Contacts of the strand formed by residues 142 - 149 (chain P) 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 ARG 142 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P LYS* 3.8 18.2 - - + +
138P TRP* 3.4 3.2 - - - -
139P ASN 2.9 21.8 + - - +
140P GLU* 4.0 4.0 - - + +
141P GLY* 1.3 79.2 - - - +
143P PRO* 1.3 81.6 + - + +
144P TYR* 3.0 67.2 - - + +
145P LEU 4.6 1.8 - - - +
146P PHE* 5.2 0.2 - - - -
156P ALA* 4.4 16.4 - - - +
157P TRP 4.6 4.4 + - - -
57Q ASP* 3.1 41.2 + - - +
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Residues in contact with PRO 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P LYS* 3.0 44.9 - - + +
40P ALA* 4.7 15.3 - - - +
42P GLY* 4.4 8.5 - - - +
43P VAL* 4.0 16.6 - - + +
137P GLY 3.4 2.0 - - - +
138P TRP* 2.3 43.3 - - + +
141P GLY 4.1 2.7 - - - +
142P ARG* 1.3 99.0 + - + +
144P TYR* 1.3 60.1 + - - +
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Residues in contact with TYR 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P VAL* 4.1 3.9 - - - +
106P THR* 3.1 24.2 - - + -
107P ALA* 5.2 7.2 - - + -
136P CYS* 3.2 4.7 - - - +
137P GLY 2.0 69.5 + - - +
139P ASN* 3.3 20.5 - - + +
140P GLU* 1.9 37.2 + - - -
142P ARG* 3.0 62.2 - - + +
143P PRO* 1.3 69.1 - - - +
145P LEU* 1.3 58.8 + - - +
146P PHE* 3.7 27.1 - + + -
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Residues in contact with LEU 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P GLY 3.5 26.0 - - - +
38P LYS* 3.9 8.1 - - + +
43P VAL* 4.0 18.4 - - + -
45P LEU* 3.7 29.4 - - + -
134P LEU* 4.7 1.3 - - + -
135P ILE 4.1 0.9 - - - -
136P CYS* 4.1 3.4 - - + -
142P ARG* 4.6 2.2 - - - +
143P PRO 4.2 1.0 + - - -
144P TYR* 1.3 75.8 - - - +
146P PHE* 1.4 63.2 + - - +
156P ALA* 3.3 5.9 - - - +
157P TRP* 2.8 43.5 + - + +
158P LYS 3.8 5.4 - - - -
159P ALA* 3.7 26.0 - - - +
160P THR* 3.8 20.2 - - + -
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Residues in contact with PHE 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P THR* 4.0 3.1 - - + -
107P ALA* 3.6 38.1 - - + -
110P VAL* 3.7 27.8 - - + -
134P LEU* 3.2 12.6 - - - +
135P ILE* 2.9 41.2 + - + +
142P ARG* 5.2 0.2 - - - -
144P TYR* 3.7 32.1 - + + -
145P LEU* 1.4 78.7 - - - +
147P GLN* 1.3 59.7 + - - +
154P TYR* 3.7 32.8 - + - -
155P PHE 3.4 2.2 - - - -
156P ALA* 3.6 34.8 - - + -
157P TRP* 5.3 1.3 - - - -
160P THR* 5.6 0.2 - - - -
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Residues in contact with GLN 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P SER* 3.1 1.4 + - - -
133P LEU 3.4 5.3 + - - -
134P LEU* 3.5 6.0 - - + +
146P PHE* 1.3 74.8 - - - +
148P SER* 1.4 70.7 + - - +
149P ASP* 2.9 35.8 + - - +
153P ALA 4.0 0.5 - - - +
154P TYR* 3.1 5.6 - - - -
155P PHE* 2.8 40.5 + - + +
157P TRP* 4.2 16.8 - - + +
160P THR* 4.0 7.3 + - - +
161P ALA 4.1 1.9 - - - +
162P MET* 2.6 50.9 - - - +
170P LYS* 4.8 6.2 + - - +
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Residues in contact with SER 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P VAL* 4.7 2.8 + - - +
113P VAL* 5.1 2.4 - - - -
114P ALA* 4.1 16.1 + - - +
117P MET* 3.6 21.6 - - - -
132P SER* 2.9 8.8 + - - -
133P LEU* 2.9 31.6 + - - -
135P ILE* 4.3 19.3 - - - +
146P PHE 4.2 0.6 - - - -
147P GLN* 1.4 70.6 + - - +
149P ASP* 1.4 69.6 + - - +
152P GLY* 4.7 0.5 - - - -
153P ALA 3.7 7.9 + - - -
154P TYR* 3.9 11.6 - - - +
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Residues in contact with ASP 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU* 5.0 6.9 - - + +
28P VAL* 5.9 1.3 - - - -
117P MET* 3.2 16.2 - - - +
132P SER* 2.1 30.8 + - - -
147P GLN* 2.9 24.4 + - - +
148P SER* 1.4 75.5 - - - +
150P PRO* 1.3 70.4 - - + +
151P SER* 3.3 6.1 - - - +
152P GLY* 3.0 18.3 + - - -
153P ALA* 3.0 17.8 + - + +
155P PHE* 4.4 11.6 - - - -
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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