Contacts of the strand formed by residues 43 - 52 (chain B) in PDB entry 5SZK
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 VAL 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A MET* 4.3 12.1 - - - +
657A ILE* 3.4 23.7 - - + +
40B THR* 4.7 2.0 - - - -
41B ILE 3.1 8.7 + - - +
42B GLY* 1.3 79.6 - - - +
44B ASP* 1.3 65.1 + - - +
62B TRP* 4.0 19.1 - - + -
63B ASP 3.1 12.6 - - - +
64B THR* 4.2 8.1 - - + -
73B ILE* 4.5 2.9 - - + +
74B THR* 3.8 21.3 - - + +
77B TYR* 3.7 46.4 - - + +
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Residues in contact with ASP 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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620A GLN* 2.7 32.1 + - - -
624A GLU* 4.8 4.5 - - - +
657A ILE* 4.3 5.3 - - - +
660A ARG* 3.2 11.8 + - - -
25B LEU* 5.9 1.1 - - + +
40B THR* 4.9 7.6 - - + -
43B VAL* 1.3 78.1 - - - +
45B PHE* 1.3 72.8 + - - +
46B LYS* 4.7 15.2 + - - +
62B TRP* 3.3 10.2 - - - -
63B ASP* 2.7 44.4 + - + +
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Residues in contact with PHE 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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657A ILE* 3.8 13.7 - - + -
660A ARG* 2.9 81.0 + - + -
661A ASP 3.9 2.7 - - - -
664A VAL* 3.8 12.6 - - + -
25B LEU* 5.0 1.1 - - - -
44B ASP* 1.3 83.9 + - - +
46B LYS* 1.3 76.4 + - - +
47B ILE* 3.9 10.8 - - + -
60B GLN* 3.3 35.4 - - + -
61B ILE 3.2 15.5 - - - +
62B TRP* 3.5 35.9 - + + -
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Residues in contact with LYS 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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660A ARG* 4.6 3.6 - - - +
25B LEU* 3.7 35.6 - - + +
26B LEU* 3.2 30.4 - - + +
29B ALA* 4.2 9.9 - - + -
30B ASP* 4.2 24.4 + - - +
44B ASP* 4.7 12.9 + - - +
45B PHE* 1.3 85.2 - - - +
47B ILE* 1.3 65.5 + - - +
59B LEU 3.5 1.4 - - - +
60B GLN* 3.8 0.9 - - - -
61B ILE* 2.9 33.3 + - - +
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Residues in contact with ILE 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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613A GLU* 6.1 0.7 - - - +
660A ARG* 5.7 0.4 - - - +
664A VAL* 4.1 10.8 - - + -
29B ALA* 4.1 13.2 - - - +
45B PHE* 3.9 16.8 - - + -
46B LYS* 1.3 74.9 - - - +
48B ARG* 1.3 68.4 + - - +
49B THR* 4.4 5.6 - - + -
58B LYS* 3.6 45.3 - - + -
59B LEU 3.3 1.8 - - - +
60B GLN* 3.8 35.2 - - + +
61B ILE* 5.6 0.2 - - - -
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Residues in contact with ARG 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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27B ARG 5.2 0.4 + - - -
28B PHE* 2.7 71.4 + - + +
29B ALA* 4.3 13.7 - - + +
46B LYS 4.1 0.2 + - - -
47B ILE* 1.3 75.2 - - - +
49B THR* 1.3 74.4 + - - +
50B ILE* 3.3 33.5 - - + +
59B LEU* 2.8 41.8 + - + +
61B ILE* 5.2 1.5 - - + +
159B GLU* 3.6 21.2 + - - +
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Residues in contact with THR 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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3B LYS* 3.2 47.1 + - + +
5B TYR* 5.4 6.1 - - + -
47B ILE* 4.4 7.0 - - + -
48B ARG* 1.3 88.1 + - - +
50B ILE* 1.3 63.5 + - - +
51B GLU* 5.6 2.1 + - - -
56B THR* 5.8 4.9 - - - +
57B ILE 3.1 11.4 - - - -
58B LYS* 3.8 25.8 - - + -
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Residues in contact with ILE 50 (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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28B PHE* 4.0 18.4 - - + -
48B ARG* 3.3 40.4 - - + +
49B THR* 1.3 76.6 - - - +
51B GLU* 1.3 73.0 + - - +
52B LEU* 4.1 0.9 - - + +
55B LYS 3.6 0.5 - - - +
56B THR* 3.3 6.2 - - - -
57B ILE* 2.8 52.4 + - + +
59B LEU* 4.3 4.9 - - + -
159B GLU* 3.8 6.3 - - - +
163B MET* 3.3 45.8 - - + -
166B ALA* 5.4 1.1 - - + -
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Residues in contact with GLU 51 (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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49B THR* 5.6 1.9 + - - -
50B ILE* 1.3 81.0 - - - +
52B LEU* 1.3 61.5 + - - +
53B ASP 4.1 4.9 + - - +
54B GLY 5.2 1.4 - - - +
55B LYS 3.6 7.8 + - - +
56B THR* 3.1 36.4 + - - +
163B MET* 4.1 6.6 - - - +
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Residues in contact with LEU 52 (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* 6.1 0.7 - - + -
50B ILE* 3.8 5.9 + - + -
51B GLU* 1.3 73.7 - - - +
53B ASP* 1.3 88.4 + - + +
54B GLY 3.1 0.3 + - - -
55B LYS* 2.9 26.5 + - - +
57B ILE* 4.7 12.1 - - + -
163B MET* 3.5 35.7 - - + +
166B ALA* 4.4 8.1 - - + +
167B ALA* 3.9 32.5 - - + +
170B LYS* 4.5 17.3 - - + -
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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