Contacts of the strand formed by residues 140 - 148 (chain D) 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 GLY 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D ASP 5.0 3.3 - - - +
136D PHE* 3.3 21.2 - - - -
137D ASP* 3.0 28.1 + - - +
141D THR* 1.3 66.9 + - - +
142D PRO* 3.9 2.9 - - - +
213D ARG* 3.3 42.9 - - - +
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 4.5 8.7 - - - +
136D PHE* 3.8 1.1 - - - -
137D ASP* 2.8 40.9 + - - +
140D GLY* 1.3 81.0 + - - +
142D PRO* 1.3 80.5 - - + +
143D ARG* 3.8 4.1 + - - -
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Residues in contact with PRO 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 2.9 56.1 - - + +
37D GLY 3.3 20.4 - - - +
38D ARG 4.3 12.1 - - - +
39D ASP 5.2 2.2 - - - +
40D ILE 4.6 0.2 - - - -
41D VAL* 3.4 26.2 - - + +
135D GLY 4.1 2.5 - - - +
136D PHE* 4.8 6.9 - - + -
140D GLY 3.9 5.6 - - - +
141D THR* 1.3 94.6 - - + +
143D ARG* 1.4 69.0 + - - +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 4.2 4.7 - - - +
41D VAL* 4.2 1.2 - - - +
104D VAL* 4.5 3.9 - - + +
105D GLU* 3.6 17.7 + - - +
133D ILE 4.3 0.2 - - - +
134D VAL* 3.4 7.6 - - - +
135D GLY 3.2 32.2 + - - +
137D ASP* 3.1 38.6 + - - +
141D THR* 3.9 5.2 - - - +
142D PRO* 1.4 86.9 - - - +
144D LEU* 1.3 63.2 + - - +
145D TYR* 3.2 46.9 + - + -
155D ALA* 3.9 9.7 - - - +
156D TRP 5.4 1.4 + - - -
60E GLU* 5.3 4.4 - - - +
63E SER* 3.3 22.0 + - - -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLY* 3.4 7.0 - - - -
35D VAL* 3.0 49.8 - - - +
36D ARG* 3.4 16.9 - - + +
41D VAL* 5.7 0.2 - - + -
42D VAL 4.4 1.6 - - - +
132D LEU* 4.5 7.2 - - + -
133D ILE 4.0 2.9 - - - -
134D VAL* 4.0 21.5 - - + -
143D ARG* 1.3 74.0 - - - +
145D TYR* 1.3 65.3 + - - +
156D TRP* 2.9 50.5 + - + +
158D ALA 4.2 2.5 - - - +
159D ASN* 4.0 22.4 - - + +
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Residues in contact with TYR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 4.6 6.3 - - + -
105D GLU* 3.2 36.0 - - + +
108D THR* 3.6 30.5 - - + +
132D LEU* 3.5 17.2 - - - +
133D ILE* 3.1 24.6 + - + +
143D ARG* 3.2 48.8 + - + -
144D LEU* 1.3 79.2 - - - +
146D GLN* 1.3 57.7 + - - +
153D TYR* 3.7 30.4 - + - -
154D HIS 3.5 16.8 - - - -
155D ALA* 3.5 18.2 - - + -
156D TRP* 4.4 1.1 - - - -
159D ASN* 5.3 0.4 + - - -
63E SER* 3.8 7.3 + - - -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA 3.7 5.2 - - - -
132D LEU* 4.8 0.2 - - - +
145D TYR* 1.3 73.1 - - - +
147D THR* 1.3 70.5 + - - +
148D ASP* 4.7 17.4 + - - +
152D THR 5.1 1.7 - - - +
153D TYR* 3.3 5.5 - - - +
154D HIS* 2.9 54.0 + - - +
156D TRP* 3.3 33.0 - - + +
159D ASN* 3.2 29.9 + - - +
161D ILE* 4.1 12.9 - - + +
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D THR* 3.5 18.9 - - - +
111D ILE* 4.4 1.3 - - + -
112D ALA* 3.8 36.1 - - + +
115D LYS* 3.7 25.1 - - + +
130D SER* 3.1 27.4 - - - -
131D ALA* 3.0 11.4 + - - -
133D ILE* 3.5 15.6 - - - +
146D GLN* 1.3 78.5 + - - +
148D ASP* 1.4 64.1 + - - +
152D THR 3.5 10.5 - - - +
153D TYR* 4.3 0.7 - - + -
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Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLN* 4.2 12.9 + - - +
115D LYS* 3.7 7.9 - - - +
129D ILE 4.3 2.7 - - - -
130D SER* 3.7 7.9 - - - +
146D GLN* 4.7 17.6 + - - +
147D THR* 1.4 73.3 - - - +
149D PRO* 1.3 74.6 - - + +
150D SER* 3.4 15.9 + - - -
151D GLY* 3.1 11.1 + - - -
152D THR* 3.1 44.1 + - - +
154D HIS* 5.8 0.5 + - - -
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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