Contacts of the strand formed by residues 20 - 27 (chain A) in PDB entry 1LNU
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 ILE 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.9 1.0 - - - +
14A TYR* 3.1 8.2 - - - -
15A GLN* 2.8 62.0 + - + +
17A PRO 3.4 20.4 - - - +
18A GLY* 3.3 17.9 - - - +
19A ASP* 1.3 70.9 - - - +
21A GLY* 1.3 64.1 + - - +
116A PRO 5.1 3.6 - - - +
117A VAL* 4.2 17.0 - - + -
169A TRP* 5.8 2.0 - - + -
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Residues in contact with GLY 21 (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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13A VAL 3.3 8.7 - - - -
14A TYR* 4.0 10.0 - - - -
19A ASP 3.8 4.0 + - - -
20A ILE* 1.3 79.5 - - - +
22A GLN* 1.3 63.2 + - - +
37A LEU* 3.3 25.9 - - - +
64A ILE* 4.5 1.6 - - - -
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Residues in contact with GLN 22 (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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11A ILE* 3.5 4.5 - - - +
12A SER* 3.7 1.0 - - - -
13A VAL* 3.0 46.4 + - + +
21A GLY* 1.3 75.2 - - - +
23A TYR* 1.3 62.5 + - - +
24A THR* 3.5 23.2 + - + +
34A TYR* 5.7 2.0 - - + -
35A VAL 5.7 0.4 - - - -
37A LEU* 3.8 3.2 - - - +
64A ILE* 3.9 3.5 - - - +
137A SER* 3.8 8.7 - - - +
138A PHE* 3.1 68.5 + - + +
146A PHE* 5.1 6.3 - - - -
148A LYS* 5.3 0.2 + - - -
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Residues in contact with TYR 23 (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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10A GLY* 3.2 23.5 - - - -
11A ILE 3.3 2.9 - - - -
12A SER* 3.1 27.8 - - - -
22A GLN* 1.3 74.4 - - - +
24A THR* 1.3 62.6 + - - +
25A PHE* 3.0 35.7 - + - -
33A PHE* 4.5 0.7 - + - -
34A TYR* 3.4 4.5 - - - +
35A VAL* 3.0 48.6 + - + -
37A LEU* 4.4 10.8 - - + +
55A PHE* 3.5 16.8 - + - -
59A GLY 4.9 0.2 - - - -
60A GLY* 3.7 25.4 - - - +
63A ASN* 3.8 13.9 - - + -
64A ILE* 4.3 10.5 - - + +
5B LYS* 3.4 19.9 - - - +
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Residues in contact with THR 24 (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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11A ILE* 2.9 66.3 + - + +
22A GLN* 3.5 36.5 + - + +
23A TYR* 1.3 82.9 - - - +
25A PHE* 1.3 70.5 + - - +
26A GLU* 4.5 7.6 + - - -
31A GLU* 5.2 3.8 - - - -
33A PHE* 3.8 8.7 - - - -
34A TYR* 4.2 5.2 - - + -
137A SER* 4.2 15.9 - - - -
138A PHE 4.9 1.9 + - - +
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Residues in contact with PHE 25 (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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8A THR 3.5 4.0 - - - -
9A TYR* 3.0 35.7 - + + -
10A GLY 3.3 17.0 - - - -
23A TYR* 3.0 33.4 - + - -
24A THR* 1.3 76.4 - - - +
26A GLU* 1.3 61.5 + - - +
31A GLU* 3.8 4.0 - - - +
32A LEU* 2.9 34.2 + - + +
33A PHE* 3.3 41.3 + + + +
55A PHE* 3.6 20.4 - + - -
3B ALA* 4.2 16.6 - - + -
4B GLN 3.6 22.7 - - - -
5B LYS* 3.9 2.9 - - - -
108B ASN* 4.4 1.1 - - - -
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Residues in contact with GLU 26 (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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8A THR* 2.6 56.9 + - - +
9A TYR* 3.8 4.5 - - - -
11A ILE* 4.0 13.6 - - + +
24A THR* 4.5 5.2 + - - +
25A PHE* 1.3 76.4 - - - +
27A PHE* 1.3 62.6 + - - +
29A GLY* 4.5 12.1 + - - +
30A ASP 3.3 11.4 - - - +
31A GLU* 4.2 6.7 - - + -
32A LEU* 4.4 2.2 - - - -
138A PHE 4.0 4.2 - - - +
139A PHE* 3.5 32.8 - - + +
140A VAL* 3.2 41.0 + - - +
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Residues in contact with PHE 27 (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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5A HIS* 3.7 20.4 - + + -
6A VAL 3.1 31.6 - - - -
7A GLY* 3.5 2.0 - - - -
9A TYR* 3.4 20.2 - - - -
26A GLU* 1.3 74.8 - - - +
28A ASP* 1.3 100.0 + - + +
29A GLY 3.2 0.4 - - - -
30A ASP* 2.6 29.9 + - - +
32A LEU* 4.0 11.2 - - + +
43B PHE* 4.5 6.3 - + - -
109B TYR* 5.2 1.3 - + - -
113B GLU* 3.7 18.8 - - + -
117B SER* 3.2 31.6 - - - +
118B LEU* 4.0 12.1 - - + -
150B TYR* 5.0 3.4 - - - -
180B TRP* 3.8 19.9 - + + -
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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