Contacts of the strand formed by residues 102 - 107 (chain U) in PDB entry 3ALQ
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 102 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120S LYS* 6.3 0.7 - - - -
151S THR* 4.2 16.8 - - + -
81U ASP* 3.3 31.9 - - + -
98U CYS* 4.0 13.8 - - + +
99U ARG* 3.1 63.6 + - + +
100U PRO* 3.7 7.7 + - - +
101U GLY* 1.3 90.4 + - - +
103U TYR* 1.3 63.2 + - - +
115U CYS* 4.0 14.6 - - + -
116U ALA* 3.4 16.8 - - - +
117U PRO* 3.2 48.4 - - + +
118U LEU* 4.2 5.3 - - - +
132U THR 4.7 2.3 - - - +
133U GLU* 3.9 13.3 - - - +
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Residues in contact with TYR 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E HIS* 5.1 6.1 + - - -
98U CYS* 3.4 5.9 - - - -
102U TRP* 1.3 73.9 - - - +
104U CYS* 1.3 69.4 + - - +
105U ALA* 4.0 20.6 - - + +
115U CYS* 3.4 5.5 - - - -
116U ALA* 2.9 72.0 + - + +
117U PRO 3.8 5.4 - - - -
118U LEU* 3.9 10.1 - - + -
132U THR 3.6 21.5 - - - +
133U GLU* 3.8 6.3 - - - +
134U THR 5.0 0.7 - - - -
135U SER* 3.8 14.4 - - - +
136U ASP* 3.4 54.5 + - + +
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Residues in contact with CYS 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U TYR* 1.3 75.3 - - - +
105U ALA* 1.3 63.0 + - - +
106U LEU 3.3 17.0 - - - -
107U SER* 3.4 23.0 + - - +
111U GLY 4.2 1.6 - - - -
112U CYS* 2.0 54.5 - - + -
133U GLU* 2.8 26.2 + - + +
134U THR* 3.8 22.0 - - + +
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Residues in contact with ALA 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E HIS* 5.0 7.2 - - + +
75E LEU* 5.5 1.9 - - + +
103U TYR* 3.5 23.5 + - + +
104U CYS* 1.3 73.3 - - - +
106U LEU* 1.3 70.2 + - + +
107U SER 4.1 0.4 + - - -
114U LEU* 3.0 32.6 + - + +
116U ALA* 4.5 12.1 - - + -
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Residues in contact with LEU 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 5.0 2.0 - - - +
75E LEU* 3.7 35.7 - - + -
77E THR* 4.1 20.4 - - + +
97E ILE* 3.6 32.8 - - + -
137E ASN* 4.4 14.8 - - + +
104U CYS* 3.3 5.0 - - - -
105U ALA* 1.3 84.3 - - - +
107U SER* 1.3 62.9 + - - +
113U ARG* 2.8 40.8 + - - +
114U LEU* 3.4 17.7 + - + +
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Residues in contact with SER 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLU* 5.5 0.7 - - - +
104U CYS* 3.4 16.6 + - - +
105U ALA 4.1 1.2 + - - -
106U LEU* 1.3 74.9 - - - +
108U LYS* 1.3 64.7 + - - +
111U GLY 3.9 7.2 + - - -
113U ARG* 4.9 0.9 - - - -
134U THR* 3.2 30.1 - - - +
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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