Contacts of the strand formed by residues 8 - 18 (chain B) 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 LEU 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLN* 1.3 78.6 + - - +
9B LEU* 1.3 68.3 + - - +
59B GLU* 3.8 4.0 - - - +
60B ILE* 2.9 61.6 + - + +
62B ARG* 4.0 32.1 - - + +
65B LEU* 3.8 23.3 - - + -
132B LEU* 4.5 19.5 - - + -
133B GLU 3.4 11.7 - - - +
134B THR* 3.8 15.7 - - + -
85C VAL* 4.8 16.8 - - + -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN 5.5 0.9 - - - +
8B LEU* 1.3 81.0 - - - +
10B ILE* 1.3 64.8 + - - +
11B VAL* 3.8 11.8 + - + -
57B ALA* 4.5 17.9 - - + -
58B TRP 3.4 7.0 - - - +
59B GLU* 3.6 38.1 - - + +
132B LEU* 3.3 6.8 - - - +
133B GLU* 2.7 49.8 + - + +
135B ASP 3.5 29.2 - - - +
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 1.3 73.6 - - - +
11B VAL* 1.3 62.5 + - - +
12B VAL* 4.8 1.1 - - + -
34B PHE* 3.7 34.3 - - + -
56B LEU 3.6 1.6 - - - +
57B ALA* 3.3 4.3 - - - -
58B TRP* 3.0 46.2 + - + +
60B ILE* 4.1 23.3 - - + -
65B LEU* 4.9 1.8 - - + -
75B ILE* 4.8 3.6 - - + -
99B LEU* 3.6 31.2 - - + -
130B ILE* 3.8 31.2 - - + -
131B ALA 3.5 5.2 - - - +
132B LEU* 4.0 10.8 - - + -
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.3 10.5 - - + +
10B ILE* 1.3 77.3 - - - +
12B VAL* 1.3 62.1 + - - +
13B SER* 3.9 6.9 + - - +
55B GLU* 3.8 37.5 - - + +
56B LEU 3.4 7.9 - - - +
57B ALA* 4.5 8.7 - - + -
106B LYS* 6.1 1.1 - - - -
129B SER 3.8 0.7 - - - +
130B ILE* 3.4 4.5 - - - -
131B ALA* 2.9 42.1 + - + +
133B GLU* 3.8 37.0 - - + +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 4.8 1.6 - - + -
11B VAL* 1.3 73.4 - - - +
13B SER* 1.3 62.4 + - - +
14B ILE* 3.8 18.7 + - + +
54B THR 3.6 1.9 - - - +
55B GLU* 3.4 1.4 - - - -
56B LEU* 2.8 46.1 + - + +
58B TRP* 3.7 24.2 - - + -
75B ILE* 4.4 6.1 - - + -
77B LEU* 4.7 5.2 - - + -
97B LEU* 3.9 15.3 - - + -
128B ILE* 3.9 23.6 - - + -
129B SER 3.5 2.9 - - - +
130B ILE* 3.8 27.8 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.9 6.1 + - - +
12B VAL* 1.3 70.5 - - - +
14B ILE* 1.3 61.7 + - - +
15B LEU* 3.8 17.8 + - - +
54B THR 3.4 6.5 - - - -
55B GLU* 3.5 24.6 + - - +
128B ILE* 3.3 7.6 - - - +
129B SER* 2.8 48.4 + - - +
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 4.0 15.5 - - + +
13B SER* 1.3 73.0 - - - +
15B LEU* 1.3 62.3 + - - +
30B VAL* 3.9 16.4 - - + -
41B THR* 4.1 8.7 - - + -
52B PHE* 3.4 26.4 - - + +
53B ALA 3.0 5.4 + - - -
54B THR* 2.8 42.7 + - - +
56B LEU* 3.7 26.7 - - + -
77B LEU* 3.7 25.4 - - + -
126B ILE* 3.7 25.8 - - + -
127B GLN 4.0 2.5 - - - -
128B ILE* 4.5 3.8 - - + -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 4.2 22.4 - - - +
14B ILE* 1.3 76.7 - - - +
16B GLU* 1.3 68.3 + - + +
51B GLU* 3.7 7.2 - - - +
52B PHE* 3.0 8.8 + - - -
53B ALA* 3.0 28.3 + - - +
54B THR 5.7 0.4 - - - +
109B PRO* 4.1 27.8 - - + -
127B GLN* 3.0 37.2 + - + +
129B SER* 5.3 2.7 - - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 1.3 84.0 - - + +
17B GLY* 1.3 68.6 + - - +
18B ARG* 5.7 0.3 - - - +
49B GLN* 4.9 10.9 - - - +
50B PRO 3.4 12.6 - - - +
51B GLU* 3.8 13.2 - - - +
52B PHE* 4.0 9.7 - - - -
111B TRP* 3.5 15.4 - - + -
126B ILE* 3.4 1.6 - - - +
127B GLN* 2.7 60.4 + - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLU* 1.3 82.4 - - - +
18B ARG* 1.3 64.3 + - - +
20B PHE* 3.8 12.8 - - - -
49B GLN* 3.2 20.1 - - - +
50B PRO* 2.9 23.3 + - - +
52B PHE* 4.0 3.0 - - - -
111B TRP* 4.0 2.7 - - - -
125B GLU 3.3 11.0 - - - -
126B ILE* 4.3 1.8 - - - -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLU* 5.7 0.2 - - - +
17B GLY* 1.3 75.3 - - - +
19B HIS* 1.3 87.2 + - + +
20B PHE* 3.2 6.2 + - - -
48B ASP 3.5 7.6 - - - -
49B GLN* 4.3 10.8 - - + +
111B TRP* 3.4 59.3 - - + +
124B SER* 3.5 0.3 - - - -
125B GLU* 2.8 62.6 + - + +
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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