Contacts of the helix formed by residues 65 - 79 (chain H) in PDB entry 2DYS
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 PRO 65 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LYS* 3.8 5.4 - - + -
100B MET* 3.9 28.3 - - + -
109B GLU* 3.4 9.9 - - - +
179B LEU* 3.8 24.2 - - + -
63H LEU 3.6 6.1 - - - +
64H CYS* 1.3 88.4 - - + +
66H ILE* 1.3 67.7 + - - +
67H SER* 4.3 2.5 - - - +
68H TRP* 3.0 57.8 + - + +
69H VAL* 3.2 10.4 + - - +
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Residues in contact with ILE 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 4.6 0.9 - - - +
109B GLU* 2.9 37.3 + - + +
111B THR* 4.5 15.9 - - + -
115B ASP* 4.8 13.2 - - + +
116B LEU 5.6 0.4 - - - -
117B SER* 3.7 27.8 - - - +
64H CYS 3.4 2.5 + - - -
65H PRO* 1.3 70.7 - - - +
67H SER* 1.3 61.3 + - - +
69H VAL* 3.3 6.5 + - - +
70H SER* 2.8 37.0 + - - -
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Residues in contact with SER 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 4.6 1.4 + - - -
157B GLU* 3.2 36.0 + - - +
65H PRO* 4.3 3.8 - - - +
66H ILE* 1.3 77.9 - - - +
68H TRP* 1.3 74.7 + - - +
70H SER* 3.8 6.5 - - - -
71H THR* 2.9 34.6 + - - -
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Residues in contact with TRP 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B MET* 4.4 8.5 - - - +
155B SER* 4.0 11.4 + - - -
156B SER 5.3 1.4 + - - -
157B GLU* 5.9 0.2 - - - +
177B GLY* 3.7 41.0 - - - +
178B ARG 3.8 12.8 - - - -
179B LEU* 4.0 8.1 - - + -
110C PRO* 5.7 0.2 - - + -
26H THR* 3.7 28.7 - - + -
29H CYS* 4.0 11.2 - - - -
64H CYS* 5.0 0.7 - - + -
65H PRO* 3.0 39.8 + - + +
67H SER* 1.3 86.3 + - - +
69H VAL* 1.3 61.5 + - - +
71H THR* 3.3 5.1 + - - -
72H TRP* 2.8 71.4 + + + +
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Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TYR* 4.1 5.4 - - + -
60H TYR* 3.6 36.6 - - + +
61H LYS* 4.5 12.6 - - + +
64H CYS* 3.4 33.4 - - + +
65H PRO 3.2 6.7 + - - +
66H ILE* 3.6 8.7 - - - +
68H TRP* 1.3 79.6 - - - +
70H SER* 1.3 58.6 + - - +
72H TRP* 3.2 9.5 + - + +
73H ASP* 2.8 46.5 + - - +
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Residues in contact with SER 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE* 2.8 24.2 + - - -
67H SER* 3.8 9.0 - - - -
69H VAL* 1.3 78.0 - - - +
71H THR* 1.3 57.4 + - - +
73H ASP* 3.3 7.2 + - - +
74H ASP* 3.0 41.9 + - - +
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H SER* 2.9 23.3 + - - -
68H TRP* 3.3 5.1 + - - -
70H SER* 1.3 76.3 + - - +
72H TRP* 1.3 67.1 + - + +
74H ASP* 3.5 8.3 + - - +
75H ARG* 3.1 62.3 + - - +
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Residues in contact with TRP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PRO* 4.1 14.9 + - + +
111C GLU* 5.8 4.6 - - - +
29H CYS* 3.6 33.4 - - - -
30H TRP* 3.4 39.2 - + + -
33H TYR* 3.2 60.7 + + + +
64H CYS* 4.2 1.8 - - - -
68H TRP* 2.8 49.2 + + + +
69H VAL* 3.7 1.8 - - - +
71H THR* 1.3 83.0 - - + +
73H ASP* 1.3 59.3 + - - +
75H ARG* 3.3 9.6 + - - +
76H ARG* 3.0 30.0 + - - +
81H PHE* 3.7 19.7 - + + -
82H PRO* 5.9 3.5 - - + +
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Residues in contact with ASP 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TYR* 2.7 30.0 + - - -
37H HIS* 4.0 2.9 + - - -
60H TYR* 4.9 2.5 + - - -
69H VAL* 2.8 33.0 + - - +
70H SER* 3.5 7.8 - - - +
72H TRP* 1.3 73.2 - - - +
74H ASP* 1.3 68.0 + - - +
76H ARG* 2.8 27.2 + - - +
77H ALA* 3.2 21.7 + - - +
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Residues in contact with ASP 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H SER* 3.0 23.1 + - - +
71H THR* 3.6 12.0 - - + +
72H TRP 3.3 0.2 - - - -
73H ASP* 1.3 77.2 - - - +
75H ARG* 1.3 60.1 + - + +
77H ALA* 3.5 8.0 - - - +
78H GLU* 3.0 27.3 + - - +
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Residues in contact with ARG 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 5.0 14.8 - - - +
51G HIS* 3.5 47.4 + - + +
71H THR* 3.1 40.8 + - - +
72H TRP* 3.8 13.8 - - - +
73H ASP 3.2 0.2 - - - -
74H ASP* 1.3 76.7 - - + +
76H ARG* 1.3 59.6 + - - +
77H ALA 3.1 1.3 - - - -
78H GLU* 4.0 7.2 - - - +
79H GLY 2.9 25.1 + - - -
80H THR* 3.0 34.1 + - - +
81H PHE* 3.3 14.4 + - + +
82H PRO* 5.0 8.1 - - - +
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Residues in contact with ARG 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TYR* 3.0 19.2 + - - -
37H HIS* 3.0 33.0 + - - +
72H TRP 3.0 13.2 + - - +
73H ASP* 2.8 34.6 + - - +
75H ARG* 1.3 75.1 - - - +
77H ALA* 1.3 61.2 + - - +
79H GLY* 3.3 11.6 + - - -
81H PHE* 3.5 29.6 - - + -
85H ILE* 3.4 28.7 - - + -
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ASP 3.2 9.9 + - - +
74H ASP* 3.5 12.8 - - - +
76H ARG* 1.3 80.4 - - - +
78H GLU* 1.3 61.3 + - - +
79H GLY* 3.3 1.0 + - - -
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Residues in contact with GLU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PRO* 4.7 12.4 - - + +
51G HIS* 3.1 22.5 + - - -
74H ASP 3.0 17.4 + - - +
75H ARG* 3.2 6.7 + - - +
77H ALA* 1.3 76.9 - - - +
79H GLY* 1.3 57.5 + - - +
80H THR* 2.6 38.5 + - + +
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Residues in contact with GLY 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 3.7 16.4 - - - +
50G TYR* 4.4 4.2 + - - -
75H ARG 2.9 5.3 + - - -
76H ARG 3.3 7.8 + - - -
77H ALA 3.1 4.4 - - - -
78H GLU* 1.3 79.1 - - - +
80H THR* 1.3 59.4 + - - +
81H PHE* 3.5 4.6 + - - +
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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