Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 1SQU
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 PHE 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 5.3 1.1 - - + -
21A LEU* 5.6 2.0 - - + -
58A TYR* 4.8 18.4 - + + -
59A SER 3.3 5.4 - - - -
60A PHE* 3.3 38.6 - + + -
64A THR* 3.5 19.7 - - + -
68A VAL* 3.5 31.2 - - + -
92A LEU* 5.2 8.1 - - + -
136A PRO* 4.1 0.5 - - - +
137A ILE* 2.9 49.1 + - + +
139A VAL* 3.1 34.8 - - + -
140A PHE* 5.1 0.7 - + - -
143A GLU* 3.2 4.2 - - - +
144A ASP* 1.3 82.8 - - - +
146A ASP* 1.3 61.0 + - - +
147A LEU* 3.9 0.9 + - + -
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Residues in contact with ASP 146 (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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36A ILE* 5.2 1.6 - - - +
37A GLU 4.7 0.4 - - - +
39A PRO* 2.8 38.8 - - + +
40A HIS* 3.6 4.3 - - + +
57A ILE 3.5 1.9 - - - +
58A TYR* 4.8 0.4 - - - -
59A SER* 2.8 51.3 + - - -
134A LYS* 4.9 10.3 - - + +
135A LEU 4.4 2.9 - - - -
136A PRO* 4.7 2.5 - - + -
143A GLU* 4.9 15.3 - - + +
144A ASP 4.4 0.2 - - - -
145A PHE* 1.3 73.5 - - - +
147A LEU* 1.3 57.9 + - - +
148A HIS* 2.9 29.1 + - + -
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Residues in contact with LEU 147 (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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9A LEU* 4.2 13.7 - - + -
13A VAL* 3.7 25.4 - - + -
56A LEU* 3.2 30.5 - - + -
57A ILE 3.5 8.1 - - - +
58A TYR* 3.3 41.7 - - + +
133A LEU 5.4 0.2 - - - +
134A LYS* 3.6 0.3 - - - +
135A LEU* 3.0 45.6 + - + +
137A ILE* 4.3 12.1 - - + -
145A PHE* 3.9 0.8 + - + -
146A ASP* 1.3 73.4 - - - +
148A HIS* 1.3 94.0 + - - +
149A LEU 4.1 0.7 - - - +
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Residues in contact with HIS 148 (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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33A VAL* 4.0 10.3 - - + +
35A HIS 4.6 0.2 + - - -
36A ILE* 3.4 57.4 - - + +
37A GLU 4.4 6.1 + - - -
55A SER 3.8 0.7 - - - +
56A LEU* 3.6 2.3 - - - -
57A ILE* 2.9 38.6 + - + +
132A ILE* 4.0 16.6 - - + -
133A LEU 3.3 4.9 - - - +
134A LYS* 3.7 37.0 + - + +
146A ASP* 2.9 26.8 + - + -
147A LEU* 1.3 86.7 - - - +
149A LEU* 1.3 59.8 + - - +
150A SER 3.9 1.9 + - - +
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.6 25.1 - - + +
5A ILE* 4.1 13.0 - - + -
9A LEU* 3.9 35.4 - - + -
48A ILE* 3.7 23.3 - - + -
52A ILE* 5.0 2.7 - - + -
55A SER 2.8 26.9 - - - +
56A LEU* 3.9 11.4 - - + -
100A LEU* 4.9 6.5 - - + -
131A VAL 3.9 0.9 - - - +
132A ILE* 4.5 0.4 - - - -
133A LEU* 2.9 35.0 + - + +
147A LEU* 4.1 0.2 - - - +
148A HIS* 1.3 74.9 - - - +
150A SER* 1.3 61.6 + - - +
151A VAL* 3.8 14.4 + - + +
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Residues in contact with SER 150 (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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36A ILE* 5.4 1.6 - - - -
54A GLY* 3.1 4.5 - - - -
55A SER* 2.9 55.0 + - - +
57A ILE* 6.0 0.4 - - - +
128A SER* 3.3 17.9 + - - -
129A PHE 3.8 16.9 + - - -
131A VAL 3.0 10.5 - - - -
132A ILE* 3.8 18.1 - - - +
148A HIS* 3.9 2.0 + - - +
149A LEU* 1.3 74.6 - - - +
151A VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 151 (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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1A MET* 3.7 33.2 - - + -
5A ILE* 5.6 5.2 - - + -
52A ILE* 4.1 24.7 - - + -
53A GLU 3.3 6.5 - - - +
54A GLY* 4.7 0.2 - - - -
129A PHE 4.5 2.2 - - - -
130A GLY* 3.0 5.7 - - - -
131A VAL* 2.6 46.0 + - + +
149A LEU* 3.8 15.0 - - + +
150A SER* 1.3 82.1 - - - +
152A LYS* 1.3 99.3 + - + +
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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