Contacts of the strand formed by residues 92 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS 2.9 6.4 + - - +
62A THR* 2.9 26.7 + - - +
63A ILE* 2.9 24.1 + - - -
83A GLU* 5.2 2.2 - - - +
91A TYR* 1.3 79.7 - - - +
93A LEU* 1.3 64.9 + - - +
107B THR* 3.7 29.4 - - + -
108B TYR* 3.6 22.9 - - + +
111B VAL* 3.9 12.9 - - + +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A THR* 4.1 1.1 - - - -
63A ILE* 3.2 36.8 - - + +
65A LEU* 4.1 12.8 - - + -
79A ALA 4.0 6.5 - - - +
82A ILE* 4.0 16.2 - - + -
83A GLU* 3.6 52.3 + - + +
86A ALA* 4.4 11.7 - - + -
92A THR* 1.3 76.2 - - - +
94A PHE* 1.3 64.4 + - - +
95A LEU* 4.0 20.4 + - + +
95B LEU 4.3 3.8 - - - +
96B CYS* 4.8 1.0 - - - -
97B ASN 5.4 0.2 + - - -
108B TYR* 3.0 29.3 + - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A THR* 3.7 17.5 - - + +
63A ILE 3.0 8.6 + - - +
64A GLY* 3.5 5.3 - - - -
65A LEU* 2.8 26.3 + - - +
93A LEU* 1.3 79.9 - - - +
95A LEU* 1.3 61.2 + - - +
96A CYS* 4.0 1.7 + - - -
112A LEU* 4.7 2.5 - - + -
117A VAL* 4.3 12.1 - - + -
94B PHE* 3.6 52.7 - + + -
95B LEU 3.9 2.2 - - - -
96B CYS* 4.0 16.2 - - - -
108B TYR* 4.8 2.2 - + - -
111B VAL* 3.6 32.1 - - + -
112B LEU* 3.9 22.7 - - + -
115B HIS* 3.9 26.0 - + + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.4 35.4 - - + +
67A VAL* 4.3 6.7 - - + -
70A ILE* 4.5 15.0 - - + -
79A ALA* 4.2 18.6 - - + -
83A GLU* 5.1 2.5 - - - +
93A LEU* 4.0 16.8 - - + +
94A PHE* 1.3 76.4 - - - +
96A CYS* 1.3 63.4 + - - +
97A ASN 4.2 0.2 - - - -
70B ILE* 4.5 21.5 - - + -
93B LEU 4.4 0.5 - - - +
94B PHE* 3.8 1.6 - - - -
95B LEU* 2.9 63.6 + - + +
97B ASN* 5.0 9.9 - - + +
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU 2.9 8.1 + - - +
66A MET* 3.4 16.7 - - + +
67A VAL* 2.8 31.8 + - - +
94A PHE 4.4 5.8 - - - -
95A LEU* 1.3 78.8 - - - +
97A ASN* 1.3 62.4 + - - +
98A THR 3.4 0.9 + - - -
108A TYR* 3.7 39.7 - - + -
112A LEU* 4.1 25.4 - - - -
93B LEU 5.0 1.1 - - - -
94B PHE* 4.0 18.2 - - - -
95B LEU* 5.5 0.7 - - - -
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 3.4 7.6 - - - -
68A PRO 2.9 18.0 - - - +
69A ASN* 3.0 27.5 + - - +
70A ILE* 5.7 3.0 - - + +
95A LEU 4.2 0.6 + - - -
96A CYS* 1.3 70.4 - - - +
98A THR* 1.3 58.8 + - - +
99A ASP* 3.3 14.7 + - - -
104A LYS* 4.4 6.6 - - - +
108A TYR* 3.7 19.3 - - - -
79B ALA* 5.2 2.0 + - - +
80B SER* 4.0 18.4 + - - +
83B GLU* 4.0 25.5 + - - +
95B LEU* 5.0 16.3 - - + +
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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