Contacts of the strand formed by residues 7 - 18 (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 GLN 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.7 4.2 + - - +
4A LYS* 3.2 35.3 + - - +
5A SER 3.1 11.1 - - - +
6A ASP* 1.3 77.4 - - - +
8A LEU* 1.3 61.8 - - - +
59A GLU* 5.4 1.9 - - - +
60A ILE 3.8 7.0 - - - +
61A ASP* 5.0 2.7 - - + +
134A THR* 4.0 1.4 - - - -
135A ASP* 3.0 47.7 + - + +
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Residues in contact with LEU 8 (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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5A SER 5.2 0.2 - - - +
6A ASP 4.3 3.6 - - - +
7A GLN* 1.3 79.0 - - - +
9A LEU* 1.3 63.0 + - - +
59A GLU* 3.5 5.9 - - - +
60A ILE* 2.8 42.7 + - + +
62A ARG* 3.6 55.6 - - + +
65A LEU* 3.6 28.7 - - + -
104A GLU* 4.3 16.4 - - + +
132A LEU* 4.7 4.9 - - + -
133A GLU 3.3 24.7 - - - +
134A THR* 4.2 5.4 - - + +
135A ASP* 3.8 8.1 - - - +
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Residues in contact with LEU 9 (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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8A LEU* 1.3 83.1 - - - +
10A ILE* 1.3 62.3 + - - +
11A VAL* 3.5 16.5 + - + -
57A ALA* 4.2 20.2 - - + -
58A TRP 3.3 8.5 - - - +
59A GLU* 3.8 25.6 - - + -
132A LEU* 3.3 8.6 - - - +
133A GLU* 2.7 49.1 + - + +
134A THR 5.0 3.6 - - - +
135A ASP* 4.0 22.2 - - + +
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Residues in contact with ILE 10 (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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8A LEU 4.3 0.4 - - - -
9A LEU* 1.3 71.4 - - - +
11A VAL* 1.3 59.3 + - - +
12A VAL* 4.5 2.7 - - + -
34A PHE* 3.6 38.6 - - + -
56A LEU 3.3 2.3 - - - +
57A ALA* 3.2 4.7 - - - -
58A TRP* 2.9 44.0 + - + +
60A ILE* 4.1 22.6 - - + +
65A LEU* 4.4 1.6 - - + -
75A ILE* 3.9 25.1 - - + -
99A LEU* 3.8 23.8 - - + -
130A ILE* 4.1 10.3 - - + -
131A ALA 3.7 4.0 - - - +
132A LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 11 (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* 4.1 20.2 - - + +
10A ILE* 1.3 74.6 - - - +
12A VAL* 1.3 64.2 + - - +
13A SER* 3.8 3.7 + - - +
55A GLU* 4.1 35.2 - - + +
56A LEU 3.2 6.7 - - - +
57A ALA* 4.2 11.2 - - + -
129A SER* 4.5 0.3 - - - -
130A ILE* 3.5 3.5 - - - -
131A ALA* 2.8 45.2 + - + +
133A GLU* 4.1 31.2 - - + +
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Residues in contact with VAL 12 (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* 4.5 1.8 - - + -
11A VAL* 1.3 73.7 - - - +
13A SER* 1.3 62.1 + - - +
14A ILE* 3.8 18.7 + - + -
54A THR 3.7 1.0 - - - +
55A GLU* 3.3 1.9 - - - -
56A LEU* 2.7 45.9 + - + +
58A TRP* 3.8 24.5 - - + -
75A ILE* 4.0 23.3 - - + -
77A LEU* 4.9 6.1 - - + -
97A LEU* 4.0 13.5 - - + -
128A ILE* 4.0 22.4 - - + -
129A SER 3.5 3.8 - - - +
130A ILE* 4.3 11.9 - - + -
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Residues in contact with SER 13 (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* 3.8 5.6 + - - +
12A VAL* 1.3 70.6 - - - +
14A ILE* 1.3 60.9 + - - +
15A LEU* 3.5 14.2 - - - +
54A THR 3.5 5.2 - - - -
55A GLU* 2.9 30.7 + - - +
128A ILE* 3.3 8.5 - - - +
129A SER* 2.9 49.0 + - - +
71B GLN* 5.1 6.3 + - - -
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Residues in contact with ILE 14 (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* 4.1 15.5 - - + +
13A SER* 1.3 73.2 - - - +
15A LEU* 1.3 62.7 + - - +
30A VAL* 3.9 21.3 - - + -
41A THR* 3.8 16.6 - - + -
52A PHE* 3.6 24.5 - - + -
53A ALA* 3.1 5.2 + - - -
54A THR* 2.8 40.0 + - - +
56A LEU* 3.7 30.3 - - + -
77A LEU* 4.3 11.2 - - + -
126A ILE* 3.6 26.9 - - + -
127A GLN 3.9 2.2 - - - -
128A ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 15 (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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13A SER* 3.5 28.9 - - - +
14A ILE* 1.3 72.5 - - - +
16A GLU* 1.3 69.2 + - + +
52A PHE* 3.0 31.0 + - - +
53A ALA* 3.0 13.5 + - - +
109A PRO* 3.9 30.3 - - + -
127A GLN* 3.0 30.4 + - - +
129A SER* 4.1 5.4 - - - +
71B GLN* 6.3 1.3 - - - +
73B THR* 6.1 4.7 - - + -
74B PRO* 5.6 9.6 - - + -
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Residues in contact with GLU 16 (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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15A LEU* 1.3 87.6 - - + +
17A GLY* 1.3 64.7 + - - +
49A GLN* 4.6 12.2 - - - +
50A PRO 3.5 6.7 - - - +
51A GLU* 3.3 34.8 - - + +
52A PHE* 4.5 3.6 - - - -
53A ALA* 5.9 1.8 - - + +
111A TRP* 3.5 12.8 - - + -
126A ILE* 3.6 0.5 - - - -
127A GLN* 2.8 33.0 + - - +
76B LYS* 3.3 31.5 + - - +
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Residues in contact with GLY 17 (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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16A GLU* 1.3 80.1 - - - +
18A ARG* 1.3 65.6 + - - +
20A PHE* 4.0 4.0 - - - -
49A GLN* 3.3 18.4 - - - +
50A PRO* 2.9 34.3 + - - +
52A PHE* 4.2 4.3 - - - -
111A TRP* 4.1 1.5 - - - -
125A GLU 3.2 10.3 - - - -
126A ILE* 4.2 2.9 - - - -
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Residues in contact with ARG 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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17A GLY* 1.3 74.4 - - - +
19A HIS* 1.3 84.1 + - + +
20A PHE* 3.3 5.9 + - - -
48A ASP 3.5 7.0 - - - -
49A GLN* 4.3 13.9 - - + +
111A TRP* 3.4 59.9 - - + +
124A SER* 3.4 0.7 - - - -
125A GLU* 2.7 64.6 + - + -
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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