Contacts of the strand formed by residues 107 - 111 (chain R) in PDB entry 2A1T
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 HIS 107 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20R GLN* 3.7 19.8 + - - -
21R SER 3.5 2.0 + - - -
22R THR* 3.6 25.4 + - + +
23R LEU* 3.4 18.9 + - - +
47R LEU* 3.6 20.0 - - + +
105R TYR* 3.4 8.5 - - - +
106R THR* 1.3 112.5 + - + +
108R ILE* 1.3 69.8 + - - +
141R PRO* 2.9 36.2 + - + +
144R PHE* 4.6 1.6 - + - -
164R LYS* 3.2 28.1 - - + +
166R PHE* 3.6 18.4 - + + -
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Residues in contact with ILE 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R LEU* 3.6 14.4 - - + +
25R ILE* 3.9 26.2 - - + -
96R ILE* 4.2 24.2 - - + -
100R GLN* 4.3 15.3 - - + +
105R TYR* 4.5 8.3 - - + -
107R HIS* 1.3 81.3 - - - +
109R CYS* 1.3 63.9 + - - +
120R LEU* 4.7 5.2 - - + -
123R VAL* 4.6 4.9 - - + -
127R LEU* 3.7 30.1 - - + -
163R VAL* 3.7 15.0 - - + -
164R LYS 2.7 10.2 + - - +
165R VAL* 3.1 35.7 - - + +
166R PHE 3.1 1.7 + - - -
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Residues in contact with CYS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R THR* 4.8 7.2 - - - -
23R LEU 3.1 14.5 + - - +
24R VAL* 4.4 10.5 - - - -
25R ILE* 3.1 28.1 + - - +
40R THR* 3.6 25.4 - - - -
43R ALA* 6.4 0.2 - - - -
44R ALA* 5.2 2.5 - - - -
108R ILE* 1.3 76.4 - - - +
110R ALA* 1.3 62.1 + - - +
120R LEU* 4.1 6.3 - - - -
166R PHE* 2.8 50.5 - - + +
168R VAL* 4.6 0.4 - - + -
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Residues in contact with ALA 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R ILE* 4.1 24.0 - - + +
40R THR* 3.5 12.1 - - - -
109R CYS* 1.3 79.7 - - - +
111R GLY* 1.3 67.9 + - - +
115R PHE* 4.8 5.8 - - + -
116R GLY* 4.2 9.4 - - - -
119R LEU* 6.3 0.4 - - + -
120R LEU* 3.7 18.4 - - + +
166R PHE 3.2 4.0 + - - -
167R SER* 3.0 5.5 - - - -
168R VAL* 2.9 26.2 + - - +
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Residues in contact with GLY 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R ILE 5.0 2.0 + - - -
27R GLU* 4.6 3.4 + - - +
36R ILE* 3.5 20.6 - - - -
37R THR* 5.6 1.2 - - - +
40R THR* 3.1 22.7 + - - -
110R ALA* 1.3 76.0 - - - +
112R ALA* 1.3 52.7 + - - -
113R SER* 2.7 20.1 + - - -
115R PHE* 5.3 0.2 - - - -
116R GLY* 3.4 18.7 + - - -
167R SER* 4.2 0.2 - - - -
168R VAL 3.7 3.6 - - - -
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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