Contacts of the helix formed by residues 105 - 121 (chain M) in PDB entry 6I3N
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 LEU 105 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28M ARG* 4.3 6.3 - - - +
29M VAL* 4.2 16.2 - - + +
32M ARG* 3.6 31.0 - - + +
33M LEU* 3.7 50.5 - - + +
36M PHE* 5.1 2.0 - - + -
90M LEU* 5.3 1.7 - - - +
101M VAL* 2.8 26.5 + - + +
102M LEU* 4.2 2.6 - - - -
104M GLU* 1.3 75.2 - - + +
106M GLY* 1.3 64.2 + - - +
107M PRO 3.7 0.2 - - - -
108M SER* 4.1 22.9 - - - -
109M ILE* 3.3 31.9 + - + +
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Residues in contact with GLY 106 (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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102M LEU* 3.3 21.6 + - - -
103M LEU 4.9 0.4 - - - -
104M GLU 3.2 4.6 - - - +
105M LEU* 1.3 80.4 - - - +
107M PRO* 1.3 67.7 - - - +
109M ILE* 4.2 1.9 - - - +
110M GLU* 3.6 24.2 + - - +
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Residues in contact with PRO 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M LEU 4.6 6.3 - - - +
104M GLU 4.0 11.0 - - - +
106M GLY* 1.3 89.8 - - - +
108M SER* 1.3 60.4 + - - +
110M GLU* 3.4 11.7 + - + +
111M GLU* 2.9 29.7 + - - +
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Residues in contact with SER 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ARG* 2.9 29.8 + - - -
29M VAL* 3.7 15.9 - - - -
104M GLU 4.4 6.2 + - - -
105M LEU* 4.1 11.9 - - - -
106M GLY 3.3 1.0 - - - -
107M PRO* 1.3 78.6 - - - +
109M ILE* 1.3 60.6 + - - +
111M GLU* 3.3 7.7 + - - +
112M ASP* 3.0 34.5 + - - +
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Residues in contact with ILE 109 (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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25M LEU* 3.9 18.6 - - + +
29M VAL* 3.7 25.6 - - + -
33M LEU* 5.4 8.7 - - + -
86M VAL* 3.7 28.9 - - + -
89M LEU* 5.6 3.4 - - + -
90M LEU* 3.8 34.5 - - + -
93M LEU* 6.1 1.1 - - + -
105M LEU* 3.3 35.4 + - + +
106M GLY 4.2 2.0 - - - +
107M PRO 3.4 0.4 - - - -
108M SER* 1.3 73.7 - - - +
110M GLU* 1.3 60.0 + - + +
112M ASP* 3.4 2.2 + - - +
113M CYS* 2.9 27.5 + - + +
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Residues in contact with GLU 110 (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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106M GLY 3.6 14.9 + - - +
107M PRO* 3.4 12.0 + - - +
108M SER 3.3 0.2 - - - -
109M ILE* 1.3 80.1 - - + +
111M GLU* 1.3 56.3 + - - +
113M CYS* 3.2 7.1 + - - +
114M GLN* 2.9 37.7 + - + +
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Residues in contact with GLU 111 (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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107M PRO 2.9 18.8 + - - +
108M SER* 3.3 8.5 + - - +
110M GLU* 1.3 76.1 - - - +
112M ASP* 1.3 77.4 + - - +
114M GLN* 3.9 5.7 + - - +
115M LYS* 2.6 46.8 + - - +
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Residues in contact with ASP 112 (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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52J GLU* 5.1 0.2 - - - +
24M ALA* 3.2 28.7 - - - +
25M LEU* 4.8 3.4 - - + -
26M ASN* 2.8 40.6 + - - +
28M ARG* 5.6 1.2 - - - +
29M VAL* 3.3 21.8 - - + +
108M SER* 3.0 12.9 + - - +
109M ILE* 3.7 4.7 - - - +
111M GLU* 1.3 89.6 - - - +
113M CYS* 1.3 63.2 + - - +
115M LYS* 3.9 14.8 + - - +
116M TYR* 3.4 16.1 + - - +
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Residues in contact with CYS 113 (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 LEU* 3.7 38.9 - - + +
