + - + -
86C LEU* 3.1 35.9 + - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 5.9 5.6 - - - +
77C ARG* 6.3 0.2 - - - +
81C LYS 2.8 16.8 + - - +
82C CYS* 1.3 71.3 - - - +
84C ARG* 1.3 71.0 + - + +
86C LEU* 3.6 12.4 + - - +
87C LYS* 3.3 22.3 + - + +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 4.8 10.0 + - - +
45B VAL* 2.9 41.0 + - - +
46B GLU 4.7 5.9 - - - +
65B ARG* 4.2 14.5 - - - +
82B CYS* 4.1 15.0 - - - +
85B ILE* 3.2 40.3 - - + +
82C CYS 3.3 0.6 - - - -
83C VAL* 1.3 85.7 - - + +
85C ILE* 1.3 66.5 + - + +
87C LYS* 3.1 8.3 + - - +
88C GLN* 3.0 22.0 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.3 68.4 - - + +
85B ILE* 4.7 2.0 - - - +
88B GLN* 3.5 27.9 - - + +
45C VAL* 4.0 11.9 - - + +
46C GLU 4.4 7.4 - - - +
47C TYR* 4.8 0.4 - - - -
48C LEU* 3.8 16.2 - - + -
82C CYS* 3.4 18.3 + - + +
84C ARG* 1.3 77.6 - - + +
86C LEU* 1.3 58.1 + - - +
88C GLN* 3.8 6.1 - - - +
89C PHE* 3.0 27.7 + - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.6 16.8 - - + -
60C TYR* 3.5 46.4 - - + +
77C ARG* 4.1 35.4 - - + +
80C LEU* 4.2 22.9 - - + +
81C LYS 5.6 0.2 - - - -
82C CYS* 3.1 28.6 + - - +
83C VAL* 3.8 10.3 - - - +
84C ARG 3.2 0.4 - - - -
85C ILE* 1.3 75.9 - - - +
87C LYS* 1.3 58.1 + - - +
89C PHE* 3.5 1.4 - - - +
90C HIS* 3.0 35.6 + - - -
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.8 25.3 + - + +
47B TYR* 4.0 21.4 - - + -
83C VAL* 3.3 11.5 + - + +
84C ARG* 3.1 11.3 + - - +
86C LEU* 1.3 76.8 - - - +
88C GLN* 1.3 60.0 + - - +
90C HIS* 3.1 8.5 + - + +
91C LYS* 2.8 72.7 + - - +
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 3.3 11.8 - - + +
48B LEU* 2.8 43.7 + - - +
85B ILE* 3.1 38.6 - - + +
88B GLN* 3.9 9.2 - - + -
89B PHE* 3.7 11.5 - - - +
84C ARG 3.0 15.5 + - - +
85C ILE* 3.8 6.7 - - - +
87C LYS* 1.3 77.3 - - - +
89C PHE* 1.3 58.0 + - - +
91C LYS* 3.3 1.3 + - - +
92C ASP* 2.9 68.3 + - - +
95C ARG* 4.2 1.2 - - - +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.6 21.6 - - - +
92B ASP* 3.7 17.0 - - - -
95B ARG* 4.6 2.9 - - - -
48C LEU* 3.7 28.0 - - + -
49C CYS 4.1 3.8 - - - -
50C ASP* 3.8 31.9 - - - -
51C TYR* 3.6 22.7 - - + -
60C TYR* 4.0 22.2 - + - -
85C ILE 3.0 19.2 + - - +
86C LEU 3.5 3.8 - - - +
88C GLN* 1.3 77.2 - - - +
90C HIS* 1.3 65.4 + + - +
92C ASP* 3.4 2.1 + - - +
93C LEU* 3.0 55.2 + - + +
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Residues in contact with HIS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 3.6 36.6 - + - -
58C GLU* 4.9 1.9 + - - -
60C TYR* 2.6 36.9 + + - -
77C ARG* 3.9 11.1 + - - -
86C LEU 3.0 26.7 + - - +
87C LYS* 3.1 7.8 + - + +
89C PHE* 1.3 79.5 - + - +
91C LYS* 1.3 72.1 + - + +
93C LEU* 3.5 12.7 + - + +
94C GLU* 3.2 22.9 + - - +
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 3.3 53.8 + - + +
87C LYS* 2.8 47.7 + - - +
88C GLN* 3.9 4.0 - - - +
90C HIS* 1.3 78.1 - - - +
92C ASP* 1.3 57.8 + - - +
94C GLU* 3.5 21.9 + - - +
95C ARG* 3.0 46.1 + - - +
