Contacts of the strand formed by residues 136 - 144 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.7 5.8 - - - +
80A MET* 3.5 32.5 - - + -
81A THR 3.3 10.8 - - - +
83A MET 4.6 0.2 - - - +
86A ASP 3.9 20.9 - - - -
87A SER* 4.1 11.0 - - - +
90A GLN* 3.4 30.0 - - - +
134A LEU* 3.0 15.3 + - - +
135A GLY* 1.4 74.7 - - - +
137A CYS* 1.4 61.8 + - - +
138A MET* 3.7 2.8 + - - +
154A CYS* 4.5 2.8 - - - +
155A ASP 5.1 0.9 - - - -
156A PRO* 4.8 5.6 - - - +
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Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.4 20.3 - - + +
79A VAL 3.5 1.6 - - - +
80A MET* 3.2 6.4 - - - -
81A THR* 3.0 37.7 + - - +
136A CYS* 1.4 72.7 - - - +
138A MET* 1.3 59.1 + - - +
139A ILE* 4.0 6.5 - - - -
153A LYS* 3.6 23.8 - - - -
154A CYS 3.4 18.6 - - - -
155A ASP* 4.3 6.1 - - - +
168A ALA* 3.4 35.0 - - + -
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 5.1 1.1 - - + -
78A CYS* 3.7 26.9 - - - -
79A VAL 3.7 2.5 - - - -
80A MET* 3.6 30.5 - - + +
90A GLN* 4.5 4.0 - - - +
94A ALA* 3.9 23.1 - - + -
118A ILE* 3.5 35.0 - - + -
136A CYS 4.5 3.1 - - - +
137A CYS* 1.3 74.6 - - - +
139A ILE* 1.3 59.5 + - - +
140A LEU* 3.4 37.3 + - + +
152A TYR 3.5 1.7 - - - +
153A LYS* 4.6 0.2 - - - -
154A CYS* 3.1 42.2 + - + -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 3.9 19.1 - - - -
40A VAL 6.0 0.2 - - - +
41A ALA* 3.9 11.2 - - + +
50A ILE* 3.3 25.6 - - + +
78A CYS* 3.2 4.2 - - - -
79A VAL* 3.0 41.6 + - + +
81A THR* 3.5 19.3 - - - +
137A CYS* 4.2 8.1 - - - +
138A MET* 1.3 70.1 - - - +
140A LEU* 1.4 63.5 + - - +
151A VAL* 4.1 1.6 - - + -
152A TYR 3.3 8.1 - - - +
153A LYS* 4.8 2.0 - - + +
166A THR* 3.5 36.3 - - + +
168A ALA* 4.0 19.7 - - + +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 6.3 0.9 - - + -
76A ILE* 4.8 7.0 - - + -
77A GLY 3.6 8.3 - - - +
78A CYS* 3.7 10.3 - - + -
111A VAL* 3.6 39.5 - - + +
114A LEU* 4.0 11.9 - - + -
115A CYS* 3.7 35.9 - - + +
138A MET* 3.4 45.1 - - + +
139A ILE* 1.4 74.4 - - - +
141A ILE* 1.3 68.9 + - - +
150A GLN 3.8 0.4 - - - +
151A VAL* 3.5 1.9 - - - -
152A TYR* 3.0 29.4 + - + +
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.3 9.4 - - + -
48A ALA* 3.1 33.4 - - + +
50A ILE* 3.4 43.5 - - + -
76A ILE* 3.8 5.0 - - - +
77A GLY 3.0 33.8 + - - +
111A VAL* 4.7 2.0 - - - -
140A LEU* 1.3 79.1 - - - +
142A GLY* 1.3 59.5 + - - +
150A GLN 3.5 12.8 - - - +
151A VAL* 4.1 15.5 - - + -
218A GLY 3.5 6.5 - - - +
220A VAL* 3.9 9.9 - - + -
227A PHE* 3.8 23.4 - - + -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.8 1.8 - - - +
75A ASN 4.0 13.7 - - - -
76A ILE* 4.8 0.2 - - - -
111A VAL* 3.5 11.9 - - - +
141A ILE* 1.3 79.3 - - - +
143A ILE* 1.3 64.0 + - - -
149A PRO* 4.6 1.1 - - - -
150A GLN* 3.0 32.5 + - - +
220A VAL* 4.1 13.9 - - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP 5.2 0.2 - - - +
75A ASN* 4.5 3.4 + - - +
108A GLU* 3.6 22.2 - - - +
111A VAL* 4.3 2.5 - - - -
142A GLY* 1.3 74.0 - - - -
144A ASP* 1.3 75.6 + - - +
148A GLY* 4.0 12.1 - - - -
149A PRO* 4.0 22.9 - - + -
220A VAL* 3.6 30.1 - - + +
221A THR 3.8 4.3 - - - +
222A VAL* 3.5 38.1 - - + +
225A PRO* 4.9 13.5 + - + +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU* 5.1 4.3 - - - -
110A PRO* 3.6 36.3 - - + +
111A VAL* 4.3 6.0 - - - +
112A ASP* 6.3 0.2 - - + -
142A GLY 3.8 2.8 + - - -
143A ILE* 1.3 86.4 - - - +
148A GLY 2.9 36.9 + - - +
150A GLN* 4.1 20.9 - - + +
72I ARG* 5.6 7.5 + - - -
75I ARG* 5.3 6.6 + - - -
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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