Contacts of the strand formed by residues 55 - 64 (chain B) in PDB entry 5SZH
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 LYS 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ASP* 3.2 20.9 - - + +
7B TYR* 3.6 37.2 + - + +
51B GLU* 3.3 4.2 - - - -
52B LEU 2.7 40.2 + - - +
53B ASP 3.0 13.1 + - - +
54B GLY* 1.3 85.0 - - - +
56B THR* 1.3 61.6 + - - +
57B ILE* 3.7 9.4 + - + +
170B LYS* 4.5 9.9 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B GLU 3.6 22.0 - - - +
5B TYR* 3.6 9.8 - - + +
6B ASP* 2.5 44.0 + - - +
7B TYR 3.4 3.8 + - - -
49B THR* 3.5 25.6 - - + -
50B ILE 3.4 5.4 - - - +
51B GLU* 4.6 4.4 - - - +
54B GLY 4.1 1.5 + - - -
55B LYS* 1.3 69.8 - - - +
57B ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 57 (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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7B TYR* 3.4 24.9 - - + +
9B PHE* 3.6 35.9 - - + -
49B THR* 3.4 3.6 - - - -
50B ILE* 2.6 50.9 + - + +
52B LEU* 3.7 25.8 - - + +
55B LYS* 3.9 7.2 - - + +
56B THR* 1.3 78.6 - - - +
58B LYS* 1.3 63.0 + - - +
59B LEU* 3.6 14.4 + - + -
166B ALA* 5.2 0.4 - - + -
170B LYS* 3.7 30.5 - - + -
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Residues in contact with LYS 58 (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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664A VAL* 4.2 16.9 + - - +
667A LEU* 3.9 27.1 - - - +
5B TYR* 3.9 43.2 + - + +
7B TYR 2.8 13.5 + - - +
8B LEU* 3.3 23.8 - - + +
9B PHE 2.9 26.3 + - - -
47B ILE* 4.0 30.3 - - + +
49B THR* 3.9 20.2 - - - +
56B THR 4.1 1.4 + - - -
57B ILE* 1.3 72.2 - - - +
59B LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 59 (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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9B PHE* 3.4 30.7 - - + +
11B LEU* 4.6 11.9 - - + -
28B PHE* 3.8 30.1 - - + -
46B LYS 3.7 0.5 - - - +
47B ILE* 3.3 8.8 - - - +
48B ARG 2.8 38.1 + - - +
50B ILE* 3.9 22.2 - - + -
57B ILE* 3.9 19.3 - - + +
58B LYS* 1.3 74.7 - - - +
60B GLN* 1.3 60.2 + - - +
61B ILE* 3.7 17.6 + - + +
162B PHE* 4.7 7.9 - - + -
166B ALA* 4.3 12.3 - - + -
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Residues in contact with GLN 60 (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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661A ASP* 2.7 23.5 + - - +
664A VAL* 4.1 13.1 - - + +
8B LEU* 4.1 12.3 - - + -
9B PHE 2.8 13.0 + - - +
10B LYS* 2.7 38.9 + - + +
11B LEU 2.8 26.7 + - - +
45B PHE* 3.5 42.0 - - + -
46B LYS 3.7 2.2 - - - -
47B ILE* 4.1 7.9 - - + -
58B LYS 3.9 1.4 + - - -
59B LEU* 1.3 72.5 - - - +
61B ILE* 1.3 58.9 + - - +
62B TRP* 3.5 20.0 + - - +
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Residues in contact with ILE 61 (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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11B LEU* 3.5 19.1 - - + +
13B LEU* 4.1 15.3 - - + -
25B LEU* 3.5 28.9 - - + +
28B PHE* 3.5 39.5 - - + -
29B ALA* 5.9 0.2 - - + -
45B PHE* 3.1 5.4 - - - -
46B LYS 2.8 36.1 + - - +
48B ARG* 5.1 3.8 - - + -
59B LEU* 3.9 22.0 - - + +
60B GLN* 1.3 76.1 - - - +
62B TRP* 1.3 61.8 + - - +
162B PHE* 4.0 24.2 - - + -
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Residues in contact with TRP 62 (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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657A ILE* 4.0 19.5 - - + -
658A GLU* 6.0 0.7 - - - -
661A ASP* 3.6 33.0 - - + -
10B LYS* 4.9 10.1 - - + +
11B LEU 2.7 23.0 + - - +
12B LEU* 3.5 19.9 - - + +
13B LEU* 2.8 33.4 + - - +
43B VAL* 4.0 13.0 - - + -
44B ASP 3.4 17.9 - - - -
45B PHE* 3.6 28.9 - + + -
60B GLN* 3.5 31.2 + - + -
61B ILE* 1.3 74.2 - - - +
63B ASP* 1.3 59.6 + - - +
64B THR* 5.2 0.2 - - + -
77B TYR* 3.5 44.4 - + + -
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Residues in contact with ASP 63 (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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13B LEU* 4.5 5.6 - - + +
21B LYS* 3.7 21.2 - - - +
22B SER* 2.4 41.9 + - - -
25B LEU* 3.6 22.3 - - + +
40B THR* 3.5 10.5 + - - +
43B VAL* 3.3 5.7 - - - +
44B ASP* 2.7 44.7 + - + +
61B ILE 3.8 0.2 + - - -
62B TRP* 1.3 75.7 - - - +
64B THR* 1.3 72.9 + - - +
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Residues in contact with THR 64 (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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12B LEU* 3.5 33.9 - - + -
13B LEU 2.8 21.0 + - - +
14B ILE* 3.8 15.6 - - + +
21B LYS* 3.1 22.3 - - - -
40B THR* 4.3 5.5 - - - -
42B GLY 3.6 4.3 - - - -
43B VAL* 4.3 12.6 - - + -
62B TRP* 4.9 0.7 - - + -
63B ASP* 1.3 85.0 + - - +
65B ALA* 1.3 62.4 + - - +
66B GLY* 5.4 0.2 - - - -
74B THR* 3.9 23.1 - - - +
77B TYR* 5.4 0.7 - - + -
78B TYR* 5.4 0.4 - - + -
102B TRP* 5.8 1.0 - - - -
301B GNP 3.9 1.6 + - - -
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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