Contacts of the strand formed by residues 51 - 61 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C LEU 4.4 0.9 - - - -
16C GLU* 1.7 43.9 - - + +
44C VAL* 3.2 24.5 - - + +
45C ASP 4.9 1.4 + - - -
47C THR* 4.9 0.4 + - - -
49C GLN 3.5 5.8 + - - +
50C PRO* 1.3 71.7 - - - +
52C PHE* 1.3 61.4 + - - +
53C ALA* 4.7 13.0 - - + +
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Residues in contact with PHE 52 (chain C).
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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14C ILE* 3.6 27.8 - - + +
15C LEU 3.3 9.0 + - - +
16C GLU 4.4 5.2 - - - -
17C GLY* 4.8 2.5 - - - -
20C PHE* 5.2 0.9 - + - -
28C LEU* 4.0 34.3 - - + -
29C VAL 5.0 0.2 - - - -
30C VAL* 4.0 26.9 - - + -
41C THR* 4.4 10.1 - - - -
42C ASP 5.3 0.2 - - - -
44C VAL* 3.9 27.9 - - + +
50C PRO* 3.8 26.9 - - + -
51C GLU* 1.3 73.5 - - - +
53C ALA* 1.3 60.6 + - - +
54C THR* 2.6 25.5 + - - +
79C CYS* 4.6 6.1 - - - -
126C ILE* 4.3 35.0 - - + -
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 4.6 9.7 + - - -
104A GLU* 4.1 5.7 - - - +
134A THR* 4.7 13.1 - - + +
14C ILE 3.2 6.0 + - - -
15C LEU* 3.0 14.9 + - - +
51C GLU* 4.7 14.4 - - + +
52C PHE* 1.3 76.1 - - - +
54C THR* 1.3 57.9 + - - +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.4 2.5 - - - -
104A GLU* 3.6 26.7 - - + +
13C SER* 3.6 3.1 - - - -
14C ILE* 2.8 36.6 + - - +
40C ALA 5.5 0.2 - - - +
41C THR* 3.9 41.4 - - + -
42C ASP* 4.5 12.1 + - + +
52C PHE* 2.6 22.3 + - - -
53C ALA* 1.3 76.0 + - - +
55C GLU* 1.3 77.7 + - - +
56C LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.4 33.1 - - - +
65A LEU* 5.1 3.2 - - - +
66A HIS* 2.5 37.2 + - - -
104A GLU* 3.2 32.0 + - - +
132A LEU* 6.1 0.2 - - - +
11C VAL* 4.7 8.9 - - + +
12C VAL 3.0 13.5 - - - +
13C SER* 4.1 14.0 + - - +
14C ILE 4.5 0.2 - - - +
54C THR* 1.3 81.9 - - - +
56C LEU* 1.3 74.2 + - - +
57C ALA* 4.3 11.8 - - + +
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE 3.5 1.6 - - - +
11C VAL* 3.5 1.3 - - - -
12C VAL* 2.6 44.9 + - + +
14C ILE* 3.8 27.6 - - + -
30C VAL 4.8 2.5 - - - +
32C ALA* 3.6 34.1 - - + +
39C LEU* 4.1 17.9 - - + +
40C ALA 4.0 18.2 - - - +
41C THR* 3.9 22.0 - - + -
54C THR* 4.5 2.2 - - + -
55C GLU* 1.3 83.1 - - - +
57C ALA* 1.3 60.4 + - - +
58C TRP* 3.8 19.5 - - + -
77C LEU* 4.1 4.0 - - + -
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 5.2 1.3 - - + +
69A ARG* 3.8 31.5 + - - +
9C LEU* 4.2 17.3 - - + -
10C ILE 3.1 8.3 - - - +
11C VAL* 4.2 9.0 - - + -
37C GLU* 4.4 2.8 - - - +
39C LEU* 3.4 18.3 - - - +
55C GLU* 4.3 11.0 - - - +
56C LEU* 1.3 74.5 - - - +
58C TRP* 1.3 63.6 + - - +
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Residues in contact with TRP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 4.7 0.4 - - - +
9C LEU* 3.4 7.5 - - - -
10C ILE* 2.7 57.1 + - + +
12C VAL* 3.8 26.0 - - + -
32C ALA* 3.6 43.5 - - + -
34C PHE* 3.8 37.3 - + + +
37C GLU* 3.0 54.3 + - + +
39C LEU* 3.7 18.0 - - + +
56C LEU* 3.8 22.4 - - + -
57C ALA* 1.3 75.8 - - - +
59C GLU* 1.3 63.8 + - - +
75C ILE* 4.2 12.3 - - + -
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 2.8 32.9 + - - +
70A LEU* 4.1 16.5 - - + +
72A ARG* 2.7 44.2 + - - -
100A ARG* 3.6 9.8 - - - +
7C GLN* 4.3 16.4 + - - +
8C LEU 3.3 4.5 - - - +
9C LEU* 3.5 20.4 - - + -
34C PHE* 5.8 1.0 - - - -
37C GLU* 4.8 9.1 + - - +
58C TRP* 1.3 76.8 - - - +
60C ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLN* 3.9 6.4 - - - +
8C LEU* 2.8 49.9 + - + +
10C ILE* 3.7 30.5 - - + -
34C PHE* 3.8 22.7 - - + -
35C ASP* 5.4 1.1 - - - +
59C GLU* 1.3 75.6 - - - +
61C ASP* 1.3 71.3 + - - +
64C ALA* 4.0 8.3 - - + -
65C LEU* 3.8 23.3 - - + +
68C HIS* 3.3 32.8 - - + +
99C LEU* 4.8 0.4 - - + -
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP 3.6 15.2 + - - +
7C GLN* 3.7 20.1 - - - +
60C ILE* 1.3 81.3 - - - +
62C ARG* 1.3 76.9 + - - +
63C LYS* 3.3 15.8 + - - +
64C ALA* 3.4 11.7 + - + +
65C LEU* 3.1 19.2 + - - +
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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