Contacts of the helix formed by residues 58 - 78 (chain A) in PDB entry 3D9M
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 TYR 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.1 32.0 + - + -
15A ASN* 3.4 27.1 + - - -
17A TYR 2.7 25.2 + - - -
19A PRO* 4.0 16.6 - - + -
21A ILE* 4.8 2.0 - - + -
50A PHE* 3.9 11.3 - + + -
54A CYS* 3.8 15.0 - - + -
55A LYS* 2.9 28.4 + - + +
57A GLU* 1.3 101.2 + - + +
59A LYS* 1.3 60.1 + - - +
60A VAL 3.5 0.9 - - - -
61A PRO* 3.4 13.1 - - + +
62A GLY* 2.9 26.0 + - - -
5B LYS* 3.1 25.8 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 2.6 28.7 + - + +
52A GLN* 3.7 10.9 + - - +
54A CYS* 3.1 36.2 + - - -
55A LYS 4.2 2.2 - - - -
56A PRO* 3.3 27.4 + - + +
58A TYR* 1.3 76.1 - - - +
60A VAL* 1.3 60.1 + - + +
62A GLY* 3.0 3.2 + - - -
63A LEU 2.9 23.9 + - - -
98A ASN* 3.6 23.0 + - - +
99A LEU* 3.1 39.6 - - + +
101A ARG* 4.6 8.9 - - - +
102A CYS* 3.9 11.2 - - + +
110A ILE* 5.8 0.2 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.9 0.4 + - - -
57A GLU 4.7 0.8 + - - -
59A LYS* 1.3 78.4 - - - +
61A PRO* 1.4 71.9 - - + +
63A LEU* 3.0 9.7 + - + +
64A TYR* 2.8 59.9 + - + +
102A CYS* 4.9 1.6 - - + -
106A ASP* 3.5 46.8 + - + +
109A LYS* 4.0 15.0 - - + -
110A ILE* 4.0 19.3 - - + -
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.6 9.0 - - + -
19A PRO* 3.9 23.8 - - + -
20A PRO* 5.9 0.2 - - + -
21A ILE* 4.0 22.9 - - + +
26A MET* 3.9 3.0 - - + +
57A GLU 3.3 24.9 - - - +
58A TYR* 3.4 18.6 - - + +
60A VAL* 1.4 91.9 - - + +
62A GLY* 1.3 60.6 + - - +
64A TYR* 3.1 14.2 + - + +
65A VAL* 3.0 27.7 + - - +
106A ASP* 5.4 0.4 - - - +
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.9 0.2 - - - -
47A VAL* 4.4 2.0 - - - +
50A PHE* 4.3 12.9 - - - -
51A ILE* 3.8 23.6 - - - +
58A TYR 2.9 18.4 + - - -
59A LYS 3.0 4.6 + - - -
61A PRO* 1.3 71.5 - - - +
63A LEU* 1.3 61.9 + - - +
65A VAL* 3.1 19.4 + - - +
66A ILE* 3.1 16.1 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS 2.9 12.2 + - - +
60A VAL* 3.0 11.0 + - + +
62A GLY* 1.3 75.3 - - - +
64A TYR* 1.3 60.5 + - + +
66A ILE* 3.0 10.9 + - + +
67A ASP* 2.8 26.0 + - - +
96A PHE* 3.7 14.8 - - + -
99A LEU* 4.0 18.9 - - + +
109A LYS 4.8 0.4 - - - +
110A ILE* 3.9 36.6 - - + -
113A VAL* 3.8 33.7 - - + -
117A TRP* 3.6 32.5 - - + -
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 6.2 3.6 - - + -
21A ILE* 6.2 2.9 - - + -
26A MET* 3.6 16.8 - - + -
60A VAL* 2.8 46.7 + - + +
61A PRO* 3.1 12.8 + - + +
63A LEU* 1.3 74.8 - - + +
65A VAL* 1.3 58.3 + - - +
67A ASP* 3.7 4.9 - - + +
68A SER* 2.8 32.4 + - - -
109A LYS* 3.9 20.9 + - + +
112A ARG* 4.5 5.9 + - - -
113A VAL* 3.7 30.3 - - + -
1Y TYR* 3.7 36.6 - + + -
3Y PRO* 3.7 23.8 - - + +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 20.9 - - + -
14A LEU* 4.2 10.8 - - + -
26A MET* 3.6 23.1 - - + -
29A ILE* 3.8 21.1 - - + -
30A THR* 5.7 0.2 - - - -
47A VAL* 4.0 17.7 - - + -
61A PRO 3.0 19.6 + - - +
62A GLY* 3.1 10.5 + - - +
64A TYR* 1.3 73.2 - - - +
66A ILE* 1.3 67.2 + - - +
68A SER* 3.3 1.3 + - - -
69A ILE* 3.0 49.6 + - + +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.7 16.2 - - + -
51A ILE* 3.7 23.1 - - + -
62A GLY 3.1 9.9 + - - +
63A LEU* 3.0 18.9 + - + +
65A VAL* 1.3 75.8 - - - +
67A ASP* 1.3 65.5 + - - +
69A ILE* 3.8 0.5 - - - +
70A VAL* 2.9 29.5 + - + +
88A PHE* 3.8 45.3 - - + -
92A ILE* 6.1 2.5 - - + -
95A THR* 4.0 16.8 - - + -
96A PHE* 5.4 2.9 - - + -
99A LEU* 5.1 0.9 - - + -
117A TRP* 4.1 21.1 - - + -
123A PHE* 4.9 1.6 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 2.8 15.2 + - - +
64A TYR* 3.7 8.3 - - + +
66A ILE* 1.3 77.2 - - - +
