Contacts of the strand formed by residues 51 - 61 (chain A) in PDB entry 4ICX
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU 4.4 2.2 - - - -
16A GLU* 3.3 21.7 - - + +
44A VAL* 3.3 23.4 - - - +
45A ASP 4.9 0.8 + - - -
49A GLN 3.5 7.2 + - - +
50A PRO* 1.3 75.1 - - - +
52A PHE* 1.3 62.5 + - - +
53A ALA* 3.6 6.9 - - + +
33B LYS* 5.6 9.0 - - - +
76B LYS* 3.4 31.3 - - - +
78B GLN* 3.6 19.3 + - - +
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Residues in contact with PHE 52 (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 ILE* 3.6 27.4 - - + +
15A LEU 3.0 17.2 + - - +
17A GLY 4.2 4.0 - - - -
20A PHE* 5.0 0.9 - + - -
28A LEU* 4.0 24.7 - - + -
30A VAL* 3.7 28.5 - - + -
41A THR* 4.3 15.6 - - + -
44A VAL* 3.7 28.4 - - + +
50A PRO* 3.7 35.2 - - + -
51A GLU* 1.3 74.4 - - - +
53A ALA* 1.3 72.0 + - - +
54A THR* 2.7 16.1 + - - +
79A CYS* 4.8 2.7 - - - -
126A ILE* 4.1 26.2 - - + -
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Residues in contact with ALA 53 (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 ILE 3.1 5.5 + - - -
15A LEU* 3.0 18.3 + - - +
16A GLU* 6.3 1.3 - - + -
51A GLU* 4.8 7.9 - - + +
52A PHE* 1.3 76.5 - - - +
54A THR* 1.3 58.4 + - - +
55A GLU* 5.9 0.2 - - - -
33B LYS* 6.0 6.1 - - - -
36B GLY* 5.8 9.5 - - - +
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Residues in contact with THR 54 (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 VAL 3.7 1.0 - - - +
13A SER* 3.5 2.1 - - - -
14A ILE* 2.8 40.4 + - - +
40A ALA 5.1 0.4 - - - +
41A THR* 4.1 32.0 - - + -
42A ASP* 4.8 5.6 + - - +
52A PHE 2.7 21.3 + - - -
53A ALA* 1.3 71.9 + - - +
55A GLU* 1.3 75.8 + - - +
56A LEU* 3.9 19.1 - - + -
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Residues in contact with GLU 55 (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 VAL* 4.1 21.5 - - + +
12A VAL 3.3 3.8 - - - -
13A SER* 2.9 21.5 + - - +
53A ALA 5.9 0.2 - - - -
54A THR* 1.3 81.6 - - - +
56A LEU* 1.3 69.2 + - - +
57A ALA* 4.3 1.0 + - + +
106A LYS* 5.0 9.9 + - - -
133A GLU* 5.3 4.1 - - - +
35B ASP* 5.4 4.0 - - - +
71B GLN* 5.6 2.1 + - - -
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Residues in contact with LEU 56 (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 ILE 3.3 1.8 - - - +
11A VAL* 3.2 4.8 - - - -
12A VAL* 2.7 44.0 + - + +
14A ILE* 3.7 29.4 - - + -
30A VAL 4.9 0.7 - - - +
32A ALA* 3.8 25.6 - - + +
39A LEU* 4.1 23.3 - - + +
40A ALA* 3.8 22.9 - - - +
41A THR* 4.6 5.6 - - + -
54A THR* 3.9 14.8 - - + -
55A GLU* 1.3 81.7 - - - +
57A ALA* 1.3 60.8 + - - +
58A TRP* 3.9 18.0 - - + -
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Residues in contact with ALA 57 (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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9A LEU* 4.2 21.0 - - + +
10A ILE 3.2 6.1 - - - +
11A VAL* 4.2 16.2 - - + -
37A GLU* 4.7 3.1 - - - +
39A LEU* 3.5 17.1 - - - +
55A GLU* 4.3 1.9 + - + +
56A LEU* 1.3 77.1 - - - +
58A TRP* 1.3 62.7 + - - +
59A GLU* 4.4 1.0 + - - +
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Residues in contact with TRP 58 (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* 3.3 5.1 - - - -
10A ILE* 2.9 54.8 + - + +
12A VAL* 3.8 25.8 - - + -
32A ALA* 3.6 44.6 - - + -
33A LYS 4.3 0.2 - - - -
34A PHE* 3.8 38.8 - + + +
37A GLU* 2.9 55.9 + - + +
39A LEU* 3.4 18.1 - - + +
56A LEU* 3.9 19.3 - - + -
57A ALA* 1.3 75.0 - - - +
59A GLU* 1.3 65.0 + - - +
60A ILE 3.9 0.2 + - - -
75A ILE* 4.1 11.4 - - + -
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Residues in contact with GLU 59 (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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7A GLN* 5.4 1.6 - - - +
8A LEU 3.5 7.2 - - - +
9A LEU* 3.8 17.7 - - + -
34A PHE* 5.5 0.9 - - - -
37A GLU* 4.9 7.2 + - - +
57A ALA 5.8 0.7 - - - +
58A TRP* 1.3 75.9 - - - +
60A ILE* 1.3 67.3 + - - +
135A ASP* 3.9 15.3 - - - +
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Residues in contact with ILE 60 (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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7A GLN* 3.8 4.5 - - - +
8A LEU* 2.8 52.4 + - + +
9A LEU 5.0 0.2 - - - -
10A ILE* 4.1 26.5 - - + +
34A PHE* 4.1 14.6 - - + -
35A ASP* 5.1 4.0 - - - +
59A GLU* 1.3 78.7 - - - +
61A ASP* 1.3 69.0 + - - +
64A ALA* 3.8 9.4 - - + -
65A LEU* 3.8 29.6 - - + +
68A HIS* 3.7 28.3 - - + +
132A LEU* 5.6 0.2 - - + -
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Residues in contact with ASP 61 (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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3A SER* 5.6 0.9 + - - -
6A ASP* 3.2 25.2 - - - +
7A GLN* 5.0 3.0 - - + +
8A LEU* 4.9 0.2 - - - -
60A ILE* 1.3 75.8 - - - +
62A ARG* 1.3 62.4 + - - +
63A LYS* 3.6 28.6 + - - +
64A ALA* 3.0 14.3 + - + +
65A LEU* 2.7 37.4 + - - +
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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