Contacts of the helix formed by residues 66 - 86 (chain A) in PDB entry 3D4S
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 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG 3.9 18.6 - - - +
64A LEU* 3.0 3.1 + - - -
65A GLN* 1.3 78.8 - - - +
67A VAL* 1.3 65.2 + - - +
68A THR* 4.0 7.1 + - - -
69A ASN* 3.1 36.1 + - - +
70A TYR* 3.1 17.7 + - - -
147A LYS* 5.1 2.7 - - - +
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Residues in contact with VAL 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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66A THR* 1.3 71.6 - - - +
68A THR* 1.3 60.7 + - - +
70A TYR* 3.2 20.8 + - - +
71A PHE* 3.2 32.4 - - + -
130A ASP* 3.9 1.6 - - - +
143A SER* 3.4 31.9 - - - +
145A LEU* 3.4 26.2 - - + +
146A THR 4.4 11.4 - - - +
147A LYS* 4.5 12.2 - - + +
150A ALA* 3.9 14.8 - - + -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.3 6.9 + - - -
67A VAL* 1.3 77.1 - - - +
69A ASN* 1.3 62.3 + - - +
70A TYR 3.2 0.2 - - - -
71A PHE* 3.2 16.1 + - - +
72A ILE* 3.1 28.7 + - + +
127A ILE* 4.9 7.6 - - + +
130A ASP* 4.3 1.4 + - - -
131A ARG* 3.4 33.7 + - - -
275A LEU* 3.8 38.8 - - + -
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.3 13.2 - - + +
64A LEU* 2.9 47.2 + - - +
66A THR* 3.1 16.6 + - - +
68A THR* 1.3 78.4 - - - +
70A TYR* 1.3 56.4 + - - +
72A ILE* 3.5 22.1 - - - +
73A THR* 2.8 35.7 + - - -
332A PHE* 3.5 28.1 - - - -
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Residues in contact with TYR 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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58A ILE* 4.9 7.0 - - + -
65A GLN* 4.1 32.7 - - + +
66A THR 3.1 25.8 + - - -
67A VAL* 3.4 14.4 - - - +
68A THR 3.2 0.6 - - - -
69A ASN* 1.3 78.2 - - - +
71A PHE* 1.3 62.2 + - - +
73A THR* 3.4 8.9 + - - -
74A SER 3.2 14.0 + - - -
147A LYS* 4.0 29.3 + - + +
150A ALA* 4.7 8.7 - - + -
151A ARG* 2.9 50.4 + - + -
154A ILE* 3.2 24.2 - - + +
402A CLR 3.4 29.6 + - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.2 30.3 - - + -
68A THR* 3.2 9.0 + - - +
70A TYR* 1.3 75.2 - - - +
72A ILE* 1.3 59.2 + - - +
74A SER* 3.2 4.5 + - - -
75A LEU* 2.8 24.5 + - - +
123A THR* 3.3 20.8 - - + +
126A VAL* 3.7 28.0 - - + -
127A ILE* 3.5 33.2 - - + -
130A ASP* 3.6 27.6 - - + -
145A LEU* 4.0 20.2 - - + -
150A ALA* 4.0 12.1 - - + -
153A ILE* 4.3 6.7 - - + -
154A ILE* 3.7 25.8 - - + -
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Residues in contact with ILE 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 VAL* 4.0 4.7 - - + -
58A ILE* 3.9 16.8 - - + -
68A THR* 3.1 13.0 + - + +
69A ASN* 3.5 29.8 - - - +
70A TYR 3.3 0.2 - - - -
71A PHE* 1.3 74.3 - - - +
73A THR* 1.3 54.8 + - - +
75A LEU* 3.3 9.0 + - + +
76A ALA* 2.7 32.6 + - - +
127A ILE* 4.7 7.2 - - + -
275A LEU* 4.0 23.6 - - + -
326A TYR* 3.2 53.1 + - + +
332A PHE* 4.6 6.3 - - + -
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Residues in contact with THR 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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55A ILE* 4.4 10.4 - - + +
58A ILE* 3.4 26.4 - - - +
69A ASN 2.8 19.1 + - - -
70A TYR* 3.4 12.6 - - - -
72A ILE* 1.3 76.9 - - - +
