Contacts of the strand formed by residues 62 - 67 (chain G) in PDB entry 3WTW
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 THR 62 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147F THR* 6.0 3.4 - - - +
149F THR* 4.8 6.1 - - + +
161F THR* 6.5 0.4 - - + -
17G PHE* 4.4 29.2 - - + -
21G LEU* 4.4 4.8 - - + +
56G ALA* 3.4 0.7 - - - -
57G PHE* 2.9 47.4 + - + +
60G THR* 2.6 28.9 + - - -
61G GLY* 1.3 74.9 - - - +
63G ASN* 1.3 68.2 + - - +
64G LEU* 4.5 9.9 - - + +
103G LEU* 5.9 0.9 - - + -
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Residues in contact with ASN 63 (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* 3.4 34.3 - - + +
107F ALA 3.3 17.7 + - - +
113F TYR 2.8 24.4 + - - -
114F SER* 3.0 26.7 + - - -
149F THR* 3.0 29.5 + - - +
30G THR* 4.1 4.3 + - - -
55G ILE 3.5 6.5 - - - +
56G ALA* 3.8 8.6 - - - +
61G GLY 2.9 11.1 + - - -
62G THR* 1.3 74.0 - - - +
64G LEU* 1.3 69.0 + - - +
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Residues in contact with LEU 64 (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* 3.3 8.3 - - - +
149F THR* 4.3 1.6 - - + -
159F VAL* 3.7 32.1 - - + -
54G GLU* 3.4 2.9 - - - -
55G ILE* 2.7 39.5 + - + +
57G PHE* 3.8 30.3 - - + -
62G THR* 4.5 9.4 - - + +
63G ASN* 1.3 85.8 - - - +
65G SER* 1.3 64.3 + - - +
66G LEU* 4.3 11.1 - - + +
101G MET* 4.1 19.1 - - + -
103G LEU* 4.2 11.0 - - + -
110G TRP* 4.2 16.6 - - + +
125G LEU* 4.5 9.0 - - + -
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Residues in contact with SER 65 (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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104F THR* 4.4 4.9 + - - -
106F MET* 3.5 20.3 - - - +
151F THR* 4.2 16.6 + - - +
153F PHE* 3.5 35.1 - - - -
157F PRO* 5.5 4.9 - - - +
159F VAL* 5.1 5.9 - - - +
53G SER 3.7 5.6 - - - -
54G GLU* 4.1 11.5 - - - +
64G LEU* 1.3 78.3 - - - +
66G LEU* 1.3 67.0 + - - +
67G GLN* 5.9 0.2 - - - -
101G MET* 5.1 3.1 - - - +
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Residues in contact with LEU 66 (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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153F PHE* 5.4 1.3 - - - -
52G ARG* 3.3 25.2 - - - +
53G SER 2.8 18.3 + - - +
55G ILE* 3.4 35.2 - - + -
64G LEU* 4.3 9.2 - - + +
65G SER* 1.3 78.6 - - - +
67G GLN* 1.3 66.9 + - - +
68G PHE* 3.7 22.0 - - + -
99G ALA* 3.6 13.9 - - + -
101G MET* 3.6 30.5 - - + -
110G TRP* 3.5 35.4 - - + -
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Residues in contact with GLN 67 (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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153F PHE* 4.3 22.0 - - + -
154F THR 5.6 1.8 + - - -
155F ASN* 5.5 7.9 + - - +
157F PRO* 3.3 37.1 - - + +
51G GLY 3.4 5.2 - - - -
52G ARG* 4.0 15.1 - - - +
65G SER 5.7 0.2 - - - +
66G LEU* 1.3 82.5 - - - +
68G PHE* 1.3 60.7 - - - +
69G PHE* 2.9 33.7 + - + +
99G ALA* 3.6 13.6 - - - +
100G PRO* 3.7 12.5 + - - +
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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