Contacts of the strand formed by residues 28 - 34 (chain B) in PDB entry 4KZZ
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 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PRO* 3.1 34.7 - - - +
25B PHE* 2.7 51.9 + - + +
27B LYS* 1.3 82.3 + - - +
29B ASP* 1.3 61.0 + - - +
30B TRP* 4.5 10.8 + - - +
48B LEU* 3.7 29.3 - - + +
49B VAL 3.2 16.6 - - - +
50B THR* 4.6 13.7 - - + -
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Residues in contact with ASP 29 (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 LYS 4.1 0.4 + - - +
28B LYS* 1.3 73.7 - - - +
30B TRP* 1.3 65.3 + - - +
31B TYR* 3.9 28.7 + - - -
47B THR 3.7 0.7 - - - +
48B LEU* 3.1 5.9 - - - -
49B VAL* 2.6 49.7 + - - +
50B THR 4.4 4.8 - - - +
51B ARG* 4.9 10.7 - - + -
52B THR* 4.7 4.9 - - - +
58B ALA* 4.3 9.0 - - - +
94B LYS* 4.6 10.2 + - - +
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Residues in contact with TRP 30 (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 LYS* 4.5 8.1 + - - +
29B ASP* 1.3 83.0 - - - +
31B TYR* 1.3 73.6 + - - +
32B ASP* 5.4 2.5 - - - +
46B LYS* 3.9 19.3 - - + -
47B THR* 3.6 37.0 - - - -
48B LEU* 4.0 29.3 - - + +
94B LYS* 4.2 12.1 + - - +
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Residues in contact with TYR 31 (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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29B ASP* 3.9 30.0 + - - -
30B TRP* 1.3 74.6 - - - +
32B ASP* 1.3 65.2 + - - +
33B VAL* 3.7 1.5 + - + -
46B LYS* 3.3 7.0 - - - +
47B THR* 3.0 40.8 + - - +
49B VAL* 4.8 3.6 - - + -
52B THR* 5.2 4.3 - - - +
58B ALA* 5.0 11.3 - - + +
59B SER* 5.4 1.9 + - - -
62B LEU* 3.1 38.8 - - + -
91B VAL* 4.0 12.4 - - + +
93B GLY* 5.1 1.7 - - - -
94B LYS* 2.7 63.4 + - + +
95B ASN 3.7 1.6 - - - -
96B CYS* 3.8 15.9 - - + -
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Residues in contact with ASP 32 (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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30B TRP* 5.4 2.4 - - - +
31B TYR* 1.3 75.8 + - - +
33B VAL* 1.3 64.2 + - - +
34B LYS* 3.2 7.8 + - - +
43B ASN* 4.2 14.3 + - - +
45B GLY 3.7 3.8 - - - -
46B LYS* 2.4 40.9 + - + +
94B LYS* 3.0 20.0 + - - +
95B ASN* 4.3 9.8 - - - +
96B CYS* 3.8 14.0 + - - -
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Residues in contact with VAL 33 (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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31B TYR* 4.8 0.9 - - + +
32B ASP* 1.3 69.9 - - - +
34B LYS* 1.3 60.2 + - - +
42B ARG 3.7 0.9 - - - +
43B ASN* 4.0 3.8 - - - +
44B ILE* 3.1 62.9 + - + +
45B GLY 3.0 15.8 + - - +
47B THR* 3.7 35.0 - - + +
67B PHE* 3.8 23.3 - - + -
86B LEU* 5.6 0.2 - - + -
88B THR* 5.5 1.6 - - - +
96B CYS* 4.0 9.4 - - + -
98B THR* 3.9 17.5 - - + -
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Residues in contact with LYS 34 (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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32B ASP 3.2 6.2 + - - +
33B VAL* 1.3 73.6 - - - +
35B ALA* 1.3 58.9 + - - +
42B ARG* 3.3 44.6 - - - +
43B ASN* 5.6 2.5 - - - +
44B ILE* 3.9 1.3 - - - -
95B ASN* 4.5 20.0 - - - +
96B CYS 2.9 17.9 + - - +
97B LEU* 3.5 27.4 - - + -
98B THR* 2.5 39.4 + - - -
232B HIS* 3.9 0.8 - - + -
233B GLY* 5.5 5.7 + - - +
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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