Contacts of the helix formed by residues 93 - 111 (chain M) in PDB entry 3J9X
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 GLY 93 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K THR* 4.6 0.4 - - - -
92M SER* 1.3 78.8 - - - +
94M PRO* 1.3 68.2 - - - -
95M ALA 3.3 1.8 - - - -
96M LEU* 2.7 30.4 + - - +
97M VAL* 3.1 14.4 + - - +
133M VAL* 4.3 18.5 - - - +
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Residues in contact with PRO 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K THR* 3.3 17.9 - - + +
65K GLN* 3.4 28.3 - - + +
66K TYR 4.6 0.7 - - - -
67K GLY* 3.8 11.0 - - - +
92M SER 4.6 0.7 - - - +
93M GLY* 1.3 85.2 - - - -
95M ALA* 1.3 62.2 + - - +
97M VAL* 3.0 12.7 + - + +
98M ASN* 2.9 25.5 + - - +
133M VAL* 4.3 8.6 - - + -
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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
----------------------------------------------------------
64K THR* 3.3 18.6 + - + +
67K GLY* 3.5 15.9 - - - -
68K ILE 3.7 20.2 - - - +
69K THR* 3.4 14.3 - - + +
90M ILE* 3.5 24.9 - - + -
93M GLY 3.1 0.8 + - - -
94M PRO* 1.3 79.4 - - - +
96M LEU* 1.3 63.0 + - - +
98M ASN* 3.3 1.3 + - - +
99M MET* 3.0 19.8 + - - +
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M VAL* 4.3 6.3 - - + +
86M ALA* 3.9 28.7 - - + +
87M LEU* 3.8 37.5 - - + +
90M ILE* 4.2 5.5 - - + +
91M GLY 3.6 11.4 - - - +
92M SER* 3.9 10.3 - - - -
93M GLY 2.7 16.8 + - - +
95M ALA* 1.3 71.2 - - - +
97M VAL* 1.3 61.7 + - + +
99M MET* 3.1 5.3 + - + +
100M ILE* 2.8 51.6 + - + +
126M THR* 4.6 13.0 - - + -
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Residues in contact with VAL 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M GLY 3.8 7.2 - - - +
94M PRO* 3.0 11.2 + - + +
96M LEU* 1.3 79.7 - - + +
98M ASN* 1.3 67.7 + - - +
100M ILE* 3.3 0.6 + - + -
101M ASN* 3.1 32.7 + - - +
130M THR* 3.4 25.0 + - - +
131M GLY* 3.6 29.4 - - - +
132M TYR 4.8 2.9 - - - +
133M VAL* 3.7 29.8 - - + -
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Residues in contact with ASN 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K GLY* 3.1 35.8 + - - -
69K THR* 4.4 8.1 - - + -
94M PRO* 2.9 13.5 + - - +
95M ALA* 3.5 7.9 - - - +
96M LEU 3.2 0.2 - - - -
97M VAL* 1.3 80.4 - - - +
99M MET* 1.3 62.9 + - - +
101M ASN* 3.5 8.8 + - - +
102M GLY 3.3 15.8 + - - -
109N SER 3.5 22.9 - - - +
110N ALA* 3.7 2.9 - - - +
112N ASN* 5.2 8.7 - - - +
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Residues in contact with MET 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768 T 4.1 11.4 - - - +
69K THR* 4.6 5.8 - - + -
82M LYS* 4.7 12.8 - - - +
83M VAL* 6.3 0.7 - - - -
86M ALA* 3.8 23.3 - - + -
90M ILE* 3.7 22.9 - - + -
95M ALA 3.0 12.6 + - - +
96M LEU* 3.1 14.1 + - + +
98M ASN* 1.3 77.5 - - - +
100M ILE* 1.3 60.1 + - + +
102M GLY* 3.2 3.5 + - - -
103M LEU* 2.8 31.6 + - + +
106N TYR* 4.7 10.1 - - - -
110N ALA* 4.2 19.4 + - - +
111N PHE* 3.8 29.8 - - + -
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Residues in contact with ILE 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M PHE* 5.0 3.6 - - + -
83M VAL* 4.3 19.1 - - + -
96M LEU* 2.8 46.8 + - + +
97M VAL* 3.3 4.0 + - + +
99M MET* 1.3 73.2 - - + +
101M ASN* 1.3 56.6 + - - +
103M LEU* 3.5 6.5 - - + +
104M LYS* 2.8 43.1 + - + +
122M VAL* 4.2 16.2 - - + -
126M THR* 4.1 22.9 - - + -
130M THR* 3.5 34.8 - - + +
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Residues in contact with ASN 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M VAL* 3.1 33.4 + - - +
98M ASN* 3.7 10.1 + - - +
99M MET 3.2 0.2 - - - -
100M ILE* 1.3 77.4 - - - +
102M GLY* 1.3 62.5 + - - +
104M LYS* 3.5 8.3 + - - +
105M GLY* 3.2 17.2 + - - -
130M THR* 3.3 21.1 - - - +
131M GLY* 4.3 7.3 + - - -
109N SER* 4.2 8.2 + - - +
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Residues in contact with GLY 102 (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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98M ASN 3.3 4.2 + - - -
99M MET 3.2 6.7 + - - -
101M ASN* 1.3 76.8 - - - +
103M LEU* 1.3 59.2 + - - +
105M GLY* 3.1 3.7 + - - -
106M TYR 2.9 23.9 + - - -
105N GLY 4.8 0.2 - - - -
106N TYR* 3.5 20.1 - - - -
109N SER* 3.0 23.5 + - - -
110N ALA* 4.0 10.1 - - - -
