Contacts of the helix formed by residues 56 - 65 (chain B) in PDB entry 5W4A
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 SER 56 (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 3.9 1.0 + - - -
55B PRO* 1.3 76.2 - - - +
57B VAL* 1.3 65.3 + - - +
58B ASP* 3.3 9.1 + - - +
59B ASP* 2.8 44.6 + - - -
60B ILE* 3.1 23.7 + - - +
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Residues in contact with VAL 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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56B SER* 1.3 73.1 - - - +
58B ASP* 1.3 66.3 + - - +
60B ILE* 3.2 4.3 + - - +
61B VAL* 2.9 38.8 + - + +
87B ASP* 4.0 32.8 - - + +
88B PHE* 3.9 36.3 - - + -
91B GLU* 6.0 3.1 - - + +
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Residues in contact with ASP 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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56B SER* 3.2 8.3 + - - +
57B VAL* 1.3 86.3 - - - +
59B ASP* 1.3 66.3 + - - +
61B VAL* 3.8 9.6 - - - +
62B GLN* 3.0 38.4 + - + +
91B GLU* 5.3 3.8 - - - +
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Residues in contact with ASP 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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41B ASN* 4.7 5.5 + - - +
42B SER* 3.6 21.0 + - - +
43B PHE* 4.3 5.7 - - - +
55B PRO* 3.6 17.0 - - + +
56B SER* 2.8 44.3 + - - +
58B ASP* 1.3 78.0 - - - +
60B ILE* 1.3 62.9 + - - +
62B GLN* 3.6 16.5 + - - +
63B ILE* 3.5 21.3 + - - +
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Residues in contact with ILE 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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19B PHE* 5.7 0.2 - - + -
43B PHE* 3.9 38.0 - - + -
55B PRO* 4.1 10.8 - - + +
56B SER 3.1 16.6 + - - +
57B VAL* 3.5 5.8 - - - +
59B ASP* 1.3 75.6 - - - +
61B VAL* 1.3 66.9 + - - +
63B ILE* 3.1 5.7 + - - +
64B LEU* 2.9 40.5 + - + +
84B LEU* 4.1 8.3 - - + -
88B PHE* 3.9 27.4 - - + -
178B ILE* 3.9 33.2 - - + -
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Residues in contact with VAL 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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57B VAL* 2.9 34.9 + - + +
58B ASP* 3.4 10.7 + - - +
60B ILE* 1.3 76.1 - - + +
62B GLN* 1.3 58.7 + - + +
64B LEU* 4.3 6.3 - - - -
65B PHE* 2.8 35.5 + - + +
81B LEU* 4.4 4.9 - - + -
88B PHE* 4.4 13.5 - - + -
91B GLU* 3.7 29.8 - - + +
95B ARG* 3.6 25.4 - - - +
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Residues in contact with GLN 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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21B ASN* 4.7 0.2 + - - -
41B ASN* 5.6 4.7 - - - +
58B ASP* 3.0 30.7 + - + +
59B ASP* 3.7 16.1 - - - +
60B ILE 3.2 0.2 - - - -
61B VAL* 1.3 77.7 - - + +
63B ILE* 1.3 63.0 + - + +
65B PHE 3.5 4.0 - - - +
66B PRO* 3.4 25.8 - - - +
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Residues in contact with ILE 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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21B ASN* 2.9 38.3 + - - +
22B LEU* 3.8 30.7 - - + +
25B TYR* 4.4 23.8 - - + -
41B ASN* 3.5 42.2 - - - +
43B PHE* 3.8 23.8 - - + -
59B ASP 3.5 6.0 + - - +
60B ILE 3.1 8.5 + - - +
62B GLN* 1.3 76.5 - - - +
64B LEU* 1.3 68.4 + - + +
66B PRO* 3.4 1.7 - - - +
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Residues in contact with LEU 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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18B PHE 4.0 20.4 - - - +
19B PHE* 4.0 20.9 - - + -
20B PRO* 6.1 0.4 - - + -
21B ASN* 5.4 1.9 - - - +
43B PHE* 4.9 5.2 - - + -
60B ILE* 2.9 39.2 + - + +
61B VAL* 3.7 0.7 - - - +
63B ILE* 1.3 81.9 - - + +
65B PHE* 1.3 70.4 + - + +
66B PRO* 3.4 6.4 - - - +
73B THR* 4.1 8.0 - - - +
77B SER* 2.7 31.7 + - - +
80B THR* 4.0 21.5 - - + -
81B LEU* 3.9 26.5 - - + -
84B LEU* 4.4 1.3 - - + -
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Residues in contact with PHE 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 VAL* 2.8 32.7 + - + +
62B GLN* 3.5 8.5 - - - +
64B LEU* 1.3 89.8 - - + +
66B PRO* 1.3 66.8 - - - +
67B SER 3.8 0.3 + - - -
69B SER* 3.7 5.8 - - - +
74B ILE* 3.7 32.3 - - + -
77B SER* 3.4 24.7 - - - -
78B MSE 3.9 2.9 - - + -
81B LEU* 3.6 39.5 - - + -
91B GLU* 4.7 0.2 - - + -
95B ARG* 3.5 53.7 + - + +
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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