Contacts of the helix formed by residues 65 - 84 (chain A) in PDB entry 5DSG
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 THR 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN 4.6 13.7 - - - +
63A LEU 3.5 2.2 - - - -
64A GLN* 1.3 80.0 - - - +
66A VAL* 1.3 57.2 + - - +
67A ASN* 4.0 9.2 + - - +
68A ASN* 2.8 40.6 + - - +
69A TYR* 2.9 18.8 + - - -
144A ARG* 5.4 7.4 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 1.3 72.7 - - - +
67A ASN* 1.3 58.4 + - - +
69A TYR* 2.9 29.1 + - - +
70A PHE* 3.0 36.5 + - + -
129A ASP* 4.6 0.2 - - - +
144A ARG* 3.7 51.7 - - + +
145A THR 4.0 15.0 - - - +
146A THR* 4.4 14.3 - - + +
149A ALA* 3.6 15.5 - - + -
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.2 9.2 + - - +
66A VAL* 1.3 75.0 - - - +
68A ASN* 1.3 62.7 + - - +
70A PHE* 3.3 12.7 + - - +
71A LEU* 2.9 33.6 + - + +
126A ILE* 5.4 2.3 - - + +
129A ASP* 2.9 14.1 - - - +
130A ARG* 3.0 35.5 - - - +
144A ARG* 2.6 31.6 + - - +
398A VAL* 4.5 16.5 - - + +
402A ILE* 5.5 5.6 - - + -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.3 14.9 - - + +
63A LEU* 2.7 59.5 + - - +
64A GLN* 4.8 0.4 - - - -
65A THR* 2.8 21.0 + - - +
67A ASN* 1.3 77.4 - - - +
69A TYR* 1.3 61.7 + - - +
71A LEU* 3.5 22.5 - - - +
72A PHE* 2.9 26.9 + - - +
460A PHE* 3.8 15.1 - - - -
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Residues in contact with TYR 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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64A GLN* 4.2 9.8 + - - +
65A THR* 2.9 36.2 + - - -
66A VAL* 2.9 13.8 + - + +
68A ASN* 1.3 78.5 - - - +
70A PHE* 1.3 63.3 + - - +
72A PHE* 3.1 7.8 + - - +
73A SER 3.0 18.2 + - - -
146A THR* 4.0 28.3 - - + +
149A ALA* 4.6 9.0 - - + -
153A ILE* 3.7 18.3 - - + +
1206A OLC 3.4 56.1 + - + +
1202B OLC 3.4 36.5 + - - -
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.0 38.6 + - + -
67A ASN* 3.4 15.9 - - - +
69A TYR* 1.3 76.1 - - - +
71A LEU* 1.3 57.3 + - - +
73A SER* 3.1 2.6 + - - -
74A LEU 2.9 14.4 + - - -
122A ASN* 2.9 26.9 + - - +
125A ILE* 3.6 31.0 - - + -
126A ILE* 3.7 32.5 - - + -
129A ASP* 3.9 21.3 - - + -
149A ALA* 3.6 35.4 - - + -
152A MET* 4.5 3.8 - - + -
153A ILE* 3.7 17.7 - - + -
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Residues in contact with LEU 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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53A VAL* 4.9 0.6 - - + +
57A ILE* 4.2 7.4 - - + +
67A ASN* 2.9 21.1 + - + +
68A ASN* 3.5 28.0 - - - +
69A TYR 3.3 0.2 - - - -
70A PHE* 1.3 75.4 - - - +
72A PHE* 1.3 56.1 + - - +
74A LEU* 3.5 7.6 + - + +
75A ALA* 2.9 29.1 + - - +
126A ILE* 4.0 21.8 - - + -
398A VAL* 6.3 2.7 - - + -
401A THR* 5.1 5.6 - - + -
402A ILE* 4.9 17.0 - - + -
405A ILE* 5.4 4.7 - - + -
453A TYR* 3.2 45.1 + - + +
460A PHE* 4.6 8.5 - - + -
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Residues in contact with PHE 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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54A MET* 3.5 44.2 - - + -
57A ILE* 3.7 25.7 - - + +
58A LYS* 3.5 35.0 - - + -
68A ASN 2.9 20.7 + - - +
69A TYR* 3.3 8.3 - - - +
70A PHE 3.1 0.2 - - - -
71A LEU* 1.3 74.7 - - - +
73A SER* 1.3 59.2 + - - +
75A ALA* 3.2 5.0 + - - +
76A CYS* 2.9 48.0 + - - -
1206A OLC 3.5 40.8 - - + +
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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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69A TYR 3.0 11.8 + - - -
70A PHE 3.3 8.5 - - - -
72A PHE* 1.3 77.5 - - - +
74A LEU* 1.3 63.4 + - - +
76A CYS* 3.0 5.4 + - - +
77A ALA* 3.0 22.1 + - - +
122A ASN* 2.9 22.4 + - - -
153A ILE* 3.3 13.4 - - - +
157A TRP* 2.9 27.1 + - - -
1206A OLC 3.7 21.1 - - - +
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Residues in contact with LEU 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 PHE 2.9 12.3 + - - +
71A LEU* 3.7 10.8 - - + +
72A PHE 3.3 0.2 - - - -
73A SER* 1.3 76.8 - - - +
75A ALA* 1.3 58.2 + - - +
77A ALA* 3.3 4.9 + - - +
78A ASP* 2.9 44.7 + - - +
119A SER* 3.9 41.7 - - - +
122A ASN* 3.8 11.3 - - + +
123A LEU* 3.7 27.1 - - + -
126A ILE* 4.6 9.0 - - + -
405A ILE* 3.8 18.2 - - + -
445A ASN* 6.0 0.9 - - - +
449A ASN* 4.2 6.7 - - - +
453A TYR* 4.1 13.0 - - - +
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Residues in contact with ALA 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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50A ASN* 3.5 23.2 - - - +
53A VAL* 4.0 18.8 - - + -
54A MET* 3.8 21.3 - - + +
