Contacts of the helix formed by residues 58 - 72 (chain B) in PDB entry 4EOH
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 ASN 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B VAL* 3.8 4.0 + - + +
57B LEU* 1.3 75.2 - - - +
59B SER* 1.3 65.1 + - - +
60B ASP* 2.7 37.7 + - - +
61B GLU* 2.9 52.3 + - - +
62B LEU* 3.0 12.1 + - - +
87B ASP* 6.0 0.2 - - - -
90B PHE* 3.9 4.0 - - - -
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Residues in contact with SER 59 (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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58B ASN* 1.3 75.4 - - - +
60B ASP* 1.3 63.5 + - - +
62B LEU* 3.7 4.5 - - - +
63B GLN* 3.1 26.5 + - - +
87B ASP* 5.3 0.8 + - - -
89B SER* 3.4 48.8 + - - -
90B PHE* 3.8 15.2 - - - +
93B MET* 3.7 17.0 - - - +
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Residues in contact with ASP 60 (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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58B ASN* 2.7 19.7 + - - +
59B SER* 1.3 77.5 + - - +
61B GLU* 1.3 60.1 + - + +
63B GLN* 3.4 17.5 + - - +
64B GLU* 2.9 29.0 + - - +
93B MET* 5.8 0.5 - - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 3.3 38.3 + - + +
56B VAL 3.9 4.7 - - - +
57B LEU* 3.5 18.8 - - + +
58B ASN* 2.9 48.8 + - - +
60B ASP* 1.3 76.3 - - + +
62B LEU* 1.3 65.4 + - - +
64B GLU* 3.4 7.5 + - - +
65B LEU* 3.0 29.3 + - - +
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Residues in contact with LEU 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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10B ILE* 4.5 9.6 - - + -
38B VAL* 3.8 29.2 - - + -
57B LEU* 4.2 7.3 - - + +
58B ASN 3.0 11.7 + - - +
59B SER 3.7 7.0 - - - +
60B ASP 3.2 0.2 - - - -
61B GLU* 1.3 77.1 - - - +
63B GLN* 1.3 64.2 + - - +
65B LEU* 3.1 7.9 + - + +
66B TYR* 3.0 21.0 + - + +
90B PHE* 3.8 31.4 - - + +
93B MET* 3.5 26.7 - - + -
94B VAL* 3.9 17.9 - - + -
97B ILE* 3.7 20.2 - - + -
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Residues in contact with GLN 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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59B SER 3.1 13.0 + - - +
60B ASP* 3.6 18.8 - - - +
62B LEU* 1.3 80.2 - - - +
64B GLU* 1.3 63.3 + - - +
66B TYR* 3.2 10.2 + - - +
67B GLU* 2.9 26.0 + - + +
93B MET* 3.6 31.4 - - + +
97B ILE* 5.1 0.2 - - - -
412B SO4 3.7 26.5 + - - +
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Residues in contact with GLU 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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53A LYS* 3.4 31.5 - - + +
54A GLY 3.9 24.8 + - - +
55A GLN* 3.9 13.0 + - - +
60B ASP 2.9 17.7 + - - +
61B GLU* 3.6 10.8 - - - +
62B LEU 3.2 0.2 - - - -
63B GLN* 1.3 78.1 - - - +
65B LEU* 1.3 61.9 + - - +
67B GLU* 3.0 22.4 + - + +
68B GLY 3.2 5.5 + - - -
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Residues in contact with LEU 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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15A ILE* 3.7 26.2 - - + -
42A GLN* 3.4 46.2 - - + +
44A SER* 3.4 22.1 - - - +
53A LYS* 3.9 7.9 - - - +
54A GLY* 3.7 15.7 - - - -
55A GLN* 3.8 7.2 - - - +
38B VAL* 4.1 6.3 - - + -
57B LEU* 4.0 19.5 - - + -
61B GLU 3.0 19.7 + - - +
62B LEU* 3.4 8.5 - - + +
64B GLU* 1.3 76.4 - - - +