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Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.4 21.0 - - - -
92B ASP* 2.3 51.2 - - + +
96B GLU* 5.5 0.2 - - - +
88C GLN* 2.9 41.5 + - - +
89C PHE 3.6 1.1 - - - +
91C LYS* 1.3 74.2 - - - +
93C LEU* 1.3 59.8 + - - +
95C ARG* 3.0 25.2 + - - +
96C GLU* 2.9 33.5 + - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 5.6 0.2 - - - -
95B ARG* 5.5 6.1 - - - +
51C TYR* 4.4 15.9 - - + -
89C PHE* 3.0 53.1 + - + +
90C HIS* 3.7 20.2 - - + +
92C ASP* 1.3 75.7 - - - +
94C GLU* 1.3 62.8 + - - +
96C GLU* 3.7 13.6 - - - +
97C LEU* 3.0 21.5 + - - +
100C ARG* 5.3 0.9 + - - -
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C HIS 3.2 14.2 + - - +
91C LYS* 3.8 21.8 - - - +
93C LEU* 1.3 78.7 - - - +
95C ARG* 1.3 64.0 + - - +
97C LEU* 3.1 10.2 + - + +
98C LEU* 3.0 45.3 + - + +
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 4.8 2.2 - - - -
48B LEU 3.1 22.8 + - - -
49B CYS* 3.0 29.6 + - - +
89B PHE* 3.6 18.4 - - - -
91C LYS* 3.0 35.6 + - - +
92C ASP* 3.0 30.8 + - - +
93C LEU 3.4 0.2 - - - -
94C GLU* 1.3 78.3 - - - +
96C GLU* 1.3 62.4 + - - +
98C LEU* 3.4 7.4 + - - +
99C ARG* 3.1 60.3 + - - +
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Residues in contact with GLU 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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92B ASP* 4.6 6.2 - - - +
95B ARG* 5.1 8.8 + - - +
96B GLU* 3.5 59.0 + - + +
99B ARG* 4.0 15.5 + - - +
92C ASP 2.9 19.3 + - - +
93C LEU* 3.7 14.7 - - + +
95C ARG* 1.3 73.0 - - - +
97C LEU* 1.3 65.5 + - - +
99C ARG* 3.2 3.2 + - - +
100C ARG* 3.0 45.7 + - - +
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Residues in contact with LEU 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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93C LEU 3.0 15.2 + - - +
94C GLU* 3.1 12.1 + - + +
96C GLU* 1.3 73.4 - - - +
98C LEU* 1.3 68.4 + - + +
100C ARG* 3.1 58.1 + - + +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 3.0 38.7 + - + +
95C ARG* 3.8 6.7 - - - +
96C GLU 3.3 0.2 - - - -
97C LEU* 1.3 86.4 - - + +
99C ARG* 1.3 57.4 + - - +
100C ARG 5.4 0.2 - - - -
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Residues in contact with ARG 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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101A HIS* 4.4 12.2 - - - -
49B CYS 5.3 0.2 + - - -
50B ASP* 5.0 9.9 + - - -
89B PHE* 6.3 0.6 - - - -
93B LEU* 3.8 18.8 - - - +
96B GLU* 2.9 36.6 + - - +
100B ARG* 3.6 19.7 + - - +
95C ARG* 3.1 52.6 + - - +
96C GLU* 3.5 6.0 - - - +
97C LEU 3.1 0.4 - - - -
98C LEU* 1.3 76.3 - - - +
100C ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.7 41.9 + - - +
93C LEU 5.3 0.6 + - - -
96C GLU* 3.0 40.7 + - - +
97C LEU* 3.1 49.9 + - + +
98C LEU 3.5 0.2 - - - -
99C ARG* 1.3 81.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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