Contacts of the helix formed by residues 74 - 94 (chain M) in PDB entry 2VGL
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 ASN 74 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ILE* 4.3 7.7 - - - +
224B ASP* 2.8 39.8 + - - +
254B ALA* 4.0 10.6 - - - +
258B SER* 3.6 8.8 + - - -
568B GLY* 4.5 13.9 - - - +
569B SER* 4.4 4.7 - - - +
1M MET* 5.6 1.3 - - - +
73M VAL* 1.3 79.6 - - - +
75M ALA* 1.3 66.8 + - - +
76M ALA* 3.2 7.1 + - - +
77M MET* 2.7 59.6 + - + +
78M VAL 3.3 2.9 + - - -
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Residues in contact with ALA 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 4.1 12.1 - - + -
568B GLY 3.4 16.6 + - - +
569B SER 3.6 14.8 - - - +
570B LEU* 4.3 3.8 - - + +
573B VAL* 3.9 20.0 - - + -
47M VAL* 6.1 0.2 - - + -
56M PHE* 3.8 21.2 - - + -
73M VAL 3.0 8.9 + - - -
74M ASN* 1.3 71.1 - - - +
76M ALA* 1.3 62.1 + - - +
77M MET 3.3 0.2 + - - -
78M VAL 3.5 7.3 + - - -
79M PHE* 3.7 17.7 + - - -
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Residues in contact with ALA 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B SER* 4.0 12.6 - - - +
254B ALA* 3.4 31.9 - - + +
257B LEU* 4.5 7.4 - - + -
298B VAL* 4.9 4.5 - - + +
301B VAL* 4.4 18.2 - - + -
568B GLY* 4.0 4.4 + - - +
74M ASN* 2.9 6.8 + - - +
75M ALA* 1.3 74.1 - - - +
77M MET* 1.3 69.8 + - - +
79M PHE* 3.5 5.2 + - - +
80M GLU* 3.3 22.7 + - - +
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Residues in contact with MET 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 4.3 7.9 - - + -
220B ILE* 4.3 15.3 - - + -
221B PHE* 4.2 15.0 - - + -
254B ALA* 3.6 10.3 - - + +
1M MET* 2.9 46.9 - - + +
2M ILE* 5.2 1.1 - - + -
73M VAL* 4.3 10.3 - - + -
74M ASN* 2.7 40.9 + - + +
76M ALA* 1.3 82.6 - - - +
78M VAL* 1.3 68.6 + - + +
80M GLU* 2.9 13.4 + - - +
81M PHE* 3.1 12.1 + - - +
119M GLY 4.6 0.4 - - - +
121M PRO* 3.8 30.1 - - + -
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Residues in contact with VAL 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ILE* 4.1 23.3 - - + -
56M PHE* 3.3 53.4 - - + -
67M ALA* 3.6 18.6 - - + -
69M THR* 5.9 0.2 - - - +
73M VAL* 3.6 30.7 - - + -
74M ASN 3.3 1.7 + - - +
75M ALA 4.0 0.4 - - - +
76M ALA 3.3 0.6 - - - -
77M MET* 1.3 82.6 - - + +
79M PHE* 1.3 63.7 + - - +
81M PHE* 3.3 9.2 - - - +
82M LEU* 3.2 22.9 + - + +
121M PRO* 5.7 0.2 - - - -
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Residues in contact with PHE 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 3.4 38.1 - - + -
298B VAL* 4.9 7.4 - - + -
300B TYR* 5.8 0.2 - + - -
301B VAL* 4.3 17.3 - - + -
46M PRO* 3.3 33.7 - - + -
47M VAL* 3.9 13.9 - - + -
56M PHE* 3.7 21.3 - + + -
57M HIS 3.8 20.2 - - - -
58M VAL* 4.5 4.3 - - + -
75M ALA 3.7 13.5 - - - -
76M ALA* 3.5 6.7 + - - +
77M MET 3.2 0.4 - - - -
78M VAL* 1.3 76.2 - - - +
80M GLU* 1.3 66.1 + - - +
82M LEU* 3.1 16.7 + - + +
83M TYR* 2.9 39.2 + - + +
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Residues in contact with GLU 80 (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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216B GLU* 4.2 10.0 - - - +
217B TRP* 3.8 19.5 - - + -
251B ALA* 4.5 5.4 - - + -
252B ASN* 4.1 16.4 + - - +
253B SER* 3.4 32.4 + - - +
254B ALA* 4.3 16.2 - - + +
298B VAL* 3.7 13.1 - - + +
76M ALA 3.3 13.2 + - - +
