Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 1IL8
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.1 43.3 - - + -
19A PRO* 2.6 34.4 + - + +
20A LYS 4.5 1.4 - - - +
21A PHE* 1.3 80.4 - - + +
23A LYS* 1.3 68.3 + - - +
24A GLU 4.0 8.3 - - - +
25A LEU* 4.7 4.5 - - + -
41A VAL* 3.5 25.8 - - + -
42A LYS 3.9 2.0 - - - -
43A LEU* 3.7 27.4 - - + -
51A LEU* 6.1 0.2 - - + -
61A VAL 6.0 0.7 - - - +
65A PHE* 3.8 33.4 - - + -
29B GLU* 4.6 3.3 - - - +
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Residues in contact with LYS 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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20A LYS 5.3 6.4 + - - +
21A PHE 3.7 1.7 + - - +
22A ILE* 1.3 81.0 + - - +
24A GLU* 1.3 63.2 + - + +
42A LYS 3.3 5.5 + - - +
44A SER* 3.6 37.5 - - - +
65A PHE* 3.7 8.0 - - - -
68A ARG* 6.2 0.2 - - - +
28B ILE* 4.0 2.3 - - - +
29B GLU* 3.2 40.8 + - + +
30B SER* 4.1 23.0 + - - +
31B GLY* 5.2 6.1 - - - -
32B PRO* 5.9 3.8 - - + -
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Residues in contact with GLU 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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22A ILE* 3.8 3.8 - - - -
23A LYS* 1.3 83.9 - - + +
25A LEU* 1.3 70.2 + - - +
26A ARG* 4.4 11.7 + - - -
41A VAL* 3.4 5.7 - - - +
42A LYS* 2.8 69.4 + - + +
65A PHE* 4.4 0.2 - - - -
26B ARG* 4.2 20.9 + - - +
27B VAL 3.5 7.0 - - - +
28B ILE* 3.1 33.8 - - + +
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Residues in contact with LEU 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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22A ILE* 4.7 4.7 - - + -
24A GLU* 1.3 77.0 - - - +
26A ARG* 1.3 72.6 + - - +
27A VAL* 3.9 24.2 - - + -
39A ILE* 4.8 4.0 - - + -
40A ILE 4.1 9.6 - - - +
41A VAL* 4.4 13.9 - - + -
51A LEU* 5.8 0.2 - - + -
62A VAL* 4.2 35.4 - - + -
65A PHE* 3.5 34.7 - - + -
66A LEU* 5.1 10.3 - - + -
25B LEU* 5.9 0.9 - - + -
26B ARG* 3.7 0.3 - - - -
27B VAL* 2.9 43.5 + - + +
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Residues in contact with ARG 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 GLN* 4.7 14.3 - - - +
24A GLU* 4.4 17.9 + - + -
25A LEU* 1.3 83.2 - - - +
27A VAL* 1.3 59.7 + - - +
28A ILE* 5.1 0.8 - - - +
39A ILE 3.4 1.0 - - - -
40A ILE* 2.5 77.3 + - + +
41A VAL 4.6 0.9 - - - +
42A LYS* 4.3 24.3 - - - +
48A GLU* 5.2 10.1 + - - +
24B GLU* 4.2 18.3 + - - +
25B LEU 3.7 3.1 - - - +
26B ARG* 3.4 31.9 - - + +
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Residues in contact with VAL 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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25A LEU* 3.9 24.0 - - + -
26A ARG* 1.3 79.6 - - - +
28A ILE* 1.3 65.9 + - - +
37A THR* 5.1 2.2 - - + -
38A GLU 3.8 4.9 - - - +
39A ILE* 4.1 27.4 - - + -
24B GLU* 3.5 1.7 - - - -
25B LEU* 2.9 48.8 + - + +
65B PHE* 4.0 23.6 - - + -
66B LEU* 5.0 16.6 - - + -
69B ALA* 4.7 12.6 - - + -
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Residues in contact with ILE 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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8A GLN* 3.3 36.8 - - + +
26A ARG* 4.2 2.2 + - - +
27A VAL* 1.3 77.6 - - - +
29A GLU* 1.3 73.5 + - - +
31A GLY* 5.8 0.2 - - - -
33A HIS* 4.1 22.2 - - + +
34A CYS* 6.1 0.4 - - + -
37A THR* 3.8 0.2 - - - -
38A GLU* 3.1 38.9 + - + +
40A ILE* 3.5 21.1 - - + -
23B LYS 4.0 6.1 - - - +
24B GLU* 3.1 36.1 - - + +
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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