Contacts of the strand formed by residues 7 - 18 (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 GLN 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.4 15.2 - - + +
72A ARG* 5.3 5.0 - - - +
6C ASP* 1.3 81.2 + - - +
8C LEU* 1.3 69.7 + - - +
59C GLU* 4.3 23.0 + - - +
60C ILE* 3.9 27.2 - - - +
61C ASP* 3.7 20.3 - - - +
134C THR* 4.4 10.7 - - - +
135C ASP* 4.1 18.5 + - - +
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Residues in contact with LEU 8 (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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70A LEU* 4.1 5.9 - - - +
7C GLN* 1.3 79.2 - - - +
9C LEU* 1.3 60.4 + - - +
10C ILE 4.2 0.2 - - - -
59C GLU* 3.3 8.3 - - - +
60C ILE* 2.8 45.6 + - + +
62C ARG* 3.6 58.3 - - + +
65C LEU* 3.6 24.0 - - + -
104C GLU* 4.9 2.7 - - - +
132C LEU* 3.8 27.6 - - + -
133C GLU 3.7 3.4 - - - +
134C THR* 3.5 19.7 - - + -
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Residues in contact with LEU 9 (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* 3.6 52.0 - - + +
69A ARG* 3.6 26.0 - - - +
70A LEU* 4.2 10.3 - - + +
8C LEU* 1.3 74.0 - - - +
10C ILE* 1.3 62.6 + - - +
11C VAL* 3.6 15.8 + - + +
57C ALA* 4.2 7.2 - - + -
58C TRP 3.4 8.7 - - - +
59C GLU* 3.5 28.9 - - + -
132C LEU* 3.3 7.9 - - - +
133C GLU* 3.0 39.8 + - + +
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Residues in contact with ILE 10 (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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9C LEU* 1.3 69.9 - - - +
11C VAL* 1.3 60.4 + - - +
12C VAL* 4.4 2.5 - - + -
34C PHE* 3.8 31.0 - - + -
56C LEU 3.5 1.6 - - - +
57C ALA* 3.1 6.8 - - - +
58C TRP* 2.7 47.4 + - + +
60C ILE* 3.7 26.7 - - + -
65C LEU* 4.6 0.7 - - + -
75C ILE* 4.2 7.9 - - + -
99C LEU* 3.8 34.3 - - + -
130C ILE* 3.8 18.4 - - + -
131C ALA 3.7 5.2 - - - +
132C LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 11 (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* 3.8 28.9 - - + +
9C LEU* 3.6 26.4 + - + +
10C ILE* 1.3 77.0 - - - +
12C VAL* 1.3 63.2 + - - +
13C SER* 3.8 8.0 + - - +
55C GLU* 4.6 8.7 - - - +
56C LEU 3.5 3.4 - - - +
57C ALA* 4.2 5.4 - - + -
129C SER 3.7 1.0 - - - +
130C ILE* 3.5 3.7 - - - -
131C ALA* 3.0 51.6 + - + +
132C LEU 4.8 0.2 - - - +
133C GLU* 3.9 18.6 - - + +
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Residues in contact with VAL 12 (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* 4.4 2.0 - - + -
11C VAL* 1.3 73.9 - - - +
13C SER* 1.3 60.7 + - - +
14C ILE* 3.8 16.7 + - + -
55C GLU* 3.0 3.6 - - - -
56C LEU* 2.6 46.0 + - + +
58C TRP* 3.8 24.7 - - + -
75C ILE* 4.4 8.3 - - + -
77C LEU* 4.7 7.6 - - + -
97C LEU* 4.1 11.9 - - + -
128C ILE* 3.9 24.7 - - + -
129C SER 3.5 2.9 - - - +
130C ILE* 3.9 25.6 - - + -
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Residues in contact with SER 13 (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* 6.1 0.2 - - - -
11C VAL* 3.8 8.4 + - - +
12C VAL* 1.3 72.2 - - - +
14C ILE* 1.3 61.5 + - - +
15C LEU* 3.5 17.1 - - - +
54C THR 3.6 7.4 - - - -
55C GLU* 4.1 13.3 + - - +
128C ILE* 3.5 6.1 - - - +
129C SER* 2.7 46.4 + - - +
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Residues in contact with ILE 14 (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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12C VAL* 3.8 13.0 + - + +
13C SER* 1.3 74.6 - - - +
15C LEU* 1.3 61.5 + - - +
30C VAL* 3.7 26.7 - - + -
41C THR* 3.8 13.2 - - + -
52C PHE* 3.6 26.7 - - + -
53C ALA* 3.2 5.2 + - - -
54C THR* 2.8 41.3 + - - +
56C LEU* 3.8 21.5 - - + -
77C LEU* 3.9 12.1 - - + -
126C ILE* 3.7 26.5 - - + -
127C GLN 4.1 2.2 - - - +
128C ILE* 4.5 7.6 - - + -
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Residues in contact with LEU 15 (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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13C SER* 3.5 30.5 - - - +
14C ILE* 1.3 73.6 - - - +
16C GLU* 1.3 71.5 + - + +
51C GLU* 4.1 0.7 - - - +
52C PHE* 3.3 9.0 + - - -
53C ALA* 3.0 26.3 + - - +
109C PRO* 4.0 19.7 - - + -
127C GLN* 3.2 42.4 + - - +
128C ILE* 4.2 0.2 - - - -
129C SER* 4.0 16.2 - - - +
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Residues in contact with GLU 16 (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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15C LEU* 1.3 86.6 - - + +
17C GLY* 1.3 65.9 + - - +
49C GLN* 4.8 10.9 - - - +
50C PRO 3.5 8.7 - - - +
51C GLU* 1.7 41.5 - - - +
52C PHE* 4.4 4.3 - - - -
111C TRP* 4.3 13.4 - - + -
126C ILE* 3.4 9.5 - - - +
127C GLN* 2.8 32.9 + - - +
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Residues in contact with GLY 17 (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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16C GLU* 1.3 79.6 - - - +
18C ARG* 1.3 63.3 + - - +
20C PHE* 4.2 7.2 - - - -
49C GLN* 3.3 22.9 - - - +
50C PRO* 3.0 26.8 + - - -
52C PHE* 4.5 1.5 - - - -
111C TRP* 4.1 3.5 - - - -
125C GLU 3.5 11.0 - - - -
126C ILE* 4.4 3.6 - - - -
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Residues in contact with ARG 18 (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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17C GLY* 1.3 75.3 - - - +
19C HIS* 1.3 97.3 + - + +
20C PHE* 3.6 5.2 - - - -
48C ASP 3.8 5.4 - - - -
49C GLN* 4.4 12.8 - - + +
111C TRP* 3.2 70.7 - - + +
123C LYS 4.1 0.2 - - - +
124C SER* 3.7 0.3 - - - -
125C GLU* 3.0 45.5 + - + -
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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