77M MET 2.9 8.1 + - - +
79M PHE* 1.3 76.6 - - - +
81M PHE* 1.3 66.6 + - - +
83M TYR* 2.9 26.6 + - - +
84M LYS* 3.0 21.1 + - - +
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Residues in contact with PHE 81 (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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217B TRP* 3.4 15.4 - + + -
2M ILE* 4.4 7.9 - - + -
5M LEU* 4.2 21.5 - - + -
77M MET 3.1 7.4 + - - +
78M VAL* 3.3 14.1 - - - +
80M GLU* 1.3 77.2 - - - +
82M LEU* 1.3 73.9 + - + +
84M LYS* 2.7 25.2 + - - +
85M MET* 2.7 42.0 + - + +
115M ILE* 3.7 32.5 - - + -
116M LEU* 3.1 39.9 - - + -
121M PRO* 4.1 25.6 - - + -
124M SER* 5.9 1.6 - - - -
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Residues in contact with LEU 82 (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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5M LEU* 3.9 28.7 - - + -
57M HIS* 4.4 8.3 - - - +
58M VAL* 4.4 27.6 - - + +
65M LEU* 4.2 25.6 - - + -
66M ALA 4.6 2.2 - - - +
67M ALA* 4.4 8.3 - - + -
78M VAL* 3.2 28.8 + - + +
79M PHE* 3.1 25.0 + - + +
81M PHE* 1.3 88.4 - - + +
83M TYR* 1.3 62.9 + - - +
85M MET* 4.1 5.2 - - - +
86M CYS* 3.2 28.8 + - - -
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Residues in contact with TYR 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.2 41.7 - - + +
297B GLU* 2.5 47.0 + - + +
298B VAL* 3.5 15.8 + - + -
58M VAL* 3.6 23.8 - - + -
60M ARG* 4.0 13.5 - - - -
79M PHE* 2.9 27.2 + - + -
80M GLU* 2.9 25.9 + - - +
82M LEU* 1.3 77.5 - - - +
84M LYS* 1.3 64.0 + - + +
86M CYS* 3.5 8.2 + - - +
87M ASP* 3.0 28.4 + - - +
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Residues in contact with LYS 84 (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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216B GLU* 3.5 28.1 + - - +
217B TRP* 4.0 22.4 - - + -
250B HIS* 5.3 4.0 + - - -
80M GLU* 3.0 21.6 + - - +
81M PHE* 2.7 12.6 + - + +
83M TYR* 1.3 73.4 - - + +
85M MET* 1.3 53.5 + - - +
86M CYS 3.1 0.9 - - - -
87M ASP* 2.9 24.6 + - + +
88M VAL* 2.7 40.0 + - + +
115M ILE* 5.0 1.3 - - + -
124M SER* 5.1 13.2 - - - +
125M GLU* 4.9 9.4 + - + +
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Residues in contact with MET 85 (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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5M LEU* 3.0 37.5 - - + -
7M ILE* 5.0 1.1 - - - -
65M LEU* 3.4 26.0 - - + -
81M PHE* 2.7 36.2 + - + +
82M LEU* 4.1 7.2 - - - +
84M LYS* 1.3 70.5 - - - +
86M CYS* 1.3 53.3 + - - +
88M VAL* 3.3 1.3 + - - +
89M MET* 2.8 60.6 + - + +
111M LEU* 6.2 0.2 - - + -
112M LEU* 3.4 29.2 - - + -
115M ILE* 3.7 29.3 - - + +
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Residues in contact with CYS 86 (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 VAL* 5.0 2.7 - - - -
60M ARG* 3.8 28.9 - - - +
65M LEU* 4.3 18.6 - - - -
82M LEU 3.2 15.3 + - - +
83M TYR* 3.5 11.7 - - - +
84M LYS 3.1 0.4 - - - -
85M MET* 1.3 74.3 - - - +
87M ASP* 1.3 64.7 + - - +
90M ALA* 3.5 19.8 + - - +
96M ILE* 3.2 33.6 - - + +
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Residues in contact with ASP 87 (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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83M TYR* 3.0 20.4 + - - +
84M LYS* 2.9 31.7 + - + +
86M CYS* 1.3 74.4 - - - +
88M VAL* 1.3 71.0 + - + +
