Contacts of the helix formed by residues 65 - 84 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG 5.9 0.2 - - - +
62B GLN 4.7 8.5 - - - +
63B LEU 3.5 2.4 + - - -
64B GLN* 1.3 83.2 - - - +
66B VAL* 1.3 57.1 + - - +
67B ASN* 4.0 10.3 + - - +
68B ASN* 2.8 39.8 + - - +
69B TYR* 2.9 17.6 + - - -
144B ARG* 5.4 5.4 - - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 1.3 72.2 - - - +
67B ASN* 1.3 57.7 + - - +
69B TYR* 2.9 27.5 + - - +
70B PHE* 3.0 36.0 + - + -
144B ARG* 3.4 58.7 - - + +
145B THR 4.2 9.2 - - - +
146B THR* 4.3 19.5 - - + +
149B ALA* 3.8 10.8 - - + -
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 3.2 9.5 + - - +
66B VAL* 1.3 74.3 - - - +
68B ASN* 1.3 63.2 + - - +
70B PHE* 3.4 11.9 + - - +
71B LEU* 2.9 33.9 + - + +
129B ASP* 3.3 8.9 - - - +
130B ARG* 5.3 4.2 - - - +
133B CYS* 5.4 1.4 - - - -
144B ARG* 2.4 41.9 + - - +
395B GLU* 5.1 5.5 + - - -
398B VAL* 4.3 27.8 - - + +
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.2 14.0 - - + +
62B GLN 5.0 0.2 + - - -
63B LEU* 2.9 60.0 + - - +
65B THR* 2.8 19.5 + - - +
67B ASN* 1.3 78.6 - - - +
69B TYR* 1.3 60.4 + - - +
71B LEU* 3.5 22.5 - - - +
72B PHE* 2.9 26.5 + - - +
460B PHE* 3.7 15.7 - - - -
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 5.6 2.7 - - + -
58B LYS* 6.2 2.2 - - - -
64B GLN* 4.2 23.6 + - + +
65B THR 2.9 36.2 + - - -
66B VAL* 2.9 13.5 + - + +
68B ASN* 1.3 74.9 - - - +
70B PHE* 1.3 60.2 + - - +
72B PHE* 3.1 9.0 + + + +
73B SER 2.9 23.6 + - - -
146B THR* 4.2 31.3 - - + +
149B ALA* 4.9 12.1 - - + -
153B ILE* 3.8 17.2 - - + +
1203B OLA 4.3 22.2 - - - -
1204B OLA 4.3 2.0 - - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.0 34.5 + - + -
67B ASN* 3.5 12.8 - - - +
69B TYR* 1.3 75.9 - - - +
71B LEU* 1.3 63.6 + - - +
73B SER* 3.1 2.6 + - - -
74B LEU 3.0 18.9 + - - -
122B ASN* 3.0 16.7 + - - +
125B ILE* 3.7 31.0 - - + -
126B ILE* 3.8 24.2 - - + -
129B ASP* 3.6 39.0 - - + -
149B ALA* 3.7 35.7 - - + -
152B MET* 4.3 7.6 - - + -
153B ILE* 4.0 16.6 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.4 7.2 - - + -
67B ASN* 2.9 21.6 + - + +
68B ASN* 3.5 26.9 - - - +
70B PHE* 1.3 76.2 - - - +
72B PHE* 1.3 57.3 + - - +
74B LEU* 3.5 4.3 + - - +
75B ALA* 2.9 28.9 + - - +
126B ILE* 4.1 19.3 - - + -
401B THR* 5.3 6.7 - - + -
402B ILE* 6.3 1.6 - - + -
405B ILE* 4.1 12.3 - - + -
453B TYR* 3.2 48.9 + - + +
460B PHE* 4.7 11.2 - - + -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.5 56.8 - - + -
57B ILE* 3.9 19.3 - - + +
58B LYS* 4.3 26.0 - - + -
68B ASN 2.9 20.6 + - - +
69B TYR* 3.1 11.0 + + + +
71B LEU* 1.3 75.1 - - - +
73B SER* 1.3 59.4 + - - +
75B ALA* 3.1 5.9 + - - +
76B CYS* 2.9 49.4 + - - -
1203B OLA 5.6 0.4 - - - -
1204B OLA 3.4 21.8 - - - -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR 2.9 10.8 + - - -
70B PHE 3.4 7.0 - - - -
72B PHE* 1.3 75.9 - - - +
74B LEU* 1.3 63.8 + - - +
76B CYS* 3.0 5.4 + - - +
77B ALA* 3.0 21.9 + - - +
122B ASN* 2.7 25.8 + - - -
153B ILE* 3.3 14.7 - - - +
157B TRP* 2.9 26.0 + - - -
1204B OLA 3.6 23.2 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE 3.0 7.8 + - - +
71B LEU* 3.7 8.5 - - - +
73B SER* 1.3 75.7 - - - +
75B ALA* 1.3 56.7 + - - +
77B ALA* 3.3 4.7 + - - +
78B ASP* 2.9 45.6 + - - +
119B SER* 4.0 39.3 - - - +
122B ASN* 3.6 18.6 - - + +
123B LEU* 3.8 26.2 - - + -
126B ILE* 4.4 8.5 - - + -
405B ILE* 4.1 8.3 - - + -
445B ASN* 5.9 0.9 - - - +
