Contacts of the strand formed by residues 143 - 148 (chain O) in PDB entry 5C7O
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 143 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O MET* 4.6 17.5 - - + -
99O VAL 5.7 0.2 - - - -
100O LYS* 3.8 33.3 + - + +
101O VAL 2.4 41.0 + - - -
102O VAL* 4.9 3.1 - - + -
138O LEU 3.5 1.2 - - - +
139O VAL* 3.3 3.6 - - - -
140O VAL 2.9 35.9 + - - +
141O ASP 3.0 4.2 + - - +
142O ASN* 1.3 76.8 - - - +
144O GLU* 1.3 82.5 + - - +
145O ILE* 3.7 19.6 + - + +
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Residues in contact with GLU 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O VAL 4.2 0.5 - - - +
102O VAL* 4.7 2.8 - - - +
134O ARG* 4.3 17.1 + - - +
135O ASN* 5.3 4.0 + - - -
137O GLN* 3.5 30.6 + - - +
138O LEU 3.8 3.4 - - - -
139O VAL* 4.2 16.8 - - + -
142O ASN 3.6 8.2 + - - +
143O HIS* 1.3 93.1 + - - +
145O ILE* 1.3 59.6 + - - +
146O SER 4.4 0.5 + - - -
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Residues in contact with ILE 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O LEU* 4.1 27.8 - - + -
95O MET* 5.3 0.2 - - - -
101O VAL* 3.5 15.7 - - + +
102O VAL 3.9 3.1 - - - -
103O ALA* 3.7 24.7 - - - +
104O VAL* 3.9 12.3 - - + -
137O GLN* 3.3 7.4 - - - +
138O LEU* 2.7 53.1 + - + +
140O VAL* 4.1 24.5 - - + -
143O HIS* 3.8 16.4 - - + +
144O GLU* 1.3 77.4 - - - +
146O SER* 1.3 73.8 + - - +
147O VAL* 3.8 0.6 - - + +
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Residues in contact with SER 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O VAL 3.0 16.1 + - - -
103O ALA* 3.2 4.5 - - - -
104O VAL 2.9 26.2 + - - +
136O GLY 4.9 0.2 - - - -
137O GLN* 3.6 22.0 + - - +
144O GLU 4.4 0.2 + - - -
145O ILE* 1.3 76.0 - - - +
147O VAL* 1.3 60.1 + - - +
148O TYR* 3.9 28.3 + - - -
161O VAL* 3.8 11.8 - - - +
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Residues in contact with VAL 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O VAL* 3.4 3.8 - - + +
111O PRO* 3.9 21.7 - - + +
114O MET* 3.6 29.4 - - + -
136O GLY 3.7 19.9 + - - +
138O LEU* 3.6 35.9 - - + +
145O ILE* 3.6 1.3 + - + +
146O SER* 1.3 78.6 - - - +
148O TYR* 1.3 69.4 + - - +
149O GLN* 3.5 28.4 - - + +
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Residues in contact with TYR 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O ALA* 3.8 23.8 - - + -
104O VAL 2.9 9.6 + - - +
105O ASN* 3.1 18.9 - - + +
106O ASP 3.1 21.7 + - - -
146O SER* 3.9 17.5 + - - -
147O VAL* 1.3 77.2 - - - +
149O GLN* 1.3 71.3 + - - +
150O CYS* 4.0 9.6 - - - -
156O ILE* 3.8 19.7 - - + -
157O PRO* 3.7 35.0 - - + -
158O TRP* 4.6 3.4 - + - -
160O ALA* 3.6 16.8 - - + +
161O VAL* 3.2 27.3 - - + +
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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