Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 1SBB
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.6 35.5 - - + -
36A ARG 3.7 2.5 - - - +
37A GLN* 3.7 12.1 + - + +
42A GLY* 1.3 70.9 - - - -
44A ARG* 1.3 60.0 + - - +
45A LEU 4.2 0.3 + - - -
91A PHE* 3.9 17.9 - - + -
101A TYR* 4.4 7.5 + - + -
108A PHE* 3.8 27.1 - - + -
42C GLY* 3.1 2.6 - - - -
43C LEU* 2.8 48.2 + - + +
101C TYR* 3.7 39.3 - - + +
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Residues in contact with ARG 44 (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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35A TYR* 3.1 7.2 - - - -
36A ARG* 3.0 40.4 + - - +
38A ASP* 2.8 27.9 + - - -
41A HIS* 3.7 45.2 + - - +
42A GLY 4.8 4.2 + - - +
43A LEU* 1.3 75.6 - - - +
45A LEU* 1.3 61.5 + - - +
46A ILE* 3.6 3.3 + - - +
59A ASP* 4.0 6.5 - - + +
60A ILE* 3.7 47.2 - - + +
40C GLY 5.1 4.0 - - - -
41C HIS* 4.5 4.0 - - - +
42C GLY* 3.7 23.6 - - - +
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Residues in contact with LEU 45 (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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33A TYR* 3.7 24.7 - - + -
34A TRP 3.5 15.5 - - - +
35A TYR* 3.6 28.7 - - + +
43A LEU 4.2 0.4 + - - -
44A ARG* 1.3 70.5 - - - +
46A ILE* 1.3 58.4 + - - +
47A HIS 3.8 11.2 - - - +
48A TYR* 3.9 13.7 - - + -
58A GLY* 4.0 6.3 - - - -
59A ASP* 2.7 43.4 + - - +
60A ILE* 3.0 10.3 + - - +
98A ARG* 3.5 47.6 - - + +
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Residues in contact with ILE 46 (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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34A TRP 2.8 18.5 + - - +
35A TYR 4.2 3.6 - - - -
36A ARG* 4.0 11.2 - - + -
44A ARG 4.1 7.9 - - - +
45A LEU* 1.3 74.4 - - - +
47A HIS* 1.3 84.9 + - + +
58A GLY* 3.0 17.4 + - - -
60A ILE* 3.8 20.4 - - + +
61A PRO* 3.6 10.2 - - - +
65A TYR* 3.7 37.9 - - + -
77A LEU* 3.8 18.4 - - + -
90A TYR* 3.7 31.6 - - + -
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Residues in contact with HIS 47 (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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34A TRP* 3.1 25.9 + - + +
45A LEU* 3.8 3.0 - - - +
46A ILE* 1.3 95.3 + - + +
48A TYR* 1.3 64.5 + - - +
55A THR* 5.8 0.9 - - - -
56A GLU 3.3 15.6 + - - +
57A LYS* 3.4 10.5 - - + -
58A GLY 4.0 2.7 - - - +
61A PRO* 3.3 30.1 + - + -
65A TYR* 2.9 32.0 + - + -
66A LYS 4.0 14.1 - - - -
67A ALA* 3.9 19.5 - - + -
75A PHE* 3.5 7.4 - - + -
77A LEU* 4.5 3.6 - - + -
20B LEU* 3.9 5.5 - - + +
177B PHE* 3.7 20.8 - + - -
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Residues in contact with TYR 48 (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 ASN* 4.8 2.0 - - - -
32A MET 3.4 5.4 - - - -
33A TYR* 3.5 35.9 - + + -
45A LEU* 3.9 14.4 - - + -
47A HIS* 1.3 75.5 - - - +
49A SER* 1.3 64.0 + - - +
50A TYR* 3.5 39.7 + + - -
55A THR* 3.4 5.7 - - - -
56A GLU* 2.7 55.3 + - + +
57A LYS 3.3 24.6 + - - -
75A PHE* 3.7 5.6 - - - -
98A ARG* 3.4 36.3 + - + +
176C PRO* 6.1 1.2 - - - +
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Residues in contact with SER 49 (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 ASN* 3.0 32.7 + - - +
32A MET 2.9 10.3 + - - +
48A TYR* 1.3 77.0 - - - +
50A TYR* 1.3 61.7 + - - +
51A GLY 2.9 10.6 + - - -
54A SER* 2.8 26.9 + - - -
56A GLU* 4.8 0.7 - - - +
69A ARG* 2.7 32.1 + - - +
75A PHE* 3.9 16.8 - - - -
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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