Contacts of the strand formed by residues 92 - 97 (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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A THR* 3.8 28.5 - - + -
108A TYR* 3.8 21.1 - - + +
111A VAL* 3.9 13.3 - - + +
61B LYS 3.0 6.3 + - - +
62B THR* 2.8 27.5 + - - +
63B ILE* 2.9 25.5 + - - +
83B GLU* 5.3 2.7 - - - +
90B GLY 5.8 0.7 - - - +
91B TYR* 1.3 77.3 - - - +
93B LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 93 (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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95A LEU 4.4 3.8 - - - +
96A CYS* 5.0 0.9 - - - -
108A TYR* 3.0 29.7 + - - -
62B THR* 4.1 0.7 - - - -
63B ILE* 3.2 35.0 - - + +
65B LEU* 4.1 10.1 - - + -
79B ALA 4.0 6.5 - - - +
82B ILE* 4.0 16.4 - - + -
83B GLU* 3.6 52.1 + - + +
86B ALA* 4.2 14.1 - - + -
92B THR* 1.3 75.1 - - - +
94B PHE* 1.3 64.2 + - - +
95B LEU* 4.1 21.2 + - + +
294B ILE* 5.3 0.2 - - + -
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Residues in contact with PHE 94 (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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94A PHE* 3.6 54.3 - + + -
95A LEU 3.9 2.2 - - - -
96A CYS* 4.0 15.7 - - - -
108A TYR* 4.8 1.6 - + - -
111A VAL* 3.7 32.1 - - + -
112A LEU* 3.9 22.7 - - + -
115A HIS* 3.8 27.4 - + + -
62B THR* 3.7 17.9 - - + +
63B ILE 2.9 9.0 + - - +
64B GLY* 3.5 5.0 - - - -
65B LEU* 2.8 25.6 + - - +
93B LEU* 1.3 80.8 - - - +
95B LEU* 1.3 62.9 + - - +
96B CYS* 3.9 2.2 + - - -
112B LEU* 4.7 0.7 - - + -
117B VAL* 4.5 11.2 - - + -
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Residues in contact with LEU 95 (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* 3.9 29.8 - - + -
93A LEU 4.3 0.5 - - - +
94A PHE* 3.8 2.1 - - - -
95A LEU* 2.9 62.8 + - + +
97A ASN* 5.0 17.3 - - + +
65B LEU* 3.4 34.1 - - + -
67B VAL* 4.1 10.3 - - + -
70B ILE* 6.3 0.2 - - + -
79B ALA* 4.1 14.4 - - + +
83B GLU* 5.1 2.9 - - - +
93B LEU* 4.1 16.4 - - + +
94B PHE* 1.3 77.0 - - - +
96B CYS* 1.3 63.7 + - - +
97B ASN 4.2 0.2 - - - -
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Residues in contact with CYS 96 (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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93A LEU 4.8 0.9 - - - -
94A PHE* 4.0 19.1 - - - -
95A LEU* 5.9 0.2 - - - -
65B LEU 2.9 8.3 + - - +
66B MET* 3.4 15.6 - - + -
67B VAL* 2.7 33.7 + - - -
94B PHE 4.3 6.5 - - - -
95B LEU* 1.3 80.0 - - - +
97B ASN* 1.3 60.9 + - - +
98B THR* 3.4 1.8 + - - +
108B TYR* 3.7 37.7 - - + -
112B LEU* 4.0 26.2 - - - -
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Residues in contact with ASN 97 (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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79A ALA 5.2 0.6 + - - -
80A SER* 4.1 15.0 + - - +
83A GLU* 3.8 26.8 + - - +
93A LEU 5.4 0.2 + - - -
95A LEU* 5.0 9.3 - - + +
67B VAL 3.5 5.5 - - - +
69B ASN* 5.1 0.2 - - - -
70B ILE* 3.6 48.7 + - + +
95B LEU 4.2 1.2 + - - -
96B CYS* 1.3 70.2 - - - +
98B THR* 1.3 61.7 + - - +
99B ASP* 3.3 20.5 + - - +
104B LYS* 4.4 7.0 - - - +
108B TYR* 3.7 19.5 - - - -
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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