Contacts of the helix formed by residues 88 - 100 (chain M) in PDB entry 1T6V
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 ILE 88 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113L ASN* 3.8 5.9 + - - +
3M PHE* 3.6 32.8 - - + -
8M LEU* 4.3 7.4 - - + -
11M ALA* 3.9 22.2 - - + -
12M MET* 4.2 18.6 - - + +
15M HIS* 3.6 26.2 - - + +
40M THR* 4.5 5.2 - - + -
55M ILE* 4.3 22.4 - - + -
85M SER 5.0 1.3 - - - +
86M SER 3.6 1.7 + - - +
87M ASP* 1.3 72.9 + - - +
89M THR* 1.3 65.4 + - - +
90M ALA 3.4 1.6 - - - -
91M SER* 3.1 9.2 + - - -
92M VAL* 2.9 38.6 + - + +
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Residues in contact with THR 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L VAL* 3.7 22.4 + - + +
112L ARG* 3.9 24.2 - - - +
113L ASN* 3.8 5.4 + - - +
15M HIS* 3.2 30.2 + - + +
87M ASP* 2.6 23.1 + - - -
88M ILE* 1.3 78.7 - - - +
90M ALA* 1.3 59.7 + - - +
92M VAL* 3.2 3.3 + - - +
93M ASN* 2.9 45.7 + - - +
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Residues in contact with ALA 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M ILE* 4.4 11.9 - - + +
82M ALA* 3.9 22.0 - - + +
83M LEU* 3.6 19.3 - - + +
87M ASP 4.7 2.4 + - - +
88M ILE 3.4 0.6 - - - -
89M THR* 1.3 81.8 - - - +
91M SER* 1.3 62.7 + - - +
93M ASN* 3.4 6.5 + - - +
94M CYS* 3.0 24.6 + - - +
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Residues in contact with SER 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M TYR 5.0 0.7 + - - -
55M ILE* 3.7 31.3 + - - +
56M LEU* 4.5 10.5 + - - +
58M ILE* 4.5 8.0 - - - +
83M LEU* 3.6 34.7 + - - +
87M ASP 5.5 0.2 + - - -
88M ILE* 3.1 11.3 + - - -
90M ALA* 1.3 77.8 - - - +
92M VAL* 1.3 58.4 + - - +
94M CYS* 3.5 3.9 + - - +
95M ALA* 2.9 30.9 + - - +
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Residues in contact with VAL 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M MET* 5.3 0.9 - - + -
15M HIS* 3.8 31.0 - - + +
17M LEU* 4.1 23.1 - - + -
55M ILE* 6.4 0.2 - - + -
56M LEU* 5.2 5.8 - - + -
88M ILE* 2.9 43.7 + - + +
89M THR 3.6 6.7 - - - +
91M SER* 1.3 74.8 - - - +
93M ASN* 1.3 63.3 + - - +
95M ALA* 3.2 5.5 + - - +
96M LYS* 2.8 52.7 + - + +
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Residues in contact with ASN 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ARG* 4.0 12.7 - - - +
15M HIS* 6.1 0.8 - - - -
89M THR* 2.9 37.2 + - - +
90M ALA* 4.0 5.9 - - - +
92M VAL* 1.3 78.3 - - - +
94M CYS* 1.3 63.7 + - - +
96M LYS* 3.4 21.7 + - - +
97M LYS* 3.2 19.8 + - - +
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Residues in contact with CYS 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M ILE* 3.6 37.2 - - + -
63M TRP* 4.1 4.3 - - - -
76M CYS* 2.0 53.8 - - + -
78M ILE* 4.1 8.5 - - + -
90M ALA 3.0 18.0 + - - +
91M SER 3.8 2.9 - - - +
93M ASN* 1.3 74.8 - - - +
95M ALA* 1.3 65.6 + - - +
97M LYS* 3.0 12.7 + - - +
98M ILE* 3.0 19.6 + - - +
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LEU* 5.4 2.2 - - + -
28M TRP* 4.1 9.4 - - + -
56M LEU* 3.9 17.7 - - + -
58M ILE* 4.5 2.8 - - + +
91M SER 2.9 17.9 + - - +
92M VAL* 3.6 5.6 - - - +
94M CYS* 1.3 75.5 - - - +
96M LYS* 1.3 63.6 + - - +
98M ILE* 3.3 3.9 + - - +
99M VAL* 2.9 28.4 + - - +
108M TRP* 3.7 31.3 - - + -
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Residues in contact with LYS 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M HIS 2.8 29.4 + - - -
16M GLY* 4.1 5.9 + - - -
17M LEU* 4.0 15.5 - - + -
20M TYR* 3.5 50.0 - - + +
92M VAL* 2.8 32.5 + - + +
93M ASN* 3.6 20.2 + - - +
94M CYS 3.2 0.2 - - - -
95M ALA* 1.3 75.2 - - - +
97M LYS* 1.4 59.7 + - - +
99M VAL* 3.5 3.5 + - - +
100M SER* 2.6 34.6 + - - -
26N ASP* 4.2 16.8 + - - -
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Residues in contact with LYS 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M TRP* 4.3 6.7 - - + -
75M LEU 3.4 28.0 - - - +
76M CYS* 4.0 22.9 - - - +
77M ASN* 5.2 3.5 - - - +
93M ASN 3.2 10.2 + - - +
94M CYS 3.0 11.2 + - - +
96M LYS* 1.4 79.9 - - - +
98M ILE* 1.3 66.0 + - - +
100M SER* 3.4 13.4 + - - -
101M ASP* 4.1 2.6 + - - +
8N ARG* 5.7 0.6 - - - +
106N ASP* 2.9 36.5 + - - +
88O ALA* 4.3 28.1 + - + +
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Residues in contact with ILE 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M ILE* 4.0 23.6 - - + -
63M TRP* 3.5 64.3 - - + +
94M CYS* 3.0 15.3 + - - +
95M ALA 3.3 5.6 + - - +
97M LYS* 1.3 77.9 - - - +
99M VAL* 1.3 59.3 + - - +
100M SER 3.2 1.0 + - - -
101M ASP* 3.1 24.4 + - - +
102M GLY* 5.1 0.3 - - - -
104M GLY 4.7 1.0 - - - +
107M ALA* 3.6 30.5 - - + -
108M TRP* 3.9 17.7 - - + -
87O VAL* 6.2 0.2 - - - +
88O ALA 5.3 0.7 + - - -
101O TYR* 5.0 2.0 - - + -
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Residues in contact with VAL 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M TYR* 3.7 27.1 - - + -
21M ARG* 3.8 10.8 - - + +
23M TYR* 3.5 36.4 - - + -
28M TRP* 3.8 15.0 - - + -
95M ALA 2.9 18.4 + - - +
96M LYS* 3.5 7.9 - - - +
98M ILE* 1.3 78.0 - - - +
100M SER* 1.3 58.7 + - - +
101M ASP 3.1 8.9 + - - +
104M GLY* 3.8 19.5 - - - -
105M MET* 3.7 16.2 - - + -
108M TRP* 4.3 3.6 - - + -
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Residues in contact with SER 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M TYR* 3.5 6.8 + - - -
21M ARG* 3.1 46.5 + - - +
96M LYS 2.6 22.0 + - - -
97M LYS* 3.8 8.3 - - - -
98M ILE 3.1 1.8 - - - -
99M VAL* 1.3 76.3 - - - +
101M ASP* 1.3 61.4 + - - +
2N ARG* 6.0 0.2 - - - -
32O GLY* 5.7 1.0 - - - -
89O GLY* 5.9 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