Contacts of the strand formed by residues 90 - 94 (chain A) in PDB entry 3CTZ
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 TRP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 2.9 20.2 + - - -
10A LEU* 3.9 16.4 - - + +
53A VAL* 3.3 24.9 - - + -
54A SER* 3.6 19.9 - - - +
63A ALA* 3.8 17.9 - - + -
65A ILE* 3.3 20.9 - - + -
70A ALA* 3.3 28.7 - - + -
71A ALA 3.7 24.2 - - - -
72A MET* 4.0 4.5 - - + -
86A MET* 3.7 42.0 - - + +
87A ASP* 3.4 31.6 - - - +
88A SER* 3.1 6.4 - - - +
89A ASN* 1.3 83.1 - - + +
91A THR* 1.3 63.5 + - - +
92A LEU 4.2 0.7 + - - -
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Residues in contact with THR 91 (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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69A HIS* 5.2 8.0 + - - +
70A ALA 2.8 16.8 + - - -
71A ALA* 3.4 7.9 - - - +
72A MET 2.9 27.0 + - - -
86A MET* 4.9 2.5 - - - -
89A ASN 4.7 2.4 + - - -
90A TRP* 1.3 74.2 + - - +
92A LEU* 1.3 67.9 + - - +
93A MET* 3.6 23.6 + - + +
106A TRP* 6.0 2.2 - - + -
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Residues in contact with LEU 92 (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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72A MET* 3.7 10.8 - - + +
74A THR* 4.0 14.6 - - + -
79A PHE* 3.5 25.1 - - - +
82A ALA* 3.9 20.9 - - + -
83A ALA* 4.3 13.2 - - + +
86A MET* 4.0 18.7 - - + +
90A TRP 4.1 2.0 + - - -
91A THR* 1.3 75.4 - - - +
93A MET* 1.3 80.2 + - - +
94A LYS* 3.8 37.9 + - + +
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Residues in contact with MET 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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71A ALA* 4.0 6.7 - - + -
72A MET 2.7 16.2 + - - +
73A TRP* 3.4 41.1 - - + +
74A THR 3.3 20.4 + - - +
91A THR* 3.8 27.1 - - + +
92A LEU* 1.3 77.6 - - - +
94A LYS* 1.3 60.2 + - - +
95A MET 3.2 6.6 + - - -
100A THR* 3.8 5.6 - - + -
101A PRO* 4.1 26.7 - - + -
106A TRP* 3.4 41.3 - - + +
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Residues in contact with LYS 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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79A PHE* 3.6 44.6 - - + -
92A LEU* 3.8 32.6 + - + +
93A MET* 1.3 67.9 - - - +
95A MET* 1.3 66.8 + - - +
97A LEU* 3.4 32.3 + - + +
100A THR* 2.6 30.7 + - - +
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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