Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 1SDS
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 SER 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY 3.0 24.4 + - - -
31A ALA* 3.7 17.8 - - - -
34A VAL* 3.7 10.5 - - - +
46A VAL* 5.0 0.2 - - - -
47A ILE 3.2 13.2 - - - -
48A ILE* 4.4 2.7 - - - -
58A VAL* 4.1 1.3 - - - +
61A LEU* 3.8 26.6 - - - +
81A LEU* 3.8 1.8 - - - -
91A ALA* 3.1 3.5 - - - +
92A SER* 1.3 93.1 + - - +
94A VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 94 (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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21A VAL* 4.1 27.4 - - + -
27A ILE* 4.1 13.0 - - + -
28A LYS 3.3 14.1 - - - +
29A LYS* 4.4 2.7 - - + -
34A VAL* 3.7 4.3 - - - -
45A LEU 4.0 0.3 - - - +
46A VAL* 3.4 4.5 - - - +
47A ILE* 2.8 34.7 + - + +
81A LEU* 3.6 31.4 - - + -
85A ALA* 4.0 19.7 - - + -
91A ALA* 4.3 5.6 - - + -
93A SER* 1.3 81.1 - - - +
95A ALA* 1.3 71.7 + - - +
96A ILE* 4.2 1.1 - - + +
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Residues in contact with ALA 95 (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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27A ILE* 3.2 6.6 - - - +
28A LYS* 2.9 42.4 + - + -
34A VAL* 3.7 24.2 - - + +
37A ALA* 4.4 2.0 - - + -
43A ALA* 4.1 23.3 - - + -
45A LEU 3.4 5.2 - - - +
46A VAL* 4.4 1.6 - - + +
94A VAL* 1.3 75.2 - - - +
96A ILE* 1.3 63.0 + - - +
97A ILE* 3.5 5.3 + - + +
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Residues in contact with ILE 96 (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 ALA* 3.8 40.6 - - + +
21A VAL* 4.1 14.6 - - + +
24A ALA* 4.1 11.2 - - + -
26A LYS 4.1 2.2 - - - -
27A ILE* 4.2 5.6 - - + -
43A ALA 3.8 0.7 - - - -
44A LYS* 2.9 33.1 + - + +
45A LEU* 2.8 37.7 + - + +
47A ILE* 4.6 2.9 - - + -
94A VAL* 5.0 1.1 - - + -
95A ALA* 1.3 73.8 - - - +
97A ILE* 1.3 61.2 + - - +
98A ASN 3.9 2.7 - - - +
99A GLU* 3.7 37.2 - - + +
105A LEU* 4.8 6.1 - - + -
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Residues in contact with ILE 97 (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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26A LYS* 2.9 36.4 + - + +
27A ILE* 4.2 3.1 - - - -
28A LYS* 3.9 23.3 - - + -
37A ALA* 3.9 13.5 - - + -
42A ILE* 3.5 50.5 - - + +
43A ALA* 3.8 12.8 - - - -
44A LYS* 3.7 23.7 - - - +
95A ALA* 4.0 7.4 - - + +
96A ILE* 1.3 76.1 - - - +
98A ASN* 1.3 61.2 + - + +
99A GLU 4.1 0.9 - - - -
215F G 5.2 0.2 + - - -
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Residues in contact with ASN 98 (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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24A ALA* 3.6 1.7 - - - +
25A GLN* 2.8 39.5 + - + +
26A LYS* 3.0 29.3 + - + +
96A ILE* 3.9 2.2 - - - -
97A ILE* 1.3 78.5 + - + +
99A GLU* 1.3 80.4 + - - +
213F G 5.6 0.2 - - - -
214F G 2.8 38.8 + - - +
215F G 3.1 25.1 + - - +
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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