24M ALA* 4.5 3.6 - - + +
86M VAL* 5.9 2.9 - - + -
109M ILE* 2.9 19.6 + - + +
110M GLU* 3.2 10.5 + - - +
112M ASP* 1.3 77.9 - - - +
114M GLN* 1.3 65.2 + - - +
116M TYR* 3.2 4.9 + - - +
117M ILE* 3.0 46.7 + - - +
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Residues in contact with GLN 114 (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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110M GLU* 2.9 23.5 + - + +
111M GLU* 4.2 5.4 - - - +
113M CYS* 1.3 83.7 - - - +
115M LYS* 1.3 57.7 + - - +
117M ILE* 3.9 24.2 - - - +
118M LEU* 3.0 44.3 + - + +
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Residues in contact with LYS 115 (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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55J ASP* 4.4 20.0 - - + +
26M ASN* 5.2 7.0 - - - +
111M GLU* 2.6 46.4 + - - +
112M ASP* 4.1 15.5 + - - +
113M CYS 3.2 0.4 - - - -
114M GLN* 1.3 76.8 - - - +
116M TYR* 1.3 60.2 + - - +
118M LEU* 3.4 5.7 + - - +
119M LYS* 2.9 27.2 + - - +
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Residues in contact with TYR 116 (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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36I PHE* 4.8 0.2 - - - -
104I GLU* 2.7 34.0 + - - -
57J GLU* 3.3 30.6 + - + -
20M LEU* 3.8 18.8 - - + -
21M PRO* 4.2 22.8 - - + +
23M ALA* 4.1 18.4 - - + +
24M ALA* 3.7 20.9 - - + +
112M ASP 3.4 12.9 + - - +
113M CYS 3.2 8.4 + - - +
115M LYS* 1.3 75.6 - - - +
117M ILE* 1.3 61.6 + - + +
119M LYS* 3.3 12.2 + - + +
120M GLN* 3.0 51.7 + - + +
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Residues in contact with ILE 117 (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 LEU* 4.5 9.2 - - + -
113M CYS* 3.0 40.1 + - - +
114M GLN* 3.9 24.0 - - - +
116M TYR* 1.3 78.2 - - + +
118M LEU* 1.3 63.9 + - + +
120M GLN* 3.1 14.7 + - - +
121M GLN 2.9 30.9 + - - +
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Residues in contact with LEU 118 (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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114M GLN* 3.0 35.8 + - + +
115M LYS* 3.4 7.4 + - + +
117M ILE* 1.3 83.0 - - + +
119M LYS* 1.3 63.9 + - - +
121M GLN* 3.2 18.2 + - - +
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Residues in contact with LYS 119 (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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32I ARG* 4.8 9.8 - - - +
55J ASP 5.0 8.1 + - - +
56J PHE* 5.4 0.2 - - - +
57J GLU* 3.3 51.2 + - + +
60J GLU* 4.0 10.3 + - - +
115M LYS* 2.9 18.2 + - + +
116M TYR* 3.6 13.7 - - + +
117M ILE 3.2 0.2 - - - -
118M LEU* 1.3 78.0 - - - +
120M GLN* 1.3 59.2 + - + +
121M GLN* 3.4 2.6 + - - +
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Residues in contact with GLN 120 (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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104I GLU* 4.1 22.0 - - + +
21M PRO* 5.8 1.2 - - - +
116M TYR* 3.0 53.3 + - + +
117M ILE* 3.1 14.9 + - + +
119M LYS* 1.3 75.3 - - + +
121M GLN* 1.3 70.3 + - - +
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Residues in contact with GLN 121 (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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117M ILE* 2.9 20.7 + - - +
118M LEU* 3.2 17.4 + - - +
119M LYS 3.2 5.7 - - - +
120M GLN* 1.3 84.4 - - - +
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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