Contacts of the strand formed by residues 50 - 55 (chain G) in PDB entry 1W4R
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 CYS 50 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G VAL* 3.7 33.2 - - + -
43G PHE* 4.3 1.8 - - - -
44G GLN* 3.9 34.3 + - - +
48G TYR 3.6 13.6 + - - -
49G LYS* 1.3 83.7 + - - +
51G LEU* 1.3 62.2 + - - +
52G VAL* 5.7 0.7 - - + -
91G VAL* 4.0 8.7 - - - +
93G VAL* 3.2 20.9 - - - +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G VAL* 5.5 0.2 - - - +
50G CYS* 1.3 76.0 - - - +
52G VAL* 1.3 76.8 + - - +
53G ILE* 4.2 20.4 - - + -
76G LEU* 4.2 17.9 - - + +
84G VAL 4.7 1.8 - - - +
87G GLU* 4.0 26.2 - - + +
88G ALA* 3.6 39.0 - - + +
91G VAL* 3.7 18.4 - - + -
93G VAL 2.9 5.5 + - - +
94G ILE* 3.2 5.6 - - + +
95G GLY 2.8 24.6 + - - +
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Residues in contact with VAL 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 4.6 9.0 - - + -
37G MET* 3.9 36.8 - - + -
40G VAL* 4.3 21.3 - - + -
50G CYS* 5.7 0.9 - - + -
51G LEU* 1.3 81.7 - - - +
53G ILE* 1.3 64.4 + - - +
75G ALA* 3.2 22.9 - - + +
76G LEU* 2.7 34.9 + - - +
95G GLY* 3.3 11.9 - - - +
97G ASP* 5.1 3.8 - - + +
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Residues in contact with ILE 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 4.2 17.0 - - + -
52G VAL* 1.3 82.6 - - - +
54G LYS* 1.3 64.8 + - - +
76G LEU* 3.2 14.1 - - + +
78G ALA* 4.0 18.2 - - + -
81G LEU* 3.9 23.3 - - + -
84G VAL* 3.6 26.5 - - + -
94G ILE* 3.8 26.7 - - + -
95G GLY 2.8 9.1 + - - +
96G ILE* 3.5 6.4 - - + +
97G ASP* 2.9 27.9 + - - +
102G PHE* 4.0 5.8 - - + -
108G PHE* 4.1 11.9 - - + -
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Residues in contact with LYS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G VAL 4.3 0.2 + - - -
53G ILE* 1.3 75.5 - - - +
55G TYR* 1.3 67.4 + - - +
56G ALA* 5.9 0.7 - - - +
58G ASP 5.5 6.3 - - - +
75G ALA* 3.0 41.9 + - + +
76G LEU 2.9 6.9 + - - -
77G PRO* 3.9 27.3 - - + +
78G ALA 2.9 26.3 + - - +
97G ASP* 4.0 20.0 - - + +
102G PHE* 3.8 6.7 - - - -
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Residues in contact with TYR 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LYS* 1.3 78.8 - - - +
56G ALA* 1.3 63.5 + - - +
57G LYS* 3.3 27.2 + - + +
58G ASP* 3.3 27.2 + - + +
78G ALA 3.4 11.7 - - - -
79G CYS* 4.4 17.0 - - + -
97G ASP 3.7 4.2 + - - -
98G GLU* 4.1 25.6 - - + +
101G PHE* 3.4 51.7 + + + +
102G PHE* 3.6 17.7 - + + -
173G GLU* 2.8 33.7 + - - -
175G ILE* 4.6 2.0 - - + -
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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