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Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M PHE* 3.6 17.0 - - + -
82M LYS* 3.5 47.1 - - + +
83M VAL* 3.6 31.4 - - + +
99M MET* 2.8 22.9 + - + +
100M ILE* 3.2 9.6 + - + +
102M GLY* 1.3 74.1 - - - +
104M LYS* 1.3 64.5 + - - +
106M TYR* 3.1 12.0 + - + +
107M TYR* 3.0 40.6 + - + -
106N TYR* 3.9 9.7 - - + -
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Residues in contact with LYS 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M PHE* 3.8 28.7 - - + -
100M ILE* 2.8 35.2 + - + +
101M ASN* 3.7 7.8 + - - +
103M LEU* 1.3 71.9 - - - +
105M GLY* 1.3 58.5 + - - +
107M TYR* 3.2 1.6 + - - +
108M ILE* 2.8 54.8 + - + +
115M PRO* 5.0 5.5 - - - +
118M LEU* 4.8 6.1 - - + -
119M ASP* 2.7 37.2 + - - +
122M VAL* 5.0 2.5 - - + -
129M PRO* 6.1 0.4 - - - +
130M THR* 4.6 11.8 - - + +
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Residues in contact with GLY 105 (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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101M ASN 3.2 8.3 + - - -
102M GLY* 3.1 8.0 + - - -
104M LYS* 1.3 77.7 - - - +
106M TYR* 1.3 58.6 + - - +
108M ILE* 4.6 6.7 - - - -
109M SER* 2.6 37.0 + - - -
102N GLY 4.4 3.1 - - - -
105N GLY* 5.9 2.7 - - - -
106N TYR 5.3 2.0 - - - -
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Residues in contact with TYR 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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2637 A 3.8 5.9 + - - -
2647 T 2.9 18.6 + - - -
82M LYS* 5.6 4.0 - - - -
102M GLY 2.9 12.1 + - - +
103M LEU* 3.2 16.4 - - + +
105M GLY* 1.3 75.6 - - - +
107M TYR* 1.3 84.7 + + - +
110M ALA* 2.8 41.1 + - + +
111M PHE* 3.7 26.9 - + - -
82N LYS* 2.8 39.7 + - - -
99N MET* 4.6 7.8 - - - +
102N GLY 3.7 15.4 + - - -
103N LEU* 4.0 13.9 - - + -
106N TYR* 3.7 30.3 - + + -
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Residues in contact with TYR 107 (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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2637 A 4.5 5.0 - - + +
2647 T 3.3 34.2 + - - -
75M ILE* 3.5 37.5 - - + -
78M GLY* 3.5 9.8 - - - -
79M PHE* 3.7 30.1 - + + -
82M LYS* 5.2 1.3 - - + -
103M LEU* 3.0 25.7 + - + +
104M LYS 4.0 1.6 - - - +
106M TYR* 1.3 98.5 - + - +
108M ILE* 1.3 66.9 + - - +
111M PHE* 3.1 41.1 + + - -
112M ASN 3.2 0.2 + - - -
113M ALA* 3.0 25.5 + - + +
118M LEU* 4.4 8.3 - - + -
71P PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (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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104M LYS* 2.8 43.7 + - + +
105M GLY* 4.1 4.9 - - - +
107M TYR* 1.3 72.7 - - - +
109M SER* 1.3 62.5 + - - +
112M ASN* 3.1 25.5 - - - +
113M ALA 3.6 15.8 + - - +
115M PRO* 3.9 31.9 - - + -
118M LEU* 3.3 21.3 - - + -
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Residues in contact with SER 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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105M GLY* 2.6 21.0 + - - -
108M ILE* 1.3 85.8 - - - +
110M ALA* 1.3 60.4 + - - +
111M PHE 3.5 0.2 - - - -
112M ASN* 4.0 10.9 - - - +
98N ASN* 3.5 17.3 - - - +
101N ASN* 4.2 6.6 + - - +
102N GLY* 2.9 21.6 - - - -
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Residues in contact with ALA 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M TYR* 2.8 25.6 + - + +
109M SER* 1.3 79.3 + - - +
111M PHE* 1.3 61.6 + - + +
112M ASN* 5.1 1.9 + - - -
98N ASN* 3.6 13.0 - - - +
99N MET* 3.9 35.2 + - - +
102N GLY* 4.1 4.7 - - - -
69P THR* 2.6 34.5 + - - +
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Residues in contact with PHE 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2637 A 3.8 25.1 - - - -
75M ILE* 4.8 13.1 - - + +
106M TYR* 3.7 34.3 - + - -
107M TYR* 3.1 47.1 + + + +
110M ALA* 1.3 78.7 - - + +
112M ASN* 1.3 75.3 + - - +
113M ALA* 3.2 1.8 + - - +
99N MET* 3.7 28.5 - - + -
69P THR* 3.4 17.9 - - - +
70P GLY* 3.5 30.5 - - - -
71P PRO* 4.6 3.8 - - + -
72P ASN* 3.3 19.4 + - - +
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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
------------------------------------------------------------
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