Contacts of the strand formed by residues 10 - 18 (chain S) in PDB entry 4UJ3
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 TYR 10 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8S TYR* 3.4 9.7 - - - -
9S ASP* 1.3 93.5 - - + +
11S LEU* 1.3 60.0 + - - +
12S PHE* 3.7 24.9 - + + -
58S LYS* 3.7 38.5 + - + +
59S THR 3.6 2.4 + - - -
60S ILE* 3.2 33.5 - - + +
61S LYS 3.2 24.3 + - - -
173S TYR* 3.7 16.1 + + - -
176S VAL* 5.2 4.5 - - + -
177S SER* 4.1 29.1 - - - -
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Residues in contact with LEU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S TYR* 3.2 33.2 - - + +
10S TYR* 1.3 71.8 - - - +
12S PHE* 1.3 70.3 + - - +
13S LYS* 4.0 1.9 + - + +
50S THR* 6.0 0.4 - - + -
61S LYS* 3.1 48.2 - - + +
63S GLN* 4.5 27.6 - - + +
85S VAL* 5.5 1.9 - - - +
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Residues in contact with PHE 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S TYR* 3.7 27.7 + + + -
11S LEU* 1.3 81.5 - - - +
13S LYS* 1.3 60.5 + - - +
14S VAL* 3.8 2.7 + - + +
60S ILE* 3.3 34.1 - - + -
61S LYS 3.4 7.7 + - - +
62S ALA* 3.7 3.3 - - - +
63S GLN* 3.0 27.4 + - - +
85S VAL* 3.7 17.7 - - + -
169S LEU* 3.8 22.2 - - + -
172S ILE* 3.2 43.7 - - + -
173S TYR* 3.7 19.5 - - - -
176S VAL* 3.8 17.7 - - + -
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Residues in contact with LYS 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LEU* 4.0 3.0 + - + +
12S PHE* 1.3 71.4 - - - +
14S VAL* 1.3 62.0 + - - +
15S VAL* 3.9 5.6 - - + -
63S GLN* 3.6 14.4 - - + +
65S TRP* 3.5 52.0 - - + +
79S ALA 3.7 9.3 + - - -
80S TYR* 3.0 24.3 + - - +
82S ARG 2.8 29.7 + - - +
83S GLY 3.7 12.4 + - - +
84S ALA* 3.4 12.3 - - + +
85S VAL* 2.9 33.6 + - - +
86S GLY 3.4 2.6 + - - -
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Residues in contact with VAL 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S PHE 4.6 4.7 - - - +
13S LYS* 1.3 80.3 - - - +
15S VAL* 1.3 70.1 + - - +
62S ALA* 5.8 0.2 - - + -
63S GLN 3.0 9.2 + - - +
64S ILE* 3.4 27.4 - - + +
65S TRP* 2.9 23.9 + - - +
86S GLY* 3.2 18.8 - - - +
87S ALA* 3.9 4.5 - - - +
88S LEU* 4.3 11.2 - - + -
168S ILE* 4.2 16.2 - - + -
169S LEU* 4.4 15.3 - - + -
172S ILE* 3.9 26.5 - - + -
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Residues in contact with VAL 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LYS* 3.9 10.8 - - - -
14S VAL* 1.3 77.5 - - - +
16S LEU* 1.3 61.4 + - - +
17S ILE* 4.5 5.8 - - + -
65S TRP* 3.9 11.9 - - + -
80S TYR* 3.4 40.2 - - + +
81S TYR* 4.3 17.0 - - + -
84S ALA* 3.8 20.6 - - + -
86S GLY 2.9 12.5 + - - +
87S ALA* 3.2 14.6 - - + +
88S LEU 2.9 24.8 + - - -
117S ILE* 5.0 0.7 - - + -
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Residues in contact with LEU 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S VAL* 5.8 0.4 - - + -
15S VAL* 1.3 70.7 - - - +
17S ILE* 1.3 65.7 + - - +
24S LYS* 3.7 39.3 + - + +
27S LEU* 5.1 5.2 - - + -
28S LEU* 3.9 15.9 - - + +
64S ILE* 3.6 26.9 - - + -
65S TRP 2.9 19.1 + - - +
66S ASP* 4.3 9.9 - - + +
67S THR* 4.7 6.9 + - - +
80S TYR* 2.8 21.4 + - - +
88S LEU* 3.4 43.5 - - + +
90S VAL* 4.6 8.7 - - + -
165S PHE* 4.9 2.7 - - + -
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Residues in contact with ILE 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 3.9 8.0 + - + -
16S LEU* 1.3 79.4 - - - +
18S GLY* 1.3 54.2 + - - +
24S LYS* 3.4 12.0 - - - +
67S THR* 6.3 0.2 - - + -
71S GLU* 5.9 1.1 - - - +
80S TYR* 4.3 9.6 - - + -
81S TYR* 3.8 31.2 - - + +
87S ALA* 4.8 2.0 - - + -
88S LEU 2.9 12.6 + - - +
89S LEU* 3.6 33.0 - - + +
90S VAL* 2.6 30.3 + - - +
105S TRP* 4.1 24.0 - - + +
109S LEU* 3.7 32.8 - - + -
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Residues in contact with GLY 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ILE* 1.3 78.0 - - - +
19S ASP* 1.3 70.0 + - - +
20S SER 3.6 0.5 + - - -
24S LYS* 3.1 13.1 - - - -
69S GLY* 3.8 3.6 - - - -
89S LEU* 4.2 1.1 - - - -
90S VAL 3.3 16.8 - - - -
105S TRP* 3.4 34.3 - - - -
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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