Contacts of the strand formed by residues 62 - 67 (chain B) in PDB entry 3CTP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.5 15.4 - - - +
115A HIS* 3.6 12.9 - - - -
60B SER* 3.2 10.5 + - - -
61B LYS* 1.3 79.7 + - - +
63B ILE* 1.3 71.6 + - - +
91B TYR* 4.0 0.2 - - - -
92B THR* 2.8 28.6 + - - +
93B LEU 4.1 0.7 - - - -
94B PHE* 3.7 39.3 - - + +
117B VAL* 3.4 6.8 - - + +
118B ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 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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62B THR* 1.3 79.2 - - - +
64B GLY* 1.3 72.2 + - - +
86B ALA* 4.5 3.4 - - + -
91B TYR* 3.7 39.3 - - + -
92B THR 2.9 6.6 + - - +
93B LEU* 3.2 22.4 - - + +
94B PHE 2.9 24.0 + - - -
119B GLY 3.4 16.8 - - - +
121B ILE* 3.9 10.5 - - + -
294B ILE* 4.3 17.3 - - + -
297B LEU* 3.7 32.3 - - + -
298B ILE* 4.7 7.4 - - + -
301B ILE* 4.7 2.2 - - + -
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Residues in contact with GLY 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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62B THR 4.3 0.4 + - - -
63B ILE* 1.3 73.6 - - - +
65B LEU* 1.3 61.9 + - - -
66B MET 3.9 0.4 - - - -
94B PHE* 3.5 7.4 - - - -
96B CYS* 5.3 0.2 - - - -
112B LEU* 3.9 31.9 - - - -
117B VAL* 4.4 4.6 - - - +
119B GLY 3.0 12.0 + - - -
120B ILE* 3.3 4.8 - - - +
121B ILE 2.8 26.7 + - - +
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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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63B ILE 3.8 0.8 + - - -
64B GLY* 1.3 72.9 - - - -
66B MET* 1.3 70.6 + - - +
67B VAL* 3.5 10.5 + - + +
78B MET* 5.6 1.3 - - + -
79B ALA* 3.8 26.9 - - + +
82B ILE* 4.0 21.3 - - + -
93B LEU* 4.1 19.5 - - + -
94B PHE 2.8 13.8 + - - +
95B LEU* 3.4 25.3 - - + -
96B CYS* 2.9 25.6 + - - -
121B ILE* 3.5 33.7 - - + -
123B SER* 5.0 2.9 - - - -
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Residues in contact with MET 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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64B GLY 3.9 0.4 - - - -
65B LEU* 1.3 80.7 - - - +
67B VAL* 1.3 58.8 + - - +
68B PRO 4.2 0.2 - - - -
96B CYS* 3.4 19.3 - - + -
98B THR* 3.7 28.9 - - + +
105B GLU* 3.9 21.8 - - + +
108B TYR* 3.6 3.4 - - + -
109B LEU* 3.3 43.1 - - + +
112B LEU* 3.4 21.1 - - + -
120B ILE* 4.1 15.5 - - + -
121B ILE 2.9 15.9 + - - +
122B ALA* 4.5 6.5 - - - -
123B SER* 3.0 29.3 - - - +
131B TYR* 4.3 7.6 - - - +
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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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70A ILE* 5.3 4.3 - - + -
65B LEU* 3.6 28.9 - - + +
66B MET* 1.3 77.6 - - - +
68B PRO* 1.3 64.4 - - + +
69B ASN 3.4 3.6 + - - +
70B ILE* 3.8 26.0 - - + +
75B PHE* 3.9 31.9 - - + +
79B ALA* 4.9 2.9 - - + -
95B LEU* 4.1 24.0 - - + -
96B CYS 2.7 12.3 + - - +
97B ASN* 3.5 4.9 - - - +
98B THR* 2.8 23.9 + - - -
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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