Contacts of the helix formed by residues 55 - 67 (chain B) in PDB entry 5H4G
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 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B LYS* 1.3 71.7 - - - +
56B ILE* 1.3 60.9 + - - +
57B GLU* 3.4 10.6 + - - +
58B ALA* 3.1 32.1 + - + +
59B GLU* 3.0 28.1 + - - +
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Residues in contact with ILE 56 (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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78A ILE* 3.6 41.7 - - + +
81A ALA* 4.6 1.8 - - + -
82A GLN* 5.8 4.0 - - + +
46B LEU* 3.8 20.6 - - + +
49B ARG* 3.7 15.7 - - + -
50B ALA* 3.4 42.4 - - + +
54B LYS 3.2 16.3 + - - +
55B ASN* 1.3 71.1 + - - +
57B GLU* 1.3 67.3 + - + +
59B GLU* 3.9 3.6 - - + +
60B PHE* 2.9 23.7 + - - +
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Residues in contact with GLU 57 (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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78A ILE* 4.4 27.1 - - + +
55B ASN* 3.4 8.2 + - - +
56B ILE* 1.3 80.1 - - - +
58B ALA* 1.3 61.9 + - - +
60B PHE* 3.3 3.3 + - - +
61B GLU* 3.1 27.6 + - + +
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Residues in contact with ALA 58 (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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55B ASN* 3.1 31.1 + - + +
57B GLU* 1.3 80.0 - - - +
59B GLU* 1.3 58.9 + - - +
61B GLU* 3.1 11.2 + - - +
62B ILE* 2.9 37.1 + - + +
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Residues in contact with GLU 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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18B HIS* 4.3 5.0 + - - -
45B TYR* 2.4 36.5 + - - -
46B LEU* 4.2 11.0 - - + -
49B ARG* 3.6 34.2 + - + +
54B LYS* 5.7 3.4 - - + -
55B ASN 3.0 17.5 + - - +
56B ILE* 4.0 4.3 - - - +
57B GLU 3.3 0.2 - - - -
58B ALA* 1.3 75.8 - - - +
60B PHE* 1.3 63.8 + - - +
62B ILE* 3.1 27.8 + - + +
63B LEU* 2.9 27.2 + - - +
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Residues in contact with PHE 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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74A ASP* 3.3 41.7 - - + -
77A ALA* 5.3 0.7 - - + -
78A ILE* 4.0 17.3 - - + -
39B ILE* 4.5 10.1 - - + -
42B VAL* 3.8 30.5 - - + -
46B LEU* 3.9 17.1 - - + +
56B ILE 2.9 18.1 + - - +
57B GLU 3.6 3.6 - - - +
58B ALA 3.2 0.2 - - - -
59B GLU* 1.3 76.8 - - - +
61B GLU* 1.3 69.2 + - - +
63B LEU* 3.2 5.9 + - + +
64B LYS* 2.8 53.5 + - + +
69B ILE* 3.9 20.6 - - + -
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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
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74A ASP* 5.1 2.1 - - - +
57B GLU* 3.1 15.0 + - + +
58B ALA* 3.1 11.1 + - - +
60B PHE* 1.3 86.5 - - - +
62B ILE* 1.3 61.2 + - - +
64B LYS* 2.9 38.1 + - - +
65B ASP* 3.2 22.9 + - - +
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Residues in contact with ILE 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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18B HIS* 5.6 2.7 - - + -
58B ALA* 2.9 25.0 + - + +
59B GLU* 3.1 34.1 + - + +
61B GLU* 1.3 75.0 - - + +
63B LEU* 1.4 63.1 + - + +
65B ASP* 3.2 19.3 + - - +
66B ILE* 3.5 22.9 + - + +
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Residues in contact with LEU 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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14B LEU* 5.4 3.8 - - + -
18B HIS* 3.8 17.5 - - + +
42B VAL* 4.0 27.4 - - + -
45B TYR* 3.8 31.4 - - + -
46B LEU* 4.3 7.6 - - + -
59B GLU* 2.9 29.2 + - - +
60B PHE* 3.5 7.2 - - - +
62B ILE* 1.4 71.4 - - + +
64B LYS* 1.3 59.5 + - - +
65B ASP 3.1 1.8 - - - -
66B ILE* 3.1 3.0 + - + -
67B TYR* 2.9 65.0 + - + +
69B ILE* 4.2 9.9 - - + -
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Residues in contact with LYS 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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74A ASP* 4.7 6.8 + - - +
60B PHE* 2.8 37.3 + - + +
61B GLU* 2.9 42.2 + - - +
63B LEU* 1.3 73.3 - - - +
65B ASP* 1.3 61.4 + - - +
66B ILE 3.3 0.5 + - - -
67B TYR 3.4 13.0 - - - +
69B ILE* 3.7 19.6 - - + +
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Residues in contact with ASP 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 GLU 3.2 13.5 + - - +
62B ILE* 3.4 13.5 - - - +
63B LEU 3.1 1.2 - - - -
64B LYS* 1.3 78.5 - - - +
66B ILE* 1.3 63.2 + - + +
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Residues in contact with ILE 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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18B HIS* 4.3 13.9 - - + -
26B LEU* 5.5 0.9 - - + -
30B LEU* 4.0 36.3 - - + +
35B VAL* 5.0 2.3 + - - +
62B ILE* 3.7 24.0 - - + +
63B LEU* 3.1 3.1 + - - +
65B ASP* 1.3 87.8 - - + +
67B TYR* 1.3 95.7 + - + +
68B ASN 4.4 0.2 + - - -
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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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9B PHE* 5.3 2.6 - + - -
14B LEU* 3.6 11.1 - - + +
17B MET* 5.4 0.2 - - - +
18B HIS* 2.7 34.3 + - - -
26B LEU* 3.5 18.1 - - + +
30B LEU* 3.8 12.3 - - + -
35B VAL* 3.6 43.1 - - + +
37B LEU* 3.5 28.5 - - + -
63B LEU* 2.9 39.4 + - + +
64B LYS* 3.4 15.6 - - - +
66B ILE* 1.3 98.2 - - + +
68B ASN* 1.3 64.8 + - - +
69B ILE* 3.5 10.1 + - + +
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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