Contacts of the helix formed by residues 60 - 70 (chain B) in PDB entry 5WRV
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B LEU* 2.8 41.9 + - - +
56B ILE 4.5 0.2 + - - -
58B ASN* 4.2 8.5 + - - +
59B GLY* 1.3 69.7 - - - +
61B PHE* 1.3 58.0 + - - +
63B GLU* 4.1 6.1 + - - -
64B ALA* 3.0 27.7 + - - +
202B SO4 3.1 31.1 + - - -
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Residues in contact with PHE 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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595A LEU* 6.0 0.2 - - + -
56B ILE* 3.6 44.2 - - + -
59B GLY* 3.3 26.4 + - - -
60B SER* 1.3 70.0 - - - +
62B LYS* 1.3 61.2 + - - +
64B ALA* 3.4 0.6 + - - -
65B LEU* 2.9 30.7 + - - +
86B TYR* 4.2 0.7 - + - -
87B CYS* 3.6 19.7 - - - +
90B ARG* 3.4 71.1 - - + -
91B LEU* 4.0 24.7 - - + -
202B SO4 3.5 1.8 + - - -
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Residues in contact with LYS 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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61B PHE* 1.3 77.3 - - - +
63B GLU* 1.3 57.3 + - - +
65B LEU* 3.3 4.6 + - - +
66B ASN* 2.9 28.9 + - - +
91B LEU* 3.8 33.4 - - + +
93B ARG* 4.6 14.4 - - - +
202B SO4 3.2 24.2 + - - +
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Residues in contact with GLU 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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31B LEU* 5.6 1.0 - - - +
51B LYS* 4.7 9.4 + - - -
55B LEU* 3.5 31.2 - - + +
60B SER* 3.9 11.8 + - - +
62B LYS* 1.3 72.2 - - - +
64B ALA* 1.3 62.6 + - - +
66B ASN* 3.2 10.5 + - + +
67B VAL* 3.0 26.0 + - + +
202B SO4 2.7 27.1 + - - +
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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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52B VAL* 3.9 11.8 - - + +
55B LEU* 3.7 24.5 - - + +
56B ILE* 3.9 12.1 - - + -
60B SER 3.0 18.5 + - - +
61B PHE 3.7 0.2 - - - +
63B GLU* 1.3 76.6 - - - +
65B LEU* 1.3 62.7 + - - +
67B VAL* 3.2 7.2 + - - +
68B ILE* 3.2 24.9 + - - +
87B CYS* 3.6 21.8 - - - -
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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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61B PHE 2.9 18.5 + - - +
62B LYS* 3.7 5.2 - - - +
64B ALA* 1.3 75.8 - - - +
66B ASN* 1.3 57.2 + - - +
68B ILE* 3.2 6.8 + - + +
69B ASN* 2.9 50.6 + - - +
84B LYS* 3.7 41.1 - - + +
87B CYS* 4.0 10.0 - - + -
88B GLU* 4.1 17.5 - - + +
91B LEU* 4.0 13.9 - - + -
93B ARG* 3.5 27.8 - - - +
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Residues in contact with ASN 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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62B LYS 2.9 14.1 + - - +
63B GLU* 3.4 14.8 + - - +
64B ALA 3.2 0.2 - - - -
65B LEU* 1.3 72.8 - - - +
67B VAL* 1.3 59.4 + - - +
69B ASN* 4.5 5.5 - - - +
70B THR* 2.7 53.4 + - - +
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Residues in contact with VAL 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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48B LEU* 3.9 31.6 - - + +
51B LYS* 3.9 31.0 - - + +
52B VAL* 3.8 19.5 - - + -
55B LEU* 3.9 11.4 - - + -
63B GLU* 3.0 22.0 + - + +
64B ALA 3.2 7.6 + - - +
66B ASN* 1.3 78.2 - - - +
68B ILE* 1.3 63.4 + - - +
70B THR* 3.9 4.0 - - - -
71B HIS* 2.7 33.5 + - + +
75B LEU* 4.5 1.1 - - + +
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Residues in contact with ILE 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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52B VAL* 3.8 26.0 - - + -
64B ALA 3.2 14.3 + - - +
65B LEU* 3.2 11.7 + - + +
67B VAL* 1.3 75.8 - - - +
69B ASN* 1.3 61.9 + - - +
71B HIS 3.2 17.2 + - - -
72B THR* 3.5 12.5 + - - -
75B LEU* 3.8 11.7 - - + +
79B SER 3.9 19.5 - - - +
80B LEU* 3.9 12.3 - - + +
83B GLU* 4.0 7.4 - - + +
84B LYS* 3.5 54.7 - - + +
87B CYS* 5.3 0.7 - - - -
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Residues in contact with ASN 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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65B LEU* 2.9 43.1 + - - +
66B ASN* 4.3 5.1 - - - +
67B VAL 3.4 0.2 - - - -
68B ILE* 1.3 78.3 - - - +
70B THR* 1.3 62.3 + - + +
71B HIS 3.4 0.4 - - - -
72B THR* 3.2 19.2 + - - -
84B LYS* 3.4 27.5 - - - +
88B GLU* 5.5 0.8 + - - -
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Residues in contact with THR 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 ASN* 2.7 45.0 + - - +
67B VAL* 3.4 1.2 + - - -
69B ASN* 1.3 79.0 - - + +
71B HIS* 1.3 83.2 + - - +
72B THR 3.7 1.3 - - - -
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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