Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 1SZB
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A THR* 4.6 6.8 - - - +
34A LEU 3.4 9.6 + - - -
35A THR* 3.7 13.2 - - - +
42A LEU* 4.6 0.4 - - - -
66A SER* 3.6 17.2 - - - -
67A GLY 5.4 6.1 - - - -
93A SER* 3.0 17.2 - - - -
95A GLY* 3.3 2.8 + - - -
96A SER* 1.3 84.4 - - - +
98A LEU* 1.3 64.9 + - - +
99A ASP* 4.7 6.3 + - - -
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Residues in contact with LEU 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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32A TRP 3.9 0.7 - - - +
33A THR* 3.6 2.4 - - - +
34A LEU* 2.8 45.4 + - + +
42A LEU* 3.7 33.2 - - + +
44A LEU* 3.9 38.6 - - + +
64A LEU* 5.5 3.6 - - + -
65A SER 3.5 13.9 - - - +
71A LEU* 3.7 25.8 - - + -
91A PHE* 5.3 3.8 - - + +
92A TYR 4.6 0.4 - - - +
93A SER* 3.8 15.7 - - - +
97A SER* 1.3 82.1 + - - +
99A ASP* 1.3 64.0 + - - +
100A ILE* 3.9 10.6 - - + +
119A TYR* 5.5 0.2 - - + -
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Residues in contact with ASP 99 (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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31A ARG* 5.5 9.0 + - - +
32A TRP 3.4 3.0 - - - +
33A THR* 2.8 34.9 + - - +
63A LYS 3.7 1.0 - - - +
64A LEU* 3.6 2.9 - - - -
65A SER* 2.6 54.1 + - - +
67A GLY* 4.8 11.6 + - - +
97A SER* 4.7 7.2 + - - -
98A LEU* 1.3 75.0 - - - +
100A ILE* 1.3 61.9 + - - +
101A THR* 5.2 2.4 + - - +
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Residues in contact with ILE 100 (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* 3.8 19.5 - - + -
31A ARG* 3.3 4.3 - - - +
32A TRP* 2.8 63.2 + - + +
34A LEU* 3.7 32.5 - - + -
44A LEU* 4.2 7.2 - - + -
46A PHE* 6.0 0.4 - - + -
62A VAL* 4.1 20.0 - - + -
63A LYS 3.4 8.3 - - - +
64A LEU* 3.7 20.2 - - + -
98A LEU* 3.9 15.7 - - + +
99A ASP* 1.3 77.2 - - - +
101A THR* 1.3 69.2 + - - +
115A PHE* 5.1 3.6 - - + -
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Residues in contact with THR 101 (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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29A GLU* 4.3 11.9 - - - +
30A ARG 3.2 15.3 - - - +
31A ARG* 3.6 24.1 + - + +
32A TRP* 4.8 0.2 - - - -
61A PHE* 3.7 11.9 - - + +
62A VAL* 3.3 6.1 - - - +
63A LYS* 3.0 48.3 + - - -
99A ASP* 5.2 2.4 + - - +
100A ILE* 1.3 85.1 + - - +
102A PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 102 (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 SER* 4.3 5.4 - - - -
18A PRO* 3.7 32.5 - - + -
24A TYR* 3.6 36.8 - + + -
28A GLN* 4.2 9.4 - - + -
29A GLU* 3.6 4.9 - - - +
30A ARG* 3.0 36.9 + - + +
32A TRP* 4.0 19.8 - - + -
51A LEU* 3.8 28.9 - - + -
60A ASP* 5.3 0.2 - - + -
61A PHE 3.4 9.4 - - - -
62A VAL* 3.9 12.3 - - + +
101A THR* 1.3 76.7 - - - +
103A ARG* 1.3 69.7 + - - +
104A SER* 4.0 19.7 - - - -
115A PHE* 4.2 13.5 - + + -
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Residues in contact with ARG 103 (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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28A GLN 3.8 1.6 - - - -
29A GLU* 3.4 28.5 + - - +
58A GLU 3.1 16.6 + - - -
59A TYR 3.0 21.7 + - - -
60A ASP* 3.1 27.2 - - - +
61A PHE* 2.9 52.0 + - + -
101A THR* 5.1 0.4 - - + -
102A PHE* 1.3 78.5 - - - +
104A SER* 1.3 77.2 + - - +
105A ASP* 3.9 12.9 - - - +
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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