71A LEU 2.9 18.1 + - - +
72A PHE* 3.2 7.4 + - - +
74A LEU* 1.3 73.8 - - - +
76A CYS* 1.3 60.2 + - - +
78A ASP* 4.4 1.1 - - - -
79A LEU* 2.9 28.9 + - - +
453A TYR* 5.1 3.8 + - + -
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Residues in contact with CYS 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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54A MET* 3.7 17.7 - - - -
72A PHE* 2.9 51.1 + - - -
73A SER* 3.0 8.3 + - - +
75A ALA* 1.3 74.9 - - - +
77A ALA* 1.3 65.1 + - - +
79A LEU* 3.1 8.6 + - - +
80A ILE* 2.9 30.7 + - + +
157A TRP* 4.8 2.7 - - + -
1206A OLC 4.2 29.8 - - + -
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Residues in contact with ALA 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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73A SER 3.0 11.8 + - - +
74A LEU* 3.5 11.0 - - - +
76A CYS* 1.3 76.3 - - - +
78A ASP* 1.3 57.2 + - - +
80A ILE* 3.2 2.8 + - - +
81A ILE* 2.9 33.2 + - - +
115A VAL* 3.5 19.4 - - + +
119A SER* 3.2 28.3 - - - +
157A TRP* 3.9 17.8 - - + -
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Residues in contact with ASP 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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46A THR* 3.6 11.1 - - - +
50A ASN* 3.1 28.6 - - - +
74A LEU* 2.9 28.3 + - - +
75A ALA* 3.8 0.9 - - - +
77A ALA* 1.3 76.5 - - - +
79A LEU* 1.3 56.6 + - - +
81A ILE* 3.7 5.2 - - - +
82A GLY 2.9 22.7 + - - -
119A SER* 4.6 6.6 + - - -
445A ASN* 4.6 2.8 - - - +
446A SER* 2.9 29.1 + - - -
449A ASN* 2.6 37.7 + - - +
453A TYR* 5.7 0.7 + - - -
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Residues in contact with LEU 79 (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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46A THR* 5.3 0.9 - - - -
47A VAL* 3.8 44.0 - - + +
50A ASN* 4.0 9.8 - - + +
51A ILE* 4.0 13.5 - - + -
54A MET* 3.9 26.0 - - + -
75A ALA 2.9 18.5 + - - +
76A CYS* 3.4 6.3 - - - +
78A ASP* 1.3 74.5 - - - +
80A ILE* 1.3 63.0 + - + +
82A GLY* 3.2 1.4 + - - -
83A ALA* 2.9 34.2 + - + +
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Residues in contact with ILE 80 (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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76A CYS* 2.9 19.9 + - + +
77A ALA 3.5 5.8 - - - +
79A LEU* 1.3 78.4 - - + +
81A ILE* 1.3 63.9 + - - +
83A ALA* 4.8 0.7 - - - -
84A PHE* 3.1 38.8 + - + +
85A SER* 3.8 1.9 + - - +
111A LEU* 3.7 33.0 - - + -
115A VAL* 3.9 18.2 - - + -
157A TRP* 4.3 8.1 - - + -
1206A OLC 3.8 35.9 - - + -
1209A OLA 4.7 11.4 - - + -
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Residues in contact with ILE 81 (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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77A ALA 2.9 22.5 + - - +
78A ASP* 3.7 2.0 - - - +
80A ILE* 1.3 77.3 - - - +
82A GLY* 1.3 62.7 + - - +
85A SER* 3.2 14.2 + - - +
86A MET* 3.2 24.3 + - + +
112A ASP* 5.6 1.6 - - - +
115A VAL* 3.7 20.9 - - + -
116A SER* 4.1 17.9 - - - +
119A SER* 4.5 10.3 - - - +
413A TRP* 5.6 6.1 - - + -
442A CYS 6.0 0.9 - - - +
443A TYR* 3.6 40.2 - - + +
446A SER* 3.4 30.5 - - - +
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Residues in contact with GLY 82 (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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43A SER* 2.9 27.7 + - - +
46A THR* 3.7 25.8 - - - -
47A VAL* 3.8 8.5 - - - +
78A ASP 2.9 12.2 + - - -
79A LEU 3.2 2.0 + - - -
81A ILE* 1.3 77.8 - - - +
83A ALA* 1.3 59.0 + - - +
86A MET* 4.0 16.0 - - - +
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Residues in contact with ALA 83 (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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43A SER* 4.8 0.2 - - - -
47A VAL* 3.9 15.2 - - + +
79A LEU* 2.9 22.6 + - + +
82A GLY* 1.3 79.2 - - - +
84A PHE* 1.3 78.8 + - + +
87A ASN* 2.6 30.1 + - - +
1203A OLA 3.7 6.8 - - - +
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Residues in contact with PHE 84 (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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80A ILE* 3.1 26.8 + - + +
83A ALA* 1.3 92.4 - - + +
85A SER* 1.3 67.8 + - - +
86A MET 3.4 0.8 + - - -
87A ASN* 3.4 2.6 + - - +
88A LEU* 3.1 36.6 + - + +
111A LEU* 3.9 18.4 - - + -
1202A OLA 5.8 3.6 - - + -
1203A OLA 4.0 23.6 - - + -
1209A OLA 3.8 55.0 - - + -
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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