Contacts of the helix formed by residues 60 - 67 (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 ASP 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B THR 3.7 2.0 + - - -
59B TRP* 1.3 76.3 - - - +
61B ILE* 1.3 66.3 + - + +
62B VAL* 3.1 12.4 + - - +
63B LYS* 2.9 39.9 + - - +
64B ALA* 2.9 19.4 + - - +
72B ARG* 5.0 1.1 - - - +
76B LEU* 3.9 2.9 - - - -
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Residues in contact with ILE 61 (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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60B ASP* 1.3 74.6 - - + +
62B VAL* 1.3 72.7 + - + +
64B ALA* 3.4 1.5 + - - +
65B THR* 2.7 30.5 + - - -
73B CYS* 3.6 32.8 - - + +
76B LEU* 3.4 22.7 - - + +
77B VAL* 4.4 4.0 - - + -
81B TYR* 3.5 47.3 - - + +
93B LEU* 3.6 23.8 - - + -
109B TYR* 3.5 18.8 - - - +
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Residues in contact with VAL 62 (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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60B ASP* 3.1 9.4 + - - +
61B ILE* 1.3 87.7 - - + +
63B LYS* 1.3 58.8 + - - +
65B THR* 3.3 4.0 + - - -
66B GLN* 3.0 49.3 + - - +
81B TYR* 4.9 5.8 - - - +
87B ASP* 4.5 21.8 - - + +
93B LEU* 4.0 21.3 - - + -
96B TRP* 3.8 18.3 - - + +
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Residues in contact with LYS 63 (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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53B ILE* 5.8 1.7 - - - +
59B TRP* 3.6 59.0 - - + +
60B ASP* 2.9 27.2 + - - +
62B VAL* 1.3 71.4 - - - +
64B ALA* 1.3 67.1 + - - +
66B GLN* 3.2 14.1 + - - +
67B TYR* 3.0 49.8 + - + +
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Residues in contact with ALA 64 (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* 4.4 7.7 - - + +
60B ASP 2.9 17.3 + - - +
61B ILE* 3.8 4.7 - - - +
63B LYS* 1.3 76.6 - - - +
65B THR* 1.3 57.3 + - - +
68B GLY 3.1 5.7 + - - -
69B ILE* 2.7 41.2 + - + +
72B ARG* 3.6 30.5 - - + -
73B CYS* 3.4 18.3 - - - +
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Residues in contact with THR 65 (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* 2.7 25.4 + - - +
62B VAL* 3.4 7.2 - - - -
64B ALA* 1.3 76.6 - - - +
66B GLN* 1.3 67.8 + - - +
68B GLY* 3.0 10.9 + - - -
73B CYS* 3.4 7.3 - - - -
93B LEU* 3.6 30.9 - - + +
96B TRP* 3.9 6.4 - - + +
97B ALA* 3.8 12.6 - - + +
102B ARG* 3.6 13.5 - - - +
105B LEU* 3.7 7.2 - - + +
109B TYR* 2.7 33.2 + - + -
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Residues in contact with GLN 66 (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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51A THR* 3.4 10.6 - - + +
52A HIS 3.4 16.2 - - - +
53A ILE* 3.4 43.1 + - - +
62B VAL* 3.0 31.0 + - - +
63B LYS* 3.2 25.9 + - - +
65B THR* 1.3 76.6 - - - +
67B TYR* 1.3 58.0 + - + +
96B TRP* 3.6 29.9 - - + -
100B ASN* 3.2 22.4 - - - +
102B ARG* 2.9 19.6 + - - -
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Residues in contact with TYR 67 (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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51A THR* 3.4 21.7 - - + -
53A ILE* 3.7 33.3 - - + +
323A SO4 2.8 32.1 + - - -
53B ILE* 5.8 1.8 - - + -
59B TRP* 3.7 24.0 - + + -
63B LYS* 3.0 50.3 + - + +
66B GLN* 1.3 77.5 - - + +
68B GLY* 1.3 60.7 + - - +
69B ILE* 3.4 12.8 + - + +
102B ARG* 3.5 11.6 + - - +
272C TRP* 4.0 19.1 - + + -
275C ASN* 2.9 20.4 - - - +
276C HIS* 3.9 16.9 - + - -
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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
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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