74A SER* 1.3 52.5 + - - +
76A ALA* 3.1 6.6 + - - +
77A CYS* 2.8 39.8 + - - -
402A CLR 3.6 16.6 - - + -
403A CLR 3.6 36.6 - - + -
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Residues in contact with SER 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 TYR 3.2 8.4 + - - -
71A PHE* 3.2 13.2 + - - -
73A THR* 1.3 78.7 - - - +
75A LEU* 1.3 61.7 + - - +
77A CYS* 3.6 0.7 + - - +
78A ALA* 3.2 17.0 + - - +
119A ALA 6.1 0.2 - - - -
123A THR* 3.4 16.4 + - - -
154A ILE* 3.5 26.4 - - - +
158A TRP* 2.9 34.5 + - - -
402A CLR 3.8 13.2 - - - +
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Residues in contact with LEU 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 PHE 2.8 15.0 + - - +
72A ILE* 3.5 8.5 - - + +
74A SER* 1.3 77.4 - - - +
76A ALA* 1.3 61.0 + - - +
78A ALA* 3.4 6.7 + - - +
79A ASP* 3.2 29.0 + - - +
120A SER* 3.7 43.1 - - - +
123A THR* 4.4 7.8 - - + +
124A LEU* 3.7 29.2 - - + -
127A ILE* 4.8 7.0 - - + -
278A ILE* 3.8 18.2 - - + -
282A PHE* 5.6 1.6 - - + -
322A ASN* 3.8 15.7 - - - +
326A TYR* 3.8 15.7 - - - +
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Residues in contact with ALA 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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51A ASN* 3.5 27.3 - - - +
54A VAL* 4.0 18.4 - - + -
55A ILE* 3.8 20.2 - - + -
72A ILE* 2.7 20.5 + - + +
73A THR* 3.1 5.8 + - - +
75A LEU* 1.3 71.6 - - - +
77A CYS* 1.3 59.5 + - - +
79A ASP* 3.4 2.0 + - - -
80A LEU* 2.8 27.7 + - - +
322A ASN* 5.8 1.1 - - - +
326A TYR* 5.9 2.0 - - + -
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Residues in contact with CYS 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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55A ILE* 3.6 18.2 - - - -
73A THR* 2.8 24.0 + - - +
74A SER 3.9 0.9 - - - +
76A ALA* 1.3 73.6 - - - +
78A ALA* 1.3 60.8 + - - +
80A LEU* 3.2 8.2 + - - +
81A VAL* 2.9 37.3 + - + +
158A TRP* 4.7 0.9 - - - -
402A CLR 3.5 35.9 - - + -
403A CLR 3.7 38.1 - - + -
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Residues in contact with ALA 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 SER 3.2 12.1 + - - +
75A LEU* 3.5 8.1 - - - +
76A ALA 3.3 0.4 - - - -
77A CYS* 1.3 78.0 - - - +
79A ASP* 1.3 58.6 + - - +
81A VAL* 4.8 0.2 - - - -
82A MET* 3.2 22.7 + - - +
116A CYS* 3.3 26.2 - - - +
119A ALA 5.2 0.2 - - - -
120A SER* 3.4 27.4 - - - +
158A TRP* 3.7 25.0 - - + -
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Residues in contact with ASP 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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47A ILE* 3.1 12.5 - - - +
51A ASN* 3.2 29.9 - - - +
75A LEU* 3.2 15.2 + - - +
76A ALA* 3.7 2.1 - - - +
77A CYS 3.2 0.4 - - - -
78A ALA* 1.3 77.6 - - - +
80A LEU* 1.3 58.3 + - - +
82A MET* 3.3 7.2 - - - +
83A GLY 3.0 22.2 + - - -
120A SER* 3.9 12.1 + - - -
282A PHE* 6.0 0.7 - - - -
318A ASN* 6.0 0.3 + - - -
319A SER* 3.5 30.1 + - - +
322A ASN* 3.1 28.2 + - - -
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Residues in contact with LEU 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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47A ILE* 5.0 1.3 - - - -
