Contacts of the helix formed by residues 64 - 81 (chain M) in PDB entry 4ADV
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 VAL 64 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4M ALA* 4.9 6.5 - - + -
21M ILE* 3.2 23.1 - - + -
23M GLY* 3.3 25.4 - - - +
24M VAL* 4.7 3.4 - - + +
59M VAL* 4.6 17.7 - - + +
62M PHE* 3.9 15.0 - - + +
63M VAL* 1.3 82.2 - - - +
65M GLU* 1.3 101.6 + - + +
67M ASP* 4.3 2.8 + - - +
68M LEU* 3.2 16.8 + - - +
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Residues in contact with GLU 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M ALA* 4.1 19.5 - - + +
5M GLY 4.4 3.4 - - - +
6M ILE* 3.8 20.8 - - + +
7M ASN* 5.4 2.1 - - - +
21M ILE* 3.3 9.5 - - + +
22M TYR* 2.7 73.3 + - + +
64M VAL* 1.3 96.2 - - + +
66M GLY* 1.3 71.6 + - - +
68M LEU* 2.9 12.4 + - - +
69M ARG* 3.3 10.5 + - - +
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Residues in contact with GLY 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M TYR* 5.5 1.2 - - - -
65M GLU* 1.3 75.1 - - - +
67M ASP* 1.3 53.1 + - - +
69M ARG* 2.8 33.2 + - - +
70M ARG* 3.1 10.2 + - - +
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Residues in contact with ASP 67 (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 VAL* 4.9 3.6 - - + -
64M VAL 4.3 3.0 + - - +
65M GLU 3.6 0.6 - - - -
66M GLY* 1.3 71.7 - - - +
68M LEU* 1.3 54.1 + - - +
70M ARG* 2.8 46.3 + - - -
71M GLU* 2.7 37.5 + - - +
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Residues in contact with LEU 68 (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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1329A A 5.1 7.6 - - - +
22M TYR 4.1 4.9 - - - +
23M GLY* 4.4 5.6 - - - +
63M VAL* 3.1 47.2 - - + +
64M VAL* 3.2 17.8 + - - +
65M GLU 2.9 11.9 + - - +
67M ASP* 1.3 78.7 - - - +
69M ARG* 1.3 81.4 + - - +
71M GLU* 3.6 7.3 - - - +
72M ILE* 2.9 52.0 + - + +
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Residues in contact with ARG 69 (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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1330A U 3.8 32.8 + - - -
1331A G 4.4 4.2 + - - -
22M TYR* 2.6 52.1 + - - +
65M GLU 3.8 13.0 + - - +
66M GLY* 2.8 12.6 + - - +
68M LEU* 1.3 97.3 - - - +
70M ARG* 1.3 54.0 + - - +
72M ILE* 3.0 10.6 + - - +
73M SER* 2.7 35.8 + - - -
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Residues in contact with ARG 70 (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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66M GLY 3.1 7.6 + - - +
67M ASP* 2.8 51.6 + - - +
69M ARG* 1.3 72.8 - - - +
71M GLU* 1.3 73.4 + - - +
72M ILE 2.9 4.4 + - - -
73M SER* 3.0 8.7 + - - -
74M MET* 2.9 57.0 + - + +
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Residues in contact with GLU 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M VAL* 4.1 16.7 - - + +
67M ASP 2.7 22.1 + - - +
68M LEU* 3.6 11.5 - - - +
70M ARG* 1.3 85.9 - - - +
72M ILE* 1.3 75.6 + - - +
74M MET* 4.1 8.1 - - + +
75M SER* 2.7 43.4 + - - +
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Residues in contact with ILE 72 (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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1309A G 4.1 23.3 - - - +
1310A G 6.0 0.9 - - - -
68M LEU* 2.9 34.8 - - + +
69M ARG* 3.0 13.4 + - - +
70M ARG 2.9 0.6 - - - -
71M GLU* 1.3 101.3 - - - +
73M SER* 1.3 59.2 + - - +
74M MET 3.0 1.6 - - - -
75M SER* 3.0 5.5 + - - +
76M ILE* 2.6 60.8 + - + +
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Residues in contact with SER 73 (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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69M ARG 2.7 19.1 + - - -
