Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 1SFE
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 ARG 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.3 16.2 + - + +
14A VAL* 1.3 78.2 - - - +
16A TYR* 1.3 60.6 + - - +
29A ALA* 3.1 4.2 - - - +
30A GLU* 2.4 75.0 + - - +
31A SER 3.7 12.5 + - - -
32A GLU* 3.6 25.1 + - - +
59A ASP 3.4 6.7 - - - +
61A ALA* 4.0 22.2 - - + -
64A ASP* 3.6 27.1 + - - -
66A MET* 6.1 2.2 - - - +
67A PHE* 3.8 20.9 - - + +
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Residues in contact with TYR 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 ARG* 1.3 75.5 - - - +
17A ALA* 1.3 64.3 + - - +
18A LEU* 3.5 31.2 - - + -
27A LEU* 3.8 20.4 - - + -
28A VAL 3.2 12.8 - - - +
29A ALA* 4.2 4.9 - - + -
48A ILE* 3.6 33.5 - - + +
51A LEU* 4.4 7.0 - - + -
52A GLN* 6.5 0.7 - - - -
58A ALA* 3.8 21.3 - - + -
59A ASP* 3.1 38.0 + - - -
60A ASN* 3.2 47.6 + - + +
61A ALA 3.6 5.4 + - - -
67A PHE* 3.5 5.9 - - - -
68A GLN* 5.2 0.2 + - - -
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Residues in contact with ALA 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 TYR* 1.3 76.9 - - - +
18A LEU* 1.3 69.1 + - - +
19A ALA* 4.2 0.6 + - - -
26A CYS 3.9 0.3 - - - +
27A LEU* 3.4 4.7 - - - +
28A VAL* 3.0 30.5 + - - +
60A ASN* 5.5 1.6 - - - -
67A PHE* 3.6 19.5 - - + -
68A GLN* 4.2 15.5 - - - +
71A VAL* 4.0 20.4 - - + +
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Residues in contact with LEU 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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16A TYR* 3.5 36.1 - - + -
17A ALA* 1.3 76.6 - - - +
19A ALA* 1.3 62.8 + - - +
25A ARG* 3.4 22.7 + - - +
26A CYS 3.5 5.6 - - - +
27A LEU* 3.8 8.1 - - + -
44A ASP* 2.9 35.4 - - - +
47A LEU* 3.8 29.8 - - + -
48A ILE* 3.7 17.3 - - + -
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Residues in contact with ALA 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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17A ALA 4.2 0.8 + - - +
18A LEU* 1.3 76.2 - - - +
20A ASP* 1.3 64.1 + - - +
25A ARG* 3.5 14.2 + - - +
26A CYS* 2.9 34.1 + - - +
28A VAL* 6.3 0.4 - - + -
71A VAL* 4.8 12.1 - - + -
75A ILE* 3.8 28.0 - - + -
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Residues in contact with ASP 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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19A ALA* 1.3 76.3 - - - +
21A CYS* 1.3 66.3 + - - +
24A GLY 3.8 3.9 - - - +
25A ARG* 2.9 38.5 + - - +
75A ILE* 3.6 15.9 - - - +
79A ASN* 4.9 0.2 + - - -
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Residues in contact with CYS 21 (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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20A ASP* 1.3 79.0 - - - +
22A GLU* 1.3 56.4 + - - +
23A LEU* 3.1 25.1 - - - -
24A GLY* 2.7 46.9 + - - +
26A CYS* 4.2 19.5 - - - -
40A LEU* 4.3 6.7 - - - -
75A ILE* 4.0 14.1 - - + -
78A LEU* 4.7 11.0 - - + -
79A ASN* 3.1 18.2 - - - +
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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