68A SER* 1.3 55.9 + - - +
70A VAL* 3.9 1.7 - - - +
71A ARG* 2.9 47.9 + - - +
113A VAL* 4.2 9.7 - - + +
116A LEU* 5.9 1.2 - - - +
117A TRP* 2.8 40.4 + - + +
1Y TYR* 2.8 22.0 + - - -
3Y PRO* 3.5 28.5 - - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 4.0 13.3 + - - +
27A THR* 5.5 0.9 - - - -
30A THR* 2.5 29.9 + - - +
64A TYR 2.8 22.5 + - - -
65A VAL 3.9 2.7 - - - -
67A ASP* 1.3 73.1 - - - +
69A ILE* 1.3 57.7 + - - +
71A ARG* 4.0 2.1 - - - +
72A GLN* 2.9 31.9 + - - +
1Y TYR* 3.5 25.3 + - - -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.2 8.5 - - + -
29A ILE* 5.1 0.4 - - + -
30A THR* 4.0 17.9 - - + +
33A ALA* 3.6 28.9 - - + -
34A ILE* 4.1 3.6 - - + +
43A VAL* 4.4 3.8 - - + -
47A VAL* 4.3 11.2 - - + -
65A VAL* 3.0 40.6 + - + +
66A ILE 3.8 2.5 - - - +
68A SER* 1.3 75.5 - - - +
70A VAL* 1.3 58.7 + - - +
72A GLN* 3.8 0.9 - - - +
73A SER* 2.9 32.4 + - - -
84A PHE* 3.6 43.5 - - + -
88A PHE* 4.3 8.1 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 2.9 26.0 + - + +
67A ASP* 4.1 3.6 - - - +
69A ILE* 1.3 77.2 - - - +
71A ARG* 1.3 57.9 + - + +
73A SER* 3.8 4.0 - - - -
74A ARG* 2.9 38.9 + - - +
82A ASP* 4.3 1.5 - - - +
84A PHE* 4.2 2.9 - - + -
85A ALA* 3.7 26.5 - - + +
88A PHE* 3.8 28.3 - - + -
117A TRP* 5.7 0.4 - - - +
122A VAL* 3.3 33.7 - - + -
123A PHE* 4.5 4.7 - - + -
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 2.9 37.5 + - - +
68A SER* 4.2 3.1 - - - +
70A VAL* 1.3 73.6 - - + +
72A GLN* 1.3 63.5 + - - +
74A ARG* 3.4 15.8 + - - +
75A HIS* 3.0 24.4 + - - +
117A TRP* 4.9 2.0 - - - +
120A ASN* 3.3 40.7 + - - +
122A VAL* 3.5 26.3 - - - +
507A SO4 2.9 32.3 + - - -
1Y TYR* 5.6 0.9 - - - +
3Y PRO 5.8 1.6 + - - -
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 3.6 18.2 - - + -
31A LYS* 6.6 0.2 - - + -
34A ILE* 4.0 14.4 - - + -
68A SER* 2.9 23.0 + - - +
69A ILE 4.0 0.9 - - - +
71A ARG* 1.3 73.4 - - - +
73A SER* 1.3 57.9 - - - +
75A HIS* 3.3 19.4 + - - +
76A GLN* 2.9 64.6 + - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.9 9.4 - - - +
69A ILE 2.9 19.2 + - - -
70A VAL 3.8 1.3 - - - -
72A GLN* 1.3 77.6 - - - +
74A ARG* 1.3 56.5 + - - +
77A PHE* 2.8 41.9 + - - +
78A GLY 3.7 0.3 + - - +
82A ASP* 2.6 27.1 + - - -
84A PHE* 3.6 15.4 - - - -
400A NH4 2.9 22.5 + - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 2.9 39.9 + - - +
71A ARG* 3.8 14.3 - - - +
73A SER* 1.3 75.5 - - - +
75A HIS* 1.3 58.5 + - - +
78A GLY* 2.9 36.4 + - - -
79A GLN* 3.4 57.9 + - + +
80A GLU* 5.1 2.6 + - - -
82A ASP* 3.7 22.5 + - + +
85A ALA* 5.4 1.2 - - - +
120A ASN 3.2 23.8 + - - -
121A ASN* 3.6 18.1 + - - +
122A VAL* 3.9 24.7 + - - +
503A SO4 3.9 3.6 + - - -
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG 3.0 17.6 + - - +
72A GLN* 3.6 24.7 - - - +
74A ARG* 1.3 80.3 - - - +
76A GLN* 1.3 64.9 + - + +
78A GLY* 4.3 2.4 + - - -
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.5 33.1 - - - +
72A GLN* 2.9 41.5 + - - +
75A HIS* 1.3 81.9 - - + +
77A PHE* 1.3 82.2 + - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.8 36.1 - - + -
37A ILE* 3.8 30.7 - - + -
73A SER* 2.8 28.5 + - - +
76A GLN* 1.3 94.9 - - + +
78A GLY* 1.3 62.1 + - - +
81A LYS* 3.4 25.0 - - + +
84A PHE* 5.6 0.2 - + - -
400A NH4 3.4 22.7 - - - +
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG 2.9 16.2 + - - +
75A HIS 4.3 2.3 + - - -
76A GLN 3.7 1.0 - - - -
77A PHE* 1.3 79.3 - - - +
79A GLN* 1.3 66.4 + - - -
80A GLU 3.2 3.1 - - - -
81A LYS* 3.2 2.8 + - - -
82A ASP* 3.1 24.3 + - - +
503A SO4 3.3 19.7 - - - -
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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