Contacts of the strand formed by residues 20 - 27 (chain B) in PDB entry 4KYI
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 CYS 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 1.3 76.6 - - - +
21B GLN* 1.3 60.3 + - - +
22B PHE* 3.3 33.2 - - + -
68B THR* 4.7 12.8 - - - -
69B THR 3.2 13.1 + - - +
70B VAL* 3.4 6.2 - - + -
71B LYS 3.0 20.8 + - - -
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Residues in contact with GLN 21 (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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468A SER* 3.6 27.7 + - - -
469A SER* 3.2 24.4 - - - +
472A ASN* 4.4 4.5 + - - +
19B ILE* 3.7 20.1 + - + +
20B CYS* 1.3 74.5 - - - +
22B PHE* 1.3 70.2 + - - +
71B LYS* 2.5 49.5 + - - +
73B GLU* 4.1 12.3 - - - +
95B GLN* 4.8 4.3 + - - -
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Residues in contact with PHE 22 (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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20B CYS* 3.3 41.3 - - + -
21B GLN* 1.3 78.9 - - - +
23B LYS* 1.3 55.5 + - - +
24B LEU 4.1 0.2 - - - -
70B VAL* 4.2 14.4 - - + -
71B LYS 2.7 13.4 + - - +
72B PHE* 3.3 10.1 - + + -
73B GLU* 2.5 38.4 + - - +
95B GLN* 3.5 31.2 - - + +
96B ALA* 6.3 0.7 - - + -
182B LEU* 3.8 54.5 - - + -
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Residues in contact with LYS 23 (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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476A GLN* 4.8 5.1 - - - +
22B PHE* 1.3 72.9 - - - +
24B LEU* 1.3 62.9 - - - +
73B GLU* 3.5 29.2 - - - +
75B TRP* 3.9 12.1 - - + +
89B MET 3.7 4.6 + - - -
90B TYR 3.2 24.1 + - - -
92B ARG* 5.0 1.8 - - - +
93B GLY* 3.6 37.0 - - - +
94B ALA* 3.4 7.8 - - + +
95B GLN* 2.5 42.1 + - - +
96B ALA* 3.4 6.3 + - - +
303B EDO 3.2 46.2 + - - +
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Residues in contact with LEU 24 (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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22B PHE 4.0 0.4 + - - -
23B LYS* 1.3 75.9 - - - +
25B VAL* 1.3 61.6 + - - +
26B LEU* 3.6 28.3 - - + -
72B PHE* 3.9 35.7 - - + -
73B GLU 2.8 12.4 + - - +
74B ILE* 4.1 9.9 - - + -
75B TRP* 2.7 32.9 + - - +
96B ALA* 3.7 22.9 - - + +
98B ILE* 3.8 20.2 - - + -
175B PHE* 4.0 15.9 - - + -
178B ILE* 4.1 18.8 - - + -
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Residues in contact with VAL 25 (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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24B LEU* 1.3 80.0 - - - +
26B LEU* 1.3 63.7 + - - +
27B LEU* 3.7 19.4 + - + +
75B TRP* 3.5 13.5 - - + +
77B THR* 3.8 19.5 - - + -
90B TYR* 3.9 22.4 - - + +
91B TYR* 4.0 8.7 - - + -
94B ALA* 3.6 19.7 - - + -
96B ALA 3.4 16.2 + - - +
97B ALA* 3.3 11.9 - - + +
98B ILE 3.0 22.9 + - - -
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Residues in contact with LEU 26 (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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24B LEU* 3.6 20.4 - - + -
25B VAL* 1.3 71.2 - - - +
27B LEU* 1.3 55.7 + - - +
34B LYS* 3.6 38.4 - - + +
37B LEU* 4.5 11.0 - - + -
38B VAL* 3.8 14.8 - - + -
74B ILE* 3.7 20.9 - - + -
75B TRP 3.1 10.3 + - - +
76B ASP* 4.1 12.1 - - - +
77B THR* 2.6 34.8 + - - +
98B ILE* 3.4 26.2 - - + +
100B VAL* 4.4 11.7 - - + -
175B PHE* 4.7 4.5 - - + -
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Residues in contact with LEU 27 (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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25B VAL* 3.9 20.6 - - + +
26B LEU* 1.3 72.8 - - - +
28B GLY* 1.3 59.1 + - - +
34B LYS* 3.3 14.5 - - - +
77B THR* 3.7 20.6 - - + +
87B ALA* 5.0 8.7 - - + -
90B TYR* 5.7 0.9 - - + -
91B TYR* 4.5 10.3 - - + -
97B ALA* 4.9 4.5 - - + -
98B ILE 2.8 11.2 + - - +
99B VAL* 4.3 5.4 - - + -
100B VAL* 2.9 23.3 + - - -
115B TRP* 4.1 43.1 - - + -
119B LEU* 4.0 36.8 - - + -
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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