Contacts of the strand formed by residues 78 - 83 (chain G) in PDB entry 3T30
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 VAL 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F LEU* 3.7 31.9 - - + +
19F TRP* 3.5 31.9 - - - +
20F GLY* 3.7 11.4 - - - +
115F LEU 4.5 0.4 - - - +
116F SER* 3.3 34.1 - - - -
117F GLY 4.8 0.2 - - - +
63G GLU* 3.1 3.3 - - - -
64G ILE* 2.8 36.1 + - + +
66G PRO* 6.2 1.3 - - + -
76G GLN 4.0 8.1 - - - +
77G PRO* 1.3 75.6 - - - +
79G THR* 1.3 61.2 + - - +
80G ILE* 3.5 9.1 + - + +
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Residues in contact with THR 79 (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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48F THR* 3.9 2.4 + - - +
50F CYS* 3.8 26.2 - - + -
114F PHE* 3.5 29.9 - - + +
115F LEU 4.5 3.9 + - - -
116F SER* 3.2 22.2 + - - -
61G ARG* 2.9 54.5 + - + -
62G VAL 3.6 5.8 - - - +
63G GLU* 4.0 5.4 + - - +
77G PRO 3.9 2.6 + - - -
78G VAL* 1.3 72.2 - - - +
80G ILE* 1.3 60.7 + - - +
81G ALA 3.9 4.3 - - - +
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Residues in contact with ILE 80 (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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18F LEU* 5.9 1.1 - - + -
48F THR* 3.0 25.7 + - + +
50F CYS* 3.8 1.6 - - - -
90F MET* 3.5 8.8 - - - +
116F SER* 4.2 8.1 - - - +
46G LEU* 3.9 10.5 - - + -
49G ILE* 3.7 23.8 - - + -
62G VAL* 2.8 24.9 + - + +
64G ILE* 3.7 38.6 - - + -
78G VAL* 3.5 13.4 + - + +
79G THR* 1.3 77.0 - - - +
81G ALA* 1.3 65.9 + - - +
93G MET* 3.7 10.0 - - - +
104G PHE* 3.8 20.6 - - + -
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Residues in contact with ALA 81 (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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50F CYS* 3.7 6.5 - - - -
90F MET* 3.7 13.5 - - + -
49G ILE* 3.8 34.8 - - + -
61G ARG* 3.3 6.8 - - - +
62G VAL* 2.9 35.2 + - + +
79G THR* 3.7 0.8 - - - -
80G ILE* 1.3 83.0 - - - +
82G SER* 1.3 63.6 + - - +
83G LEU* 4.2 5.8 - - + -
91G VAL* 4.3 5.2 - - + -
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Residues in contact with SER 82 (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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50F CYS* 3.4 18.7 - - - +
51F LEU 2.7 28.1 + - - -
89F PRO* 3.6 19.8 - - - +
90F MET* 3.4 25.1 - - - +
59G MET* 4.1 10.5 - - - -
60G HIS 3.2 8.7 - - - -
61G ARG* 3.8 12.6 - - - +
81G ALA* 1.3 73.8 + - - +
83G LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 83 (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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89F PRO* 4.6 2.7 - - - -
90F MET* 4.0 9.2 - - - -
49G ILE* 3.5 43.5 - - + +
50G CYS* 4.2 2.9 - - - +
51G LEU* 4.0 23.1 - - + +
59G MET* 3.5 3.4 - - - +
60G HIS* 2.8 35.2 + - + +
62G VAL* 6.0 0.9 - - + -
81G ALA* 4.6 5.6 - - + -
82G SER* 1.3 83.6 - - - +
84G GLN* 1.3 63.8 + - - +
88G LEU* 3.5 21.3 - - + +
89G PRO 4.1 9.6 - - - +
90G MET 3.6 25.8 - - - +
91G VAL* 4.0 2.5 - - + +
113G VAL* 4.7 2.7 - - + -
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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