Contacts of the strand formed by residues 41 - 50 (chain B) 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 ARG 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ALA* 5.4 0.9 - - - -
40B TYR* 1.3 74.7 - - - +
42B LEU* 1.3 65.5 + - - +
92B TYR* 3.7 39.8 - - - +
93B SER* 3.8 11.7 + - - +
95B GLY 3.4 20.0 - - - +
96B SER* 4.6 2.5 - - - +
121B ALA* 3.1 4.7 - - - -
122B GLU* 2.8 63.2 + - + +
123B ASP 5.2 0.4 + - - -
124B ILE* 3.5 32.3 - - + +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO 5.7 1.6 - - - +
11B VAL 4.8 2.0 - - - +
34B LEU* 3.3 52.3 - - + +
35B THR* 4.0 5.4 - - - +
36B ALA* 4.2 12.6 - - + +
41B ARG* 1.3 74.7 - - - +
43B ARG* 1.3 61.3 + - - +
44B LEU 4.2 0.4 - - - -
91B PHE 3.8 0.3 - - - +
92B TYR* 3.2 10.0 - - - +
93B SER* 2.7 43.3 + - - +
96B SER 4.7 3.4 - - - +
98B LEU* 4.0 16.6 - - + +
119B TYR* 4.4 13.7 - - + -
120B ALA 3.5 3.6 - - - +
121B ALA* 3.5 33.9 - - + +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 3.2 45.1 + - - +
144A HIS* 4.7 1.8 - - - +
41B ARG 4.1 0.4 + - - -
42B LEU* 1.3 73.6 - - - +
44B LEU* 1.3 63.0 + - - +
45B TYR* 3.5 31.1 + - + -
90B THR* 3.5 26.2 - - + -
91B PHE 3.4 4.9 - - - -
92B TYR* 3.7 15.7 - - + -
119B TYR* 3.0 3.9 - - - +
120B ALA* 2.8 49.8 + - - +
121B ALA 4.9 1.0 + - - -
122B GLU* 2.9 41.9 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.2 14.8 - - + -
34B LEU* 4.3 0.4 - - + -
43B ARG* 1.3 76.8 - - - +
45B TYR* 1.3 71.8 + - - +
46B PHE* 3.8 32.3 - - + -
64B LEU* 4.1 12.6 - - + -
90B THR* 3.9 0.7 - - - +
91B PHE* 2.8 37.6 + - + +
98B LEU* 4.1 18.2 - - + -
100B ILE* 4.0 30.7 - - + -
117B ALA* 4.4 6.5 - - + -
118B PHE 3.2 12.3 - - - +
119B TYR* 3.8 15.0 - - + -
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A CYS 3.9 4.8 + - - -
142A HIS* 2.6 56.2 + + - +
143A ASN 4.4 1.2 + - - -
43B ARG* 3.5 38.9 + - + -
44B LEU* 1.3 84.9 - - - +
46B PHE* 1.3 73.3 + - - +
47B THR* 4.1 5.1 + - + -
88B LYS 4.8 4.9 - - - +
89B ASP 3.9 17.3 - - - +
90B THR* 4.6 7.2 - - + +
91B PHE* 4.8 0.2 - - - -
117B ALA* 3.4 1.7 - - - -
118B PHE* 2.9 47.3 + - + +
119B TYR* 5.1 2.4 - - - -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.8 18.6 - - + -
45B TYR* 1.3 81.3 - - - +
47B THR* 1.3 62.7 - - - +
48B HIS 4.2 8.3 - - - +
49B PHE* 3.8 17.0 - + + -
62B VAL* 4.0 19.7 - - + -
64B LEU* 3.9 22.0 - - + -
74B LEU* 3.9 19.7 - - + -
86B PRO* 3.6 25.4 - - + -
87B GLY 3.9 15.3 + - - +
88B LYS* 5.0 4.7 - - - +
89B ASP 4.9 2.0 + - - -
91B PHE* 4.0 10.1 - + - -
100B ILE* 6.0 0.4 - - + -
115B PHE* 3.7 33.7 - + - -
116B GLU 3.4 6.7 - - - +
117B ALA* 3.7 11.2 - - + -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS* 3.6 46.0 + - + +
142A HIS* 3.8 13.7 - - + -
151A SER* 4.6 0.4 - - - +
152A CYS 5.9 0.2 - - - -
153A ARG* 5.9 0.3 - - - +
45B TYR* 4.1 6.3 + - + -
46B PHE* 1.3 76.1 - - - +
48B HIS* 1.3 63.0 + - - +
116B GLU* 2.8 38.6 + - - +
118B PHE* 3.6 24.5 - - + -
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 3.9 28.8 + - + +
20B PHE* 3.4 31.5 - + + -
46B PHE* 3.4 3.2 - - - +
47B THR* 1.3 84.4 + - - +
49B PHE* 1.3 67.0 + - - +
50B ASP* 4.0 5.8 - - + +
113B THR* 3.0 29.1 + - + -
114B GLY 3.7 13.7 - - - -
115B PHE* 3.1 5.5 - - - +
116B GLU* 2.9 34.8 + - + +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.8 17.3 - + + -
48B HIS* 1.3 74.9 + - - +
50B ASP* 1.3 61.9 + - - +
51B LEU* 3.7 16.6 - - + -
62B VAL* 3.5 26.2 - - + -
74B LEU* 3.5 25.8 - - + -
75B CYS* 3.6 18.4 - - - -
76B GLY 3.4 24.8 - - - +
77B GLN* 4.1 14.0 - - - +
85B ALA* 5.3 0.9 - - + -
86B PRO* 3.4 40.4 - - + -
87B GLY 5.7 1.1 - - - +
114B GLY 3.6 2.0 - - - -
115B PHE* 3.8 14.4 - - + -
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 4.0 6.7 - - + +
49B PHE* 1.3 76.4 - - - +
51B LEU* 1.3 61.1 + - - +
76B GLY 4.1 0.2 - - - -
77B GLN* 2.7 39.7 + - + +
110B LYS* 4.9 7.4 + - - -
111B PRO 4.3 1.6 - - - +
112B PHE* 3.4 15.1 - - - +
113B THR* 2.5 44.1 + - - +
114B GLY 2.6 31.4 + - - +
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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