449B ASN* 3.9 16.6 - - - +
453B TYR* 3.5 19.1 - - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 3.5 24.2 - - - +
53B VAL* 4.1 18.4 - - + -
54B MET* 3.8 20.6 - - + +
71B LEU 2.9 17.9 + - - +
72B PHE* 3.1 7.2 + - - +
74B LEU* 1.3 74.4 - - - +
76B CYS* 1.3 60.4 + - - +
78B ASP* 4.3 1.1 - - - -
79B LEU* 2.9 29.1 + - - +
453B TYR* 4.9 3.6 + - + -
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Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.7 22.9 - - - -
72B PHE* 2.9 49.2 + - - -
73B SER 3.0 7.8 + - - +
75B ALA* 1.3 73.8 - - - +
77B ALA* 1.3 65.3 + - - +
79B LEU* 3.1 5.3 + - - +
80B ILE* 2.9 32.0 + - + +
157B TRP* 4.5 0.9 - - + -
1204B OLA 4.1 31.6 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER 3.0 11.4 + - - +
74B LEU* 3.6 10.1 - - - +
76B CYS* 1.3 77.3 - - - +
78B ASP* 1.3 57.5 + - - +
80B ILE* 3.2 2.3 + - - -
81B ILE* 2.9 34.0 + - - +
115B VAL* 3.5 21.0 - - + +
118B ALA 5.3 0.4 - - - -
119B SER* 3.3 29.4 - - - +
122B ASN* 6.5 0.4 - - + -
157B TRP* 3.9 16.9 - - + -
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 3.5 11.1 - - - +
50B ASN* 3.2 29.0 - - - +
74B LEU* 2.9 27.0 + - - +
75B ALA* 4.3 0.5 - - - -
76B CYS 3.3 0.2 - - - -
77B ALA* 1.3 76.8 - - - +
79B LEU* 1.3 55.3 + - - +
81B ILE* 3.8 1.7 - - - +
82B GLY 2.9 22.9 + - - -
119B SER* 4.5 9.5 + - - -
445B ASN* 4.7 2.3 - - - +
446B SER* 2.9 35.8 + - - -
449B ASN* 2.9 33.1 + - - +
453B TYR* 5.3 0.7 + - - -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 5.3 0.7 - - - -
47B VAL* 3.9 27.8 - - + +
50B ASN* 4.0 9.8 - - + +
51B ILE* 3.8 29.2 - - + -
54B MET* 3.7 28.3 - - + -
75B ALA 2.9 19.2 + - - +
76B CYS* 3.1 6.0 + - - +
78B ASP* 1.3 73.9 - - - +
80B ILE* 1.3 63.0 + - + +
82B GLY* 3.3 1.4 + - - -
83B ALA* 2.9 38.4 + - + +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B CYS* 2.9 19.7 + - + +
77B ALA 3.2 5.8 + - - +
79B LEU* 1.3 77.7 - - + +
81B ILE* 1.3 63.1 + - - +
83B ALA* 4.7 0.7 - - - -
84B PHE* 3.1 40.0 + - + +
85B SER* 3.7 2.2 + - - +
111B LEU* 3.8 34.1 - - + -
115B VAL* 3.9 19.1 - - + -
157B TRP* 4.2 7.0 - - + -
1204B OLA 3.7 40.8 - - + -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA 2.9 20.8 + - - +
78B ASP* 3.8 0.7 - - - +
80B ILE* 1.3 76.2 - - + +
82B GLY* 1.3 59.9 + - - +
85B SER* 3.2 15.7 + - - +
86B MET* 3.1 27.5 + - + +
112B ASP* 5.5 0.9 - - - +
115B VAL* 3.7 19.3 - - + -
116B SER* 3.9 22.0 - - - +
119B SER* 4.3 13.0 - - - +
413B TRP* 5.6 5.8 - - + -
442B CYS 6.0 1.1 - - - +
443B TYR* 3.5 38.8 - - + +
446B SER* 3.5 28.7 - - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER* 2.9 28.6 + - - -
46B THR* 3.7 20.2 - - - -
47B VAL* 3.8 8.1 - - - +
78B ASP 2.9 17.7 + - - -
79B LEU 3.3 1.1 + - - -
81B ILE* 1.3 77.1 - - - +
83B ALA* 1.3 58.6 + - - +
86B MET* 3.8 16.4 - - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.9 15.9 - - + -
79B LEU* 2.9 23.2 + - + +
82B GLY* 1.3 78.4 - - - +
84B PHE* 1.3 79.1 + - + +
87B ASN* 2.5 30.2 + - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.1 33.3 + - + +
83B ALA* 1.3 92.4 - - + +
85B SER* 1.3 67.6 + - - +
86B MET 3.4 0.6 + - - -
87B ASN* 3.5 2.3 + - - +
88B LEU* 3.1 40.4 + - + +
111B LEU* 4.0 22.9 - - + -
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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
------------------------------------------------------------
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