70M ARG* 3.6 9.9 - - - -
72M ILE* 1.3 71.9 - - - +
74M MET* 1.3 57.5 + - - +
76M ILE* 3.5 14.4 - - - +
77M LYS* 3.1 24.9 + - - +
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Residues in contact with MET 74 (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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70M ARG* 2.9 45.0 + - + +
71M GLU* 4.1 6.7 - - + +
73M SER* 1.3 76.8 - - - +
75M SER* 1.3 55.0 + - - +
77M LYS* 2.9 14.9 + - + +
78M ARG* 2.7 33.3 + - - +
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Residues in contact with SER 75 (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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1309A G 5.9 0.7 - - - -
1310A G 5.2 9.6 - - - -
71M GLU* 2.7 29.1 + - - +
72M ILE* 3.0 9.3 + - - +
74M MET* 1.3 78.0 - - - +
76M ILE* 1.3 64.1 + - - +
78M ARG* 2.9 16.7 - - - +
79M LEU* 2.9 26.0 - - - +
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Residues in contact with ILE 76 (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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1308A U 4.7 5.2 - - - +
1309A G 4.0 30.7 - - - +
72M ILE* 2.6 51.5 + - + +
73M SER* 3.5 11.0 - - - +
75M SER* 1.3 73.3 - - - +
77M LYS* 1.3 52.5 + - - +
79M LEU* 3.1 10.2 + - - +
80M MET* 2.7 42.8 + - + +
90M HIS* 4.0 33.9 - - + +
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Residues in contact with LYS 77 (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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73M SER 3.1 10.8 + - - +
74M MET* 2.9 16.9 + - + +
76M ILE* 1.3 79.3 - - - +
78M ARG* 1.3 62.0 + - - +
80M MET* 3.5 30.5 - - + -
81M ASP* 2.4 53.1 + - + +
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Residues in contact with ARG 78 (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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74M MET 2.7 14.9 + - - +
75M SER* 2.9 19.0 + - - +
77M LYS* 1.3 77.7 - - - +
79M LEU* 1.3 93.8 + - - +
81M ASP* 2.5 25.1 - - - +
82M LEU* 3.2 22.8 - - - +
64S GLU* 3.0 45.0 + - - +
68S HIS* 5.5 2.6 + - - -
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Residues in contact with LEU 79 (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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1310A G 4.2 17.3 - - - +
75M SER* 2.9 31.6 - - - +
76M ILE* 3.1 5.6 + - - +
78M ARG* 1.3 114.3 - - - +
80M MET* 1.3 61.5 + - - +
81M ASP 3.4 0.2 - - - -
82M LEU* 3.4 20.2 - - + +
84M CYS* 3.4 18.9 - - - -
86M ARG* 3.1 37.2 - - - +
68S HIS* 5.3 8.1 - - + +
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Residues in contact with MET 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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76M ILE* 2.7 27.4 + - + +
77M LYS* 2.9 27.3 + - + +
79M LEU* 1.3 75.7 - - - +
81M ASP* 1.3 70.8 + - - +
82M LEU 3.1 10.0 - - - +
86M ARG* 6.2 0.7 - - + -
87M GLY* 3.6 34.7 - - - +
90M HIS* 4.2 12.3 - - + -
91M ARG* 4.7 19.5 - - + +
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Residues in contact with ASP 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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77M LYS* 2.4 49.5 + - - +
78M ARG* 2.5 27.0 - - - +
80M MET* 1.3 73.9 - - - +
82M LEU* 1.3 85.7 + - - +
83M GLY* 3.5 1.9 + - - -
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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
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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