Contacts of the strand formed by residues 52 - 57 (chain G) in PDB entry 3WTV
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 ARG 52 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PHE* 6.3 1.6 - - - -
47G ALA* 2.9 50.6 + - - +
48G CYS* 3.5 2.1 + - - -
50G ASP* 4.0 25.9 + - + +
51G GLY* 1.3 79.5 - - - +
53G SER* 1.3 68.2 + - - +
66G LEU 3.1 13.7 - - - +
67G GLN* 4.4 13.2 - - - +
68G PHE* 3.7 4.6 - - - -
69G PHE* 5.9 0.4 - - + -
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Residues in contact with SER 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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29G TYR* 3.8 5.5 - - - -
44G PHE* 3.3 23.0 - - - -
47G ALA* 5.1 4.0 - - - -
48G CYS* 4.2 7.2 - - - -
52G ARG* 1.3 81.8 - - - +
54G GLU* 1.3 67.6 + - - +
55G ILE* 3.1 18.7 - - - +
65G SER* 3.5 2.1 - - - -
66G LEU* 2.6 37.8 + - - +
68G PHE* 3.7 21.7 - - - -
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Residues in contact with GLU 54 (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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106F MET* 4.7 13.2 - - - +
29G TYR* 3.5 16.3 - - + -
30G THR* 3.1 35.4 + - - +
31G GLY* 3.9 19.3 + - - -
32G PHE* 5.8 3.9 - - - -
53G SER* 1.3 81.4 + - - +
55G ILE* 1.3 63.0 + - - +
64G LEU 3.4 9.2 - - - +
65G SER* 3.9 18.4 + - - +
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Residues in contact with ILE 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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27G ILE* 3.4 32.3 - - + -
28G LYS 3.7 10.3 - - - +
29G TYR* 4.7 0.4 - - - -
30G THR* 4.7 0.9 - - - -
44G PHE* 4.3 2.0 - - + -
53G SER* 3.1 29.8 + - - +
54G GLU* 1.3 76.5 - - - +
56G ALA* 1.3 66.0 + - - +
57G PHE* 5.4 1.5 - - + -
62G THR 4.3 0.3 - - - +
64G LEU* 3.0 33.8 + - - +
66G LEU* 3.5 21.0 - - + +
97G LEU* 4.7 1.6 - - + -
110G TRP* 3.5 25.9 + - + +
114G ILE* 3.4 31.6 - - + -
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Residues in contact with ALA 56 (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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113F TYR* 4.0 9.0 - - + +
27G ILE* 3.5 1.4 - - - -
28G LYS* 3.2 25.5 + - - +
30G THR* 4.0 15.7 - - + +
55G ILE* 1.3 80.8 - - - +
57G PHE* 1.3 60.7 + - - +
58G VAL* 2.9 11.0 + - - +
62G THR 3.2 5.2 - - - +
63G ASN* 3.4 39.7 - - - +
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Residues in contact with PHE 57 (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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21G LEU* 3.3 33.2 - - + -
25G CYS* 4.0 20.2 - - + -
26G GLU 3.7 6.5 - - - +
27G ILE* 4.0 11.7 - - + +
55G ILE* 5.5 1.3 - - + -
56G ALA* 1.3 69.6 - - - +
58G VAL* 1.3 53.6 + - - +
59G ALA* 3.3 3.1 - - + +
60G THR* 3.0 19.0 + - + +
61G GLY* 2.7 32.1 + - - -
62G THR* 2.9 25.1 + - - +
64G LEU* 3.5 26.0 - - + -
110G TRP* 3.3 32.5 - + - -
123G GLY 4.2 15.9 - - - -
124G CYS* 4.4 7.0 - - - -
125G LEU* 4.2 12.1 - - + -
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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