Contacts of the helix formed by residues 65 - 79 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98O LYS* 4.0 5.8 - - + +
100O MET* 3.9 29.2 - - + -
109O GLU* 3.4 10.5 - - - +
179O LEU* 3.8 20.4 - - + -
29U CYS* 4.4 0.2 - - - -
63U LEU 3.6 5.8 - - - +
64U CYS* 1.3 85.5 - - - +
66U ILE* 1.3 67.5 + - - +
67U SER* 4.3 2.9 - - - +
68U TRP* 3.0 61.5 + - + +
69U VAL* 3.2 10.0 + - - +
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Residues in contact with ILE 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O LYS* 4.6 1.6 - - - +
109O GLU* 3.0 38.1 + - + +
111O THR* 4.1 20.0 - - + -
115O ASP* 4.6 13.9 - - + +
116O LEU 5.5 0.2 - - - -
117O SER* 3.9 20.4 - - - +
64U CYS 3.4 2.2 + - - +
65U PRO* 1.3 70.5 - - - +
67U SER* 1.3 58.1 + - - +
69U VAL* 3.2 8.6 + - + +
70U SER* 2.8 33.2 + - - -
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Residues in contact with SER 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O MET* 4.1 4.7 - - - +
109O GLU* 4.9 1.4 + - - -
157O GLU* 2.9 35.3 + - - +
65U PRO* 4.3 1.2 - - - +
66U ILE* 1.3 79.3 - - - +
68U TRP* 1.3 70.8 + - - +
70U SER* 3.9 6.5 - - - -
71U THR* 2.9 33.9 + - - -
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Residues in contact with TRP 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O MET* 4.3 9.3 - - - +
155O SER* 3.9 12.7 + - - -
156O SER 5.4 1.2 + - - -
177O GLY* 3.8 28.2 - - - +
178O ARG 3.9 10.1 - - - -
179O LEU* 3.7 26.9 - - + -
110P PRO* 5.9 0.4 - - + -
26U THR* 3.9 25.4 - - + -
29U CYS* 3.8 12.8 - - - -
64U CYS* 5.0 0.4 - - + -
65U PRO* 3.0 40.8 + - + +
67U SER* 1.3 85.5 - - - +
69U VAL* 1.3 62.0 + - - +
71U THR* 3.2 5.7 + - - -
72U TRP* 2.8 71.9 + + + +
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Residues in contact with VAL 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U TYR* 4.1 4.9 - - + -
60U TYR* 3.6 36.1 - - + +
61U LYS* 5.4 6.3 - - - +
64U CYS* 3.5 33.2 - - + +
65U PRO 3.2 5.3 + - - +
66U ILE* 3.6 8.3 - - - +
68U TRP* 1.3 77.4 - - - +
70U SER* 1.3 57.3 + - - +
72U TRP* 3.2 9.5 + - + +
73U ASP* 2.8 53.8 + - - +
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Residues in contact with SER 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U ILE* 2.8 26.8 + - - -
67U SER* 3.9 8.1 - - - -
69U VAL* 1.3 75.4 - - - +
71U THR* 1.3 57.7 + - - +
73U ASP* 3.3 7.2 + - - +
74U ASP* 3.0 46.5 + - - +
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Residues in contact with THR 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U SER* 2.9 23.3 + - - -
68U TRP* 3.2 6.7 + - - +
70U SER* 1.3 78.3 + - - +
72U TRP* 1.3 68.7 + - + +
74U ASP* 3.5 8.7 + - - +
75U ARG* 3.1 61.2 + - - +
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Residues in contact with TRP 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P PRO* 4.2 14.6 - - + +
111P GLU* 6.2 1.8 - - - +
29U CYS* 3.7 22.9 - - - -
30U TRP* 3.6 35.1 - + + -
33U TYR* 3.1 59.9 - + + +
64U CYS* 4.2 3.6 - - + -
68U TRP* 2.8 59.5 + + + +
69U VAL* 3.6 2.5 - - - +
71U THR* 1.3 84.6 - - + +
73U ASP* 1.3 60.4 + - - +
75U ARG* 3.3 8.6 + - - +
76U ARG* 3.0 33.1 + - - +
81U PHE* 3.7 20.6 - + + -
82U PRO* 5.9 3.0 - - + +
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Residues in contact with ASP 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U TYR* 2.6 29.7 + - - -
37U HIS* 4.2 2.3 + - - -
60U TYR* 5.0 1.6 + - - -
69U VAL* 2.8 38.6 + - - +
70U SER* 3.6 7.2 - - - +
72U TRP* 1.3 75.9 - - - +
74U ASP* 1.3 65.3 + - - +
76U ARG* 3.2 34.1 + - - +
77U ALA* 3.2 13.7 + - - +
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Residues in contact with ASP 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70U SER* 3.0 32.4 + - - +
71U THR* 3.6 8.2 - - - +
73U ASP* 1.3 77.7 - - - +
75U ARG* 1.3 59.2 + - + +
77U ALA* 3.6 7.1 - - - +
78U GLU* 3.1 26.8 + - - +
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Residues in contact with ARG 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P GLU* 5.2 13.5 - - - +
51T HIS* 3.4 45.8 + - + +
71U THR* 3.1 42.4 + - - +
72U TRP* 3.8 13.4 - - - +
73U ASP 3.2 0.2 - - - -
74U ASP* 1.3 77.4 - - + +
76U ARG* 1.3 60.6 + - - +
77U ALA 3.1 1.3 - - - -
78U GLU* 4.1 5.2 - - - +
79U GLY 2.9 23.9 + - - -
80U THR* 3.0 34.1 + - - +
81U PHE* 3.3 16.2 + - + +
82U PRO* 5.3 8.8 - - - +
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Residues in contact with ARG 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U TYR* 3.1 17.9 + - - -
37U HIS* 2.8 41.2 + - - +
40U GLU* 5.3 0.8 + - - -
72U TRP 3.0 16.0 + - - +
73U ASP* 3.2 24.3 + - - +
75U ARG* 1.3 74.8 - - - +
77U ALA* 1.3 62.6 + - - +
79U GLY* 3.3 12.1 + - - -
81U PHE* 3.4 26.7 - - + -
85U ILE* 3.7 29.7 - - - +
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Residues in contact with ALA 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73U ASP 3.2 9.6 + - - +
74U ASP* 3.6 11.2 - - - +
75U ARG 3.1 0.4 - - - -
76U ARG* 1.3 80.4 - - - +
78U GLU* 1.3 60.9 + - - +
79U GLY* 3.3 0.7 + - - -
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Residues in contact with GLU 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T PRO* 4.3 15.3 - - + +
51T HIS* 2.9 24.2 + - - -
74U ASP 3.1 16.2 + - - +
75U ARG* 3.2 9.5 + - - +
77U ALA* 1.3 76.7 - - - +
79U GLY* 1.3 57.7 + - - +
80U THR* 2.9 34.1 + - + +
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Residues in contact with GLY 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T ILE* 3.7 18.8 - - - +
50T TYR* 4.7 3.3 + - - -
75U ARG 2.9 4.9 + - - -
76U ARG 3.3 8.7 + - - -
77U ALA 3.1 5.3 - - - -
78U GLU* 1.3 78.6 - - - +
80U THR* 1.3 60.7 + - - +
81U PHE* 3.5 5.1 + - - +
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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