Contacts of the strand formed by residues 143 - 147 (chain C) in PDB entry 6A5T
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 LEU 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ARG* 3.9 10.9 + - - +
112C ASP* 4.0 20.4 - - + +
114C TYR* 3.3 33.0 - - + +
141C GLY 4.9 0.9 - - - +
142C ILE* 1.3 78.1 - - - +
144C LEU* 1.3 63.8 + - - +
145C CYS 3.1 6.9 + - - +
146C LYS* 4.8 11.0 - - - -
2J ILE* 3.3 36.2 - - + +
3J ILE* 4.7 15.3 - - + -
15J GLY* 5.0 5.2 - - - +
16J ASP* 4.9 2.4 - - - +
18J TRP* 4.5 15.0 - - + -
19J ASP* 4.5 15.7 - - - +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 4.2 4.7 - - - +
62C ILE* 4.0 23.6 - - + +
65C ARG* 4.0 34.0 + - + +
66C LEU* 3.5 42.8 - - + +
69C ILE* 4.3 7.2 - - + -
100C LEU* 5.1 8.1 - - + -
113C VAL* 3.2 18.8 + - + +
114C TYR 3.4 22.4 - - - +
115C SER* 4.2 8.3 - - - -
118C LEU* 4.8 3.6 - - + -
142C ILE* 3.6 12.5 - - + -
143C LEU* 1.3 73.3 - - - +
145C CYS* 1.3 63.5 + - + +
155C ILE* 6.0 1.6 - - + -
2J ILE* 4.9 1.1 - - - +
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Residues in contact with CYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 4.4 10.5 - - - -
57C LEU* 4.2 18.8 - - + -
62C ILE* 4.1 10.8 - - + -
112C ASP* 3.7 4.3 - - - -
113C VAL* 2.9 34.0 + - + +
143C LEU* 3.1 7.0 + - - +
144C LEU* 1.3 84.2 - - + +
146C LYS* 1.3 94.4 + - - +
147C LEU* 3.6 19.3 - - - -
153C LEU* 4.4 9.4 - - + -
2J ILE* 4.5 5.6 - - - -
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL* 4.9 5.4 + - - +
110C THR* 4.2 14.7 - - + +
111C THR 3.5 4.0 - - - -
112C ASP* 3.6 24.7 - - - +
143C LEU* 4.8 13.9 - - + -
145C CYS* 1.3 92.0 - - - +
147C LEU* 1.3 61.8 + - - +
151C GLN* 4.5 0.3 - - - +
2J ILE* 4.5 11.7 - - + +
18J TRP* 6.0 1.8 - - - +
54J ASP* 4.3 9.1 + - - -
56J ILE* 4.0 23.0 - - + +
57J GLU* 2.3 39.6 + - - +
60J LEU* 4.2 25.6 - - + +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C SER* 3.9 17.0 - - - -
102C ALA* 4.3 10.5 - - + +
104C HIS* 4.0 20.3 - - + +
110C THR* 3.3 11.4 - - - +
111C THR* 3.0 32.8 + - - +
113C VAL* 3.7 22.7 - - + -
145C CYS* 3.6 15.7 - - - -
146C LYS* 1.3 82.9 - - - +
148C ARG* 1.3 61.7 + - - +
151C GLN* 3.1 39.9 - - + +
153C LEU* 4.3 17.0 - - + -
60J LEU* 4.9 0.9 - - - -
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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