Contacts of the strand formed by residues 17 - 32 (chain A) in PDB entry 4ILW
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 VAL 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.8 0.3 - - - +
16A ASP* 1.3 85.9 - - + +
18A VAL* 1.3 66.8 + - - +
19A ILE* 3.9 19.7 - - + -
52A MET* 4.7 1.6 - - + -
54A LYS 3.4 5.6 - - - +
56A PRO* 4.2 14.8 - - + -
60A ILE* 4.0 10.8 - - + -
86A ILE 3.6 0.5 - - - +
87A ALA* 3.3 2.6 - - - -
88A GLY 2.9 31.5 + - - +
89A LYS 4.1 1.8 - - - -
90A ALA* 3.6 34.5 - - + +
96A MET* 3.5 31.4 - - + -
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Residues in contact with VAL 18 (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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12A PHE* 3.9 38.8 - - + +
15A ALA* 4.1 9.9 - - + -
17A VAL* 1.3 79.6 - - - +
19A ILE* 1.3 61.1 + - - +
53A PHE* 2.9 35.2 + - + -
54A LYS* 2.8 30.8 + - + +
85A LEU* 3.8 26.5 - - + -
86A ILE 3.3 6.5 - - - +
87A ALA* 4.0 17.9 - - + -
118A LEU* 4.6 2.5 - - + -
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Residues in contact with ILE 19 (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* 3.9 12.8 - - + -
18A VAL* 1.3 80.5 - - - +
20A ARG* 1.3 61.7 + - - +
21A ALA* 4.2 10.8 - - + -
47A ILE* 4.2 15.9 - - + -
49A GLN* 3.9 19.3 - - + +
51A LYS 3.2 14.6 - - - +
52A MET* 3.9 11.7 - - + -
53A PHE* 4.2 1.8 - - - -
60A ILE* 4.0 15.7 - - + -
63A ILE* 4.7 3.6 - - + -
84A TYR 3.6 0.5 - - - +
85A LEU* 3.4 8.9 - - - +
86A ILE* 2.7 50.1 + - + +
96A MET* 3.7 26.0 - - - -
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Residues in contact with ARG 20 (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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19A ILE* 1.3 73.3 - - - +
21A ALA* 1.3 64.3 + - - +
49A GLN* 3.9 1.4 - - - -
50A ILE* 2.9 46.5 + - + +
51A LYS* 2.9 26.7 + - + +
53A PHE* 3.9 14.0 - - + -
83A GLU* 2.5 33.5 + - + +
84A TYR 3.2 6.7 - - - +
85A LEU* 4.5 1.3 - - - +
107A TRP* 3.5 62.1 - - + +
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Residues in contact with ALA 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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19A ILE* 4.0 13.2 - - + -
20A ARG* 1.3 77.1 - - - +
22A LYS* 1.3 63.8 + - - +
47A ILE* 4.0 22.7 - - + -
48A LYS 3.5 13.5 - - - +
50A ILE* 4.1 5.8 - - - -
82A LYS 3.9 0.5 - - - +
83A GLU* 3.3 2.4 - - - -
84A TYR* 2.6 43.7 + - - +
86A ILE* 4.4 13.7 - - + -
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Residues in contact with LYS 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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21A ALA* 1.3 72.9 - - - +
23A ALA* 1.3 63.7 + - - +
24A VAL* 3.9 4.7 + - + +
47A ILE* 3.3 6.3 - - - +
48A LYS* 3.0 38.1 + - + +
50A ILE* 4.1 7.3 - - + +
81A LYS* 3.5 40.0 + - - +
82A LYS 3.6 11.0 - - - +
83A GLU* 2.9 49.2 + - + +
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Residues in contact with ALA 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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22A LYS* 1.3 74.9 - - - +
24A VAL* 1.3 61.3 + - - +
25A SER 5.1 0.2 - - - +
45A TYR* 4.3 6.3 - - + -
46A GLU 3.6 8.1 - - - +
47A ILE* 3.9 11.6 - - + +
76A LEU* 4.2 21.8 - - + -
77A ASP 4.0 7.4 + - - +
78A VAL* 3.7 25.2 - - + -
79A GLY* 3.4 20.5 + - - +
80A GLY 4.7 1.4 - - - +
82A LYS 4.2 6.3 + - - -