90M ALA* 3.1 8.2 + - - +
91M ALA* 3.1 17.4 + - - +
126M THR* 5.1 6.2 + - - +
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Residues in contact with VAL 88 (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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84M LYS 2.7 23.7 + - - +
85M MET* 3.5 6.7 - - - +
87M ASP* 1.3 73.2 - - + +
89M MET* 1.3 56.7 + - + +
91M ALA* 2.6 38.4 + - - +
92M TYR* 3.3 16.5 + - + -
111M LEU* 3.1 37.5 - - + -
115M ILE* 4.8 7.9 - - + -
124M SER 3.5 24.7 - - - +
126M THR* 4.6 14.1 - - - +
129M LEU* 4.4 9.4 - - + -
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Residues in contact with MET 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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7M ILE* 4.0 16.8 - - + -
65M LEU* 5.0 3.6 - - - -
85M MET* 2.8 51.2 + - + +
88M VAL* 1.3 74.3 - - + +
90M ALA* 1.3 57.6 + - - +
92M TYR* 2.9 22.6 + - - +
93M PHE* 3.1 43.5 + - + -
96M ILE* 4.2 23.8 - - + -
101M ILE* 4.7 9.0 - - - -
108M ILE* 3.9 34.3 - - + -
111M LEU* 5.0 10.3 - - + -
112M LEU* 4.6 2.7 - - + -
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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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86M CYS 3.5 18.7 + - - +
87M ASP* 3.1 6.2 + - - +
89M MET* 1.3 78.2 - - - +
91M ALA* 1.3 56.8 + - - +
92M TYR 3.2 1.4 + - - -
94M GLY* 3.1 42.9 + - - +
95M LYS* 5.3 0.7 - - - -
96M ILE* 5.0 5.1 - - + +
139M LYS* 5.8 2.3 + - - -
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Residues in contact with ALA 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M ASP 3.1 9.4 + - - +
88M VAL* 2.6 18.9 + - - +
90M ALA* 1.3 69.7 - - - +
92M TYR* 1.3 66.4 + - + -
126M THR* 3.9 34.1 - - + +
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Residues in contact with TYR 92 (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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88M VAL* 3.5 30.5 - - + -
89M MET* 2.9 7.5 + - - +
91M ALA* 1.3 91.3 - - + +
93M PHE* 1.3 61.7 + - + +
94M GLY 3.9 1.1 - - - -
107M LEU* 3.3 46.9 - - + -
111M LEU* 4.3 6.1 - - + -
126M THR* 4.9 11.6 + - + -
129M LEU* 4.5 10.7 - - + +
130M LYS* 4.7 8.3 + - - +
133M ILE* 3.5 26.4 + - + +
135M GLN 3.8 12.3 - - - -
136M GLN* 4.7 0.9 - - - -
137M GLY* 3.6 28.2 + - - +
139M LYS* 4.4 13.1 + - - +
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Residues in contact with PHE 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M MET* 3.1 42.9 + - + -
92M TYR* 1.3 78.8 - - + +
94M GLY* 1.3 56.9 + - - +
95M LYS 3.7 13.0 - - - -
96M ILE* 5.1 2.0 - - - -
100M ASN* 2.7 59.7 + - + +
101M ILE* 4.5 9.6 - - + -
104M ASN* 3.2 38.1 - - + +
107M LEU* 3.7 20.6 - - + -
108M ILE* 4.2 19.5 - - + -
111M LEU* 5.4 0.4 - - + -
138M ILE 3.7 22.5 - - - +
139M LYS* 4.6 12.7 - - - +
140M SER 4.9 0.7 + - - -
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Residues in contact with GLY 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M ALA* 3.1 40.8 + - - +
92M TYR 3.9 0.8 - - - -
93M PHE* 1.3 74.4 - - - +
95M LYS* 1.3 74.4 - - - +
139M LYS* 4.9 12.8 - - - +
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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
------------------------------------------------------------
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