66B TYR* 1.3 62.8 + - - +
68B GLY 3.2 9.2 + - - -
69B LEU* 3.3 11.8 + - - +
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Residues in contact with TYR 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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8B LEU* 5.4 3.6 - - + -
62B LEU* 3.0 12.0 + - + +
63B GLN* 3.2 9.6 + - - +
65B LEU* 1.3 72.8 - - - +
67B GLU* 1.3 57.6 + - - +
69B LEU* 3.1 19.2 + - + +
70B ARG* 2.8 42.2 + - + +
75B ASN* 3.1 36.1 + - + +
77B TYR* 6.1 0.2 - + - -
97B ILE* 3.9 37.2 - - + -
100B GLU* 2.7 44.5 + - + +
101B LEU* 3.7 19.4 - - + +
412B SO4 4.0 25.1 - - - -
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Residues in contact with GLU 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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53A LYS* 4.5 10.1 - - + -
63B GLN* 2.9 17.9 + - + +
64B GLU* 3.0 17.7 + - - +
66B TYR* 1.3 79.6 - - - +
68B GLY* 1.3 51.1 + - - +
70B ARG* 2.8 46.9 + - - +
71B LEU* 2.7 55.4 + - + +
412B SO4 4.6 10.0 + - - -
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Residues in contact with GLY 68 (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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44A SER* 3.5 22.4 - - - -
45A ASN* 4.1 0.2 - - - -
52A TRP* 4.8 2.5 - - - -
53A LYS* 3.7 17.2 - - - +
64B GLU 3.2 7.5 + - - -
65B LEU 3.2 2.1 + - - -
67B GLU* 1.3 80.3 - - - +
69B LEU* 1.3 60.2 + - - +
71B LEU* 3.6 5.7 + - - +
72B ASN* 2.9 32.6 + - - -
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Residues in contact with LEU 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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15A ILE* 4.2 19.7 - - + -
16A ARG* 3.9 11.4 - - + -
44A SER* 3.6 20.8 - - - +
8B LEU* 4.5 9.6 - - + -
65B LEU 3.3 12.9 + - - +
66B TYR* 3.1 25.0 + - + +
68B GLY* 1.3 76.6 - - - +
70B ARG* 1.3 58.8 + - - +
72B ASN 3.2 2.8 + - - -
73B ASN 3.1 3.5 + - - -
74B MET* 2.7 68.2 + - + +
75B ASN* 4.7 1.3 - - + +
77B TYR* 3.9 23.1 - - + +
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Residues in contact with ARG 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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66B TYR* 2.8 28.5 + - + +
67B GLU* 2.8 38.8 + - - +
69B LEU* 1.3 72.9 - - - +
71B LEU* 1.3 79.6 + - - +
73B ASN* 2.7 25.6 + - - +
75B ASN* 4.0 28.2 - - - +
100B GLU* 3.8 16.8 - - - +
412B SO4 5.5 2.5 - - - -
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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
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51A HIS* 3.6 53.1 + - + +
53A LYS* 3.9 29.2 - - - +
67B GLU* 2.7 34.9 + - + +
68B GLY* 3.9 2.5 - - - +
70B ARG* 1.3 99.0 - - - +
72B ASN* 1.3 57.3 + - - +
73B ASN* 3.4 2.8 + - - +
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Residues in contact with ASN 72 (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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45A ASN* 3.0 15.5 + - - +
49A TYR* 3.6 18.2 - - + +
50A ALA* 3.9 3.5 + - - +
51A HIS* 2.8 51.6 + - - +
287A MET* 3.3 10.7 - - - +
68B GLY 2.9 18.2 + - - -
69B LEU 3.2 1.4 + - - +
70B ARG 3.1 1.4 - - - -
71B LEU* 1.3 75.4 - - - +
73B ASN* 1.3 72.4 + - - +
74B MET* 3.1 30.0 + - + +
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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