Contacts of the helix formed by residues 69 - 79 (chain B) in PDB entry 3EU9
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 ILE 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 3.4 48.7 - - + +
59B TRP* 4.3 3.4 - - + -
64B ALA* 2.7 27.4 + - + +
67B TYR* 3.7 26.7 - - + +
68B GLY* 1.3 69.2 - - - -
70B TYR* 1.3 63.6 + - - +
71B GLU* 3.5 2.0 - - + +
72B ARG* 3.1 24.6 + - + +
73B CYS* 3.1 23.1 + - - -
271C VAL* 3.7 27.8 - - + -
272C TRP* 4.2 11.2 - - - +
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Residues in contact with TYR 70 (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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68B GLY 3.0 10.3 + - - +
69B ILE* 1.3 69.4 - - - +
71B GLU* 1.3 83.9 + - + +
73B CYS* 2.9 20.1 + - - +
74B ARG* 2.9 29.0 + - + +
104B ASP* 3.0 53.8 + - + +
105B LEU* 3.5 25.5 - - + +
108B TYR* 3.7 29.9 - + + +
271C VAL* 5.0 2.6 - - - +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.5 2.8 - - + +
70B TYR* 1.3 100.8 - - + +
72B ARG* 1.3 57.4 + - - +
74B ARG* 2.6 40.4 + - - +
75B GLU* 3.0 30.0 + - - +
271C VAL* 6.5 1.8 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR 4.0 8.7 - - - +
57B SER* 3.2 30.0 + - - +
58B THR* 3.5 15.2 + - - +
59B TRP 2.8 24.2 + - - +
60B ASP* 5.0 1.0 - - - +
64B ALA* 3.6 19.1 - - + -
69B ILE* 3.1 28.3 + - + +
71B GLU* 1.3 79.3 - - - +
73B CYS* 1.3 62.0 + - - +
75B GLU* 2.9 28.6 + - - +
76B LEU* 3.2 38.3 + - + +
323B SO4 2.8 42.4 + - - -
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Residues in contact with CYS 73 (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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61B ILE* 3.6 10.6 - - - +
64B ALA* 3.4 9.9 - - - -
65B THR* 3.4 32.8 - - - -
69B ILE 3.1 17.4 + - - -
70B TYR 2.9 8.6 + - - +
72B ARG* 1.3 75.2 - - - +
74B ARG* 1.3 64.9 + - - +
76B LEU 3.4 0.7 + - - -
77B VAL* 3.1 30.2 + - - +
105B LEU* 3.6 16.8 - - + -
108B TYR* 4.8 1.1 - - - -
109B TYR* 3.2 28.0 - - + +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 2.9 35.4 + - + +
71B GLU* 2.6 38.1 + - - +
73B CYS* 1.3 75.1 - - - +
75B GLU* 1.3 66.4 + - - +
77B VAL* 2.8 26.6 - - - +
78B GLU* 3.0 38.7 + - - +
108B TYR* 3.8 28.2 - - + +
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Residues in contact with GLU 75 (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 SER 4.6 0.9 - - - +
71B GLU 3.0 19.3 + - - +
72B ARG* 2.9 41.8 + - - +
74B ARG* 1.3 81.3 - - - +
76B LEU* 1.3 58.9 + - + +
78B GLU* 3.5 9.7 + - - +
79B ALA* 3.1 29.1 + - + +
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Residues in contact with LEU 76 (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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59B TRP 3.8 3.4 - - - +
60B ASP* 3.9 1.6 - - - -
61B ILE* 3.4 45.5 - - + +
72B ARG* 3.2 44.8 + - + +
73B CYS 4.0 3.4 - - - +
74B ARG 3.3 0.2 - - - -
75B GLU* 1.3 78.9 - - + +
77B VAL* 1.3 63.2 + - - +
79B ALA* 3.4 14.9 + - + +
80B GLY 3.4 1.0 + - - -
81B TYR* 3.0 26.6 + - + +
323B SO4 3.1 29.2 - - - +
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Residues in contact with VAL 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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61B ILE* 4.4 9.6 - - + -
73B CYS 3.1 14.7 + - - +
74B ARG 2.8 19.3 - - - +
76B LEU* 1.3 73.9 - - - +
78B GLU* 1.3 63.3 + - - +
80B GLY* 3.0 11.8 + - - -
81B TYR* 3.5 24.4 + - + +
83B VAL* 3.7 28.0 - - + -
93B LEU* 5.0 0.2 - - + -
108B TYR* 2.7 37.9 - - + +
109B TYR* 4.0 14.4 - - + -
112B LYS* 4.8 5.6 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.0 52.3 + - - +
75B GLU* 3.8 6.9 - - - +
77B VAL* 1.3 78.4 - - - +
79B ALA* 1.3 57.9 - - - +
80B GLY 3.2 3.8 + - - -
108B TYR* 3.8 13.7 + - - +
112B LYS* 4.8 11.1 + - - +
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Residues in contact with ALA 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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75B GLU* 3.1 20.3 + - + +
76B LEU* 3.7 14.4 - - + +
77B VAL 3.2 0.6 - - - -
78B GLU* 1.3 75.1 - - - +
80B GLY* 1.3 56.2 + - - +
81B TYR 3.9 0.2 - - - -
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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