Contacts of the strand formed by residues 136 - 144 (chain O) in PDB entry 5A0Q
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 CYS 136 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32O ILE* 3.7 6.1 - - - +
80O MET* 3.5 33.4 - - + -
81O THR 3.3 10.5 - - - +
83O MET 4.6 0.2 - - - +
86O ASP 3.9 21.1 - - - -
87O SER* 4.1 10.8 - - - +
90O GLN* 3.4 28.9 - - - +
134O LEU* 3.0 16.3 + - - +
135O GLY* 1.4 73.4 - - - +
137O CYS* 1.4 62.4 + - - +
138O MET* 3.7 2.9 + - - +
154O CYS* 4.5 2.6 - - - +
155O ASP 5.1 1.2 - - - -
156O PRO* 4.8 5.4 - - - +
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Residues in contact with CYS 137 (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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32O ILE* 3.4 19.7 - - + +
79O VAL 3.5 1.4 - - - +
80O MET* 3.2 6.2 - - - -
81O THR* 3.0 38.5 + - - +
136O CYS* 1.4 72.6 - - - +
138O MET* 1.3 58.9 + - - +
139O ILE* 4.0 5.4 - - - -
153O LYS* 3.6 24.5 - - - -
154O CYS 3.4 18.6 - - - -
155O ASP* 4.3 6.1 - - - -
168O ALA* 3.4 34.1 - - + -
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Residues in contact with MET 138 (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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72O ILE* 5.1 1.1 - - + -
78O CYS* 3.7 26.0 - - - -
79O VAL 3.7 2.2 - - - -
80O MET* 3.6 32.1 - - + +
90O GLN* 4.5 4.5 - - - +
94O ALA* 3.9 23.6 - - + -
115O CYS* 5.9 0.4 - - - -
118O ILE* 3.5 34.8 - - + -
136O CYS 4.5 3.1 - - - +
137O CYS* 1.3 74.8 - - - +
139O ILE* 1.3 60.4 + - - +
140O LEU* 3.4 37.1 + - + +
152O TYR 3.5 1.7 - - - +
153O LYS* 4.6 0.2 - - - -
154O CYS* 3.1 41.6 + - + -
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Residues in contact with ILE 139 (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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39O SER* 3.9 19.3 - - - -
40O VAL 5.7 0.4 - - - -
41O ALA* 3.9 11.0 - - + +
50O ILE* 3.3 25.7 - - + +
78O CYS* 3.2 4.1 - - - -
79O VAL* 3.0 41.9 + - + +
81O THR* 3.5 18.6 - - - +
137O CYS* 4.2 8.5 - - - +
138O MET* 1.3 70.6 - - - +
140O LEU* 1.4 63.4 + - - +
141O ILE* 4.8 0.2 - - + -
151O VAL* 4.1 1.6 - - + -
152O TYR 3.3 8.3 - - - +
153O LYS* 5.2 2.0 - - + -
166O THR* 3.5 36.3 - - + +
168O ALA* 4.0 19.5 - - + +
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Residues in contact with LEU 140 (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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72O ILE* 6.3 0.9 - - + -
76O ILE* 4.8 7.2 - - + -
77O GLY 3.6 7.4 - - - +
78O CYS* 3.7 10.1 - - + -
111O VAL* 3.6 39.5 - - + +
114O LEU* 4.0 12.1 - - + -
115O CYS* 3.7 36.3 - - + +
138O MET* 3.4 45.1 - - + +
139O ILE* 1.4 74.0 - - - +
141O ILE* 1.3 67.2 + - - +
150O GLN 3.8 0.2 - - - +
151O VAL* 3.5 2.1 - - - -
152O TYR* 3.0 28.7 + - + +
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Residues in contact with ILE 141 (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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41O ALA* 4.3 9.6 - - + -
48O ALA* 3.1 33.2 - - + +
49O VAL 4.5 0.2 - - - +
50O ILE* 3.4 43.5 - - + -
76O ILE* 3.8 5.1 - - - +
77O GLY 3.0 34.2 + - - +
111O VAL* 4.7 2.7 - - - -
139O ILE 3.9 0.2 + - - -
140O LEU* 1.3 78.5 - - - +
142O GLY* 1.3 59.3 + - - +
150O GLN 3.5 13.9 - - - +
151O VAL* 4.1 15.5 - - + -
218O GLY 3.5 6.3 - - - +
220O VAL* 3.9 9.2 - - + -
227O PHE* 3.8 23.4 - - + -
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Residues in contact with GLY 142 (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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48O ALA* 4.8 1.6 - - - +
75O ASN 4.0 14.1 - - - -
76O ILE* 4.8 0.2 - - - -
111O VAL* 3.5 11.5 - - - +
141O ILE* 1.3 78.1 - - - +
143O ILE* 1.3 64.6 + - - -
149O PRO* 4.6 1.1 - - - -
150O GLN* 3.0 31.9 + - - +
220O VAL* 4.1 13.7 - - - +
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Residues in contact with ILE 143 (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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46O ASP 5.2 0.4 - - - +
75O ASN* 4.5 3.8 + - - +
108O GLU* 3.6 22.2 - - - +
111O VAL* 4.3 3.1 - - - -
142O GLY* 1.3 72.6 - - - -
144O ASP* 1.3 76.4 + - - +
148O GLY* 4.0 12.6 - - - -
149O PRO* 4.0 23.1 - - + -
220O VAL* 3.6 31.4 - - + +
221O THR 3.8 3.8 - - - +
222O VAL* 3.5 37.5 - - + +
225O PRO* 4.9 14.1 + - + +
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Residues in contact with ASP 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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108O GLU* 5.1 3.1 - - - -
110O PRO* 3.6 35.3 - - + +
111O VAL* 4.3 6.2 - - - +
112O ASP* 5.8 0.7 - - + +
142O GLY 3.8 2.8 + - - -
143O ILE* 1.3 85.6 - - - +
148O GLY 2.9 36.9 + - - +
150O GLN* 4.1 20.1 - - + +
72W ARG* 5.6 7.2 + - - -
75W ARG* 5.3 6.8 + - - -
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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