48A VAL* 3.9 23.3 - - + +
51A ASN* 4.0 6.7 - - + +
52A VAL* 3.6 32.8 - - + +
55A ILE* 3.8 22.9 - - + -
76A ALA 2.8 17.3 + - - +
77A CYS* 3.2 7.1 + - - +
79A ASP* 1.3 75.0 - - - +
81A VAL* 1.3 59.0 + - - +
83A GLY* 3.4 0.9 + - - -
84A LEU* 3.0 49.3 + - + +
403A CLR 3.6 26.2 - - + -
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Residues in contact with VAL 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 CYS* 2.9 22.3 + - + +
78A ALA* 5.0 0.4 - - - -
80A LEU* 1.3 74.7 - - - +
82A MET* 1.3 59.9 + - - +
85A ALA* 2.9 27.9 + - + +
86A VAL* 3.5 3.3 + - - +
112A ILE* 3.6 26.9 - - + -
116A CYS* 3.8 13.9 - - - -
158A TRP* 5.4 1.3 - - + -
402A CLR 4.5 27.6 - - + -
403A CLR 3.7 49.6 - - + -
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Residues in contact with MET 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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78A ALA 3.2 14.1 + - - +
79A ASP* 3.3 10.1 - - - +
80A LEU 3.2 0.2 - - - -
81A VAL* 1.3 77.2 - - - +
83A GLY* 1.3 57.4 + - - +
86A VAL* 3.2 23.4 + - + +
87A VAL* 2.8 35.9 + - + +
113A ASP* 3.2 24.5 - - - +
116A CYS* 3.7 21.7 - - - -
117A VAL* 3.8 21.5 - - + -
286A TRP* 4.1 7.2 - - + -
316A TYR* 3.4 28.3 - - + +
319A SER* 3.4 24.7 - - - +
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Residues in contact with GLY 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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44A VAL* 3.3 28.8 - - - +
47A ILE* 3.8 28.9 - - - +
48A VAL* 3.7 11.4 - - - +
79A ASP 3.0 11.3 + - - -
80A LEU 3.4 2.7 + - - -
82A MET* 1.3 77.9 - - - +
84A LEU* 1.3 55.7 + - - +
87A VAL* 4.6 3.4 - - - -
88A PRO* 3.3 8.6 - - - +
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Residues in contact with LEU 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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44A VAL* 6.2 0.7 - - + -
48A VAL* 3.6 29.4 - - + -
80A LEU* 3.0 39.3 + - + +
83A GLY* 1.3 78.0 - - - +
85A ALA* 1.3 59.8 + - - +
86A VAL 3.8 0.2 - - - -
88A PRO* 3.5 16.4 - - - +
89A PHE* 4.3 5.9 - - - -
403A CLR 3.9 27.8 - - + -
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Residues in contact with ALA 85 (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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81A VAL* 2.9 23.4 + - + +
84A LEU* 1.3 73.4 - - - +
86A VAL* 1.3 59.3 + - - +
88A PRO* 4.3 0.2 - - - -
89A PHE* 3.3 24.6 - - + -
105A TRP* 3.8 10.5 - - + -
109A TRP* 3.3 12.0 - - - -
112A ILE* 4.5 12.7 - - + +
403A CLR 3.5 33.2 - - + -
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Residues in contact with VAL 86 (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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81A VAL 3.9 5.8 - - - +
82A MET* 3.2 23.7 + - - +
84A LEU 3.8 0.4 - - - -
85A ALA* 1.3 82.0 - - - +
87A VAL* 1.3 68.4 + - - +
88A PRO* 3.4 1.1 - - - -
89A PHE 3.4 1.7 + - - -
90A GLY* 3.0 10.7 + - - -
109A TRP* 2.9 28.1 + - - +
112A ILE* 3.7 26.7 - - + -
113A ASP* 3.6 43.7 - - + +
116A CYS* 4.9 0.2 - - - -
316A TYR* 3.7 19.5 - - + +
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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