84A TYR* 5.3 3.5 - - + -
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Residues in contact with VAL 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 LYS* 4.3 11.2 - - + +
23A ALA* 1.3 75.8 - - - +
25A SER* 1.3 64.1 + - - +
46A GLU* 2.9 22.7 + - + +
47A ILE 4.7 1.6 - - - -
48A LYS* 4.4 17.0 - - + +
78A VAL* 3.1 12.0 - - - +
79A GLY* 3.2 14.7 + - - +
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Residues in contact with SER 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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24A VAL* 1.3 82.9 - - - +
26A GLU* 1.3 63.5 + - - +
27A LYS* 3.5 23.1 + - - -
44A GLN 4.7 0.2 - - - -
45A TYR* 3.4 7.1 - - - +
46A GLU* 2.9 52.0 + - - +
78A VAL* 3.3 9.1 - - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 1.3 77.0 - - - +
27A LYS* 1.3 77.2 + - - +
43A ILE* 3.9 33.2 - - + +
44A GLN 3.7 4.7 - - - -
45A TYR* 4.1 16.1 + - + -
76A LEU 4.9 2.3 - - - +
78A VAL* 3.7 24.1 - - + +
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Residues in contact with LYS 27 (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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25A SER* 3.5 23.0 + - - -
26A GLU* 1.3 85.6 - - - +
28A GLU* 1.3 66.2 + - - +
29A VAL* 4.4 4.0 - - + -
43A ILE* 4.5 6.1 - - - -
44A GLN* 2.8 55.9 + - - +
46A GLU* 5.1 6.2 + - - +
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Residues in contact with GLU 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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27A LYS* 1.3 78.9 - - - +
29A VAL* 1.3 66.6 + - - +
30A ASP* 4.6 4.3 - - - +
41A LYS* 3.3 44.6 + - - +
42A ARG 3.7 6.1 - - - +
43A ILE* 3.8 21.5 - - + +
67A PRO* 4.2 13.1 - - - +
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Residues in contact with VAL 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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27A LYS* 4.0 6.1 - - + +
28A GLU* 1.3 81.3 - - - +
30A ASP* 1.3 67.6 + - - +
31A SER* 3.9 20.2 - - - +
41A LYS* 3.3 7.6 - - - +
42A ARG* 2.9 40.9 + - + +
44A GLN* 3.7 35.7 - - + +
64A TYR* 4.1 16.8 - - + -
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Residues in contact with ASP 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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28A GLU* 4.6 3.5 - - - +
29A VAL* 1.3 83.1 - - - +
31A SER* 1.3 61.8 + - - +
32A GLY 4.8 6.7 - - - +
39A PRO* 5.3 10.3 - - + +
40A ILE 4.0 7.9 - - - +
41A LYS* 4.1 23.4 + - - +
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Residues in contact with SER 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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29A VAL* 3.9 16.4 + - - +
30A ASP* 1.3 74.0 - - - +
32A GLY* 1.3 57.2 + - - +
33A ASN* 4.0 4.9 + - - +
40A ILE 3.7 5.3 + - - -
42A ARG* 3.9 26.9 + - - +
64A TYR* 4.9 1.7 - - - -
170D PHE* 3.3 31.9 - - - -
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Residues in contact with GLY 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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30A ASP* 3.5 4.9 - - - +
31A SER* 1.3 79.6 + - - +
33A ASN* 1.3 74.6 + - - -
39A PRO* 3.4 7.9 - - - +
40A ILE 2.5 35.3 + - - +
170D PHE* 3.4 12.1 - - - -
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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