Contacts of the strand formed by residues 13 - 20 (chain A) in PDB entry 1SOI
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.2 8.0 - - - +
12A GLU* 1.3 87.8 - - + +
14A ARG* 1.3 64.5 + - - +
87A PHE* 3.9 18.6 - - + -
91A VAL* 3.9 23.8 - - + -
92A LEU 3.1 8.2 + - - +
93A ILE* 3.1 19.1 - - + -
94A LEU 2.9 22.5 + - - -
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Residues in contact with ARG 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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11A VAL* 3.4 37.4 + - - +
12A GLU 5.5 0.2 - - - -
13A LEU* 1.3 78.3 - - - +
15A ALA* 1.3 61.5 + - - +
51A ALA* 3.6 6.1 - - - +
52A VAL* 2.9 44.9 + - + +
58A PRO* 4.9 11.0 - - - +
93A ILE* 4.6 2.7 - - - -
94A LEU* 3.3 26.6 - - + +
96A HIS* 3.9 26.1 + - - +
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Residues in contact with ALA 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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14A ARG* 1.3 74.7 - - - +
16A ALA* 1.3 61.8 + - - +
49A SER* 4.2 2.9 - - - +
50A GLY 3.2 15.3 - - - +
51A ALA* 4.8 0.9 - - - -
52A VAL* 3.7 2.0 - - - -
93A ILE* 4.2 11.9 - - + +
94A LEU 3.0 6.1 + - - -
95A ARG* 3.8 36.1 - - + +
96A HIS* 2.8 31.7 + - - -
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Residues in contact with ALA 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 ALA* 1.3 76.0 - - - +
17A GLY* 1.3 59.3 + - - +
49A SER* 3.0 13.9 + - - -
50A GLY 2.8 20.8 + - - +
52A VAL* 3.5 14.3 - - + +
58A PRO* 3.2 28.7 - - + +
61A ALA* 4.2 1.3 - - + -
62A ALA* 3.7 20.5 - - + +
65A GLU* 4.3 2.4 - - - +
96A HIS* 3.5 5.4 - - + -
98A TRP* 4.0 7.4 - - + -
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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 ALA* 1.3 75.2 - - - +
18A VAL* 1.3 68.1 + - - +
47A ILE* 4.1 9.9 - - - -
48A PRO 3.1 14.8 - - - -
49A SER* 3.5 8.4 + - - -
62A ALA* 4.1 4.7 - - - +
96A HIS 2.8 11.0 + - - +
97A VAL* 3.4 2.9 - - - -
98A TRP* 3.1 24.6 + - - -
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Residues in contact with VAL 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 80.2 - - - +
19A VAL* 1.3 63.1 + - - +
20A LEU* 4.2 18.2 - - + -
28A LEU* 5.9 0.4 - - + -
47A ILE* 3.4 23.2 - - - +
48A PRO* 3.1 20.4 + - + +
62A ALA* 4.1 25.1 - - + +
63A VAL* 5.1 0.4 - - - +
66A ALA* 4.1 19.7 - - + -
74A VAL* 4.5 9.6 - - + -
76A PRO* 5.7 2.9 - - + -
97A VAL* 4.6 0.2 - - - -
98A TRP* 3.2 16.2 - - + +
100A ALA* 3.8 23.1 - - + -
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Residues in contact with VAL 19 (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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18A VAL* 1.3 72.1 - - - +
20A LEU* 1.3 57.7 + - - +
21A LEU* 4.0 8.1 - - + -
27A ILE* 4.0 22.9 - - + -
28A LEU 5.8 0.2 - - - -
47A ILE* 4.5 13.5 - - + -
80A LEU* 4.1 8.1 - - + -
97A VAL* 3.7 23.1 - - + -
98A TRP 2.8 10.5 + - - +
99A LEU* 3.5 8.0 - - - +
100A ALA 2.9 21.5 + - - -
141A THR 5.2 1.1 - - - +
144A PHE* 3.8 21.1 - - + -
145A TYR* 4.3 5.8 - - - +
148A ALA* 3.5 27.4 - - + -
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Residues in contact with LEU 20 (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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18A VAL* 3.6 15.2 + - + -
19A VAL* 1.3 72.8 - - - +
21A LEU* 1.3 64.2 + - - +
26A ASP 3.7 0.3 - - - +
27A ILE* 3.5 5.8 - - - +
28A LEU* 3.1 48.6 + - + +
48A PRO* 5.7 0.4 - - + -
72A LEU* 5.3 0.7 - - + -
74A VAL* 3.8 21.1 - - + -
100A ALA* 3.4 13.5 - - + +
101A GLU 3.3 10.3 - - - +
102A PRO* 3.2 44.0 - - + -
121A PHE* 3.6 29.8 - - + -
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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