Contacts of the strand formed by residues 26 - 34 (chain A) in PDB entry 1I5L
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 GLU 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.7 18.9 - - + +
19A VAL 3.2 12.8 - - - +
20A ARG* 2.5 49.7 + - + +
24A GLY 4.4 0.2 - - - +
25A ARG* 1.3 77.0 - - - +
27A PHE* 1.3 69.5 + - - +
47A GLU* 3.4 8.8 - - - +
48A ILE* 2.9 53.8 + - + +
69A PHE* 6.4 1.1 - - - -
55B ARG* 5.0 4.9 + - - -
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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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17A VAL 3.8 0.5 - - - +
18A ILE* 3.3 6.6 - - - +
19A VAL* 2.7 45.8 + - + +
21A LEU* 3.8 28.7 - - + -
26A GLU* 1.3 81.1 - - - +
28A ARG* 1.3 62.4 + - - +
42A LEU* 3.8 14.1 - - + +
45A ALA* 4.2 8.7 - - + -
46A GLU 3.3 14.8 - - - -
47A GLU* 4.1 27.6 - - + -
57A VAL* 4.7 8.5 - - + -
60A VAL* 3.8 33.7 - - + -
62A ILE* 4.0 12.6 - - + -
69G PHE* 3.6 38.1 - + - -
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Residues in contact with ARG 28 (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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16A PRO* 6.4 0.4 - - - +
17A VAL 3.5 4.8 + - - +
18A ILE* 3.9 35.0 - - + +
27A PHE* 1.3 76.3 - - - +
29A GLY* 1.3 58.9 + - - +
42A LEU* 4.8 0.9 - - - -
44A ASP 3.9 0.5 - - - +
45A ALA* 3.0 6.4 - - - -
46A GLU* 2.9 54.9 + - + +
48A ILE* 3.3 33.4 - - + -
73A ALA 5.1 4.6 + - - -
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Residues in contact with GLY 29 (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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16A PRO* 3.4 5.6 - - - +
17A VAL* 2.9 35.2 + - - +
27A PHE 4.3 0.4 - - - -
28A ARG* 1.3 75.8 - - - +
30A THR* 1.3 63.9 + - - -
42A LEU* 4.4 9.1 - - - +
43A LEU 4.1 1.1 - - - -
44A ASP 3.6 14.4 - - - -
45A ALA* 4.1 5.6 - - - -
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Residues in contact with THR 30 (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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14A LYS* 3.9 21.5 + - + +
15A SER* 3.6 12.5 + - - -
16A PRO* 4.3 5.2 - - - +
29A GLY* 1.3 72.0 - - - -
31A LEU* 1.3 75.0 + - - +
32A ASP* 3.2 3.4 + - - +
42A LEU* 3.3 4.5 - - - -
43A LEU* 2.9 56.0 + - + +
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Residues in contact with LEU 31 (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* 3.6 43.7 - - + +
12A SER* 4.0 18.2 - - - +
13A LEU* 3.9 17.3 - - + -
14A LYS* 2.9 29.3 + - - -
15A SER 3.2 7.9 + - - -
17A VAL* 4.0 19.0 - - + +
29A GLY 3.7 2.8 + - - -
30A THR* 1.3 71.2 - - - +
32A ASP* 1.3 60.1 + - - +
33A GLY 3.2 27.8 - - - +
34A TYR* 4.6 1.8 - - + -
40A LEU* 4.5 16.4 - - + -
41A VAL 3.7 7.9 - - - +
42A LEU* 3.9 8.9 - - + +
70A VAL* 5.7 1.8 - - + -
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Residues in contact with ASP 32 (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 LEU* 3.5 15.8 - - - +
14A LYS* 5.1 7.1 - - - +
30A THR* 3.2 2.4 + - - +
31A LEU* 1.3 74.6 - - - +
33A GLY* 1.3 56.7 + - - +
41A VAL* 2.8 34.6 + - + +
43A LEU* 3.7 34.8 - - + +
3G PRO* 3.8 34.9 - - - +
8G VAL* 5.0 3.3 - - - +
11G ARG* 5.2 3.8 + - - -
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Residues in contact with GLY 33 (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 LEU* 4.3 6.3 - - - -
31A LEU* 3.2 10.2 - - - +
32A ASP* 1.3 82.1 - - - +
34A TYR* 1.3 67.4 + - - +
40A LEU* 3.5 0.5 - - - -
41A VAL* 3.1 29.9 + - - +
3G PRO* 4.3 17.0 - - - -
4G ARG 4.6 0.4 - - - -
5G PRO* 4.2 2.9 - - - -
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Residues in contact with TYR 34 (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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6A LEU* 3.6 27.8 + - + +
9A LEU* 3.9 20.6 - - + -
10A ASN* 2.8 53.3 + - + +
13A LEU* 3.9 18.4 - - + -
31A LEU* 4.6 3.1 - - + -
33A GLY* 1.3 78.9 - - - +
35A ASP* 1.3 73.7 + - - +
38A MET 5.1 0.4 - - - -
39A ASN 3.0 16.8 - - - +
40A LEU* 3.9 13.0 - - + -
3G PRO 5.2 2.0 - - - +
4G ARG* 5.0 5.8 - - - +
5G PRO* 3.6 14.4 - - - +
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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