Contacts of the strand formed by residues 68 - 77 (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 THR 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ILE 5.5 2.2 - - - +
20B CYS* 4.7 14.8 - - - -
64B CYS* 3.5 3.2 - - - -
65B LEU* 2.7 42.7 + - + +
66B ASP* 2.8 13.1 + - - -
67B ASP* 1.3 85.2 + - - +
69B THR* 1.3 73.4 + - - +
70B VAL* 4.8 2.7 - - + -
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Residues in contact with THR 69 (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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19B ILE* 3.6 36.0 - - + +
20B CYS 3.2 19.8 + - - -
62B THR* 3.6 29.2 - - + -
63B VAL 4.1 2.7 - - - +
64B CYS* 3.9 6.3 - - + -
67B ASP 4.3 0.7 + - - -
68B THR* 1.3 79.9 - - - +
70B VAL* 1.3 68.8 + - - +
62D THR 5.5 1.6 + - - -
63D VAL* 5.5 1.9 - - - -
64D CYS* 3.6 19.4 + - - -
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Residues in contact with VAL 70 (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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19B ILE 5.8 0.2 - - - -
20B CYS* 3.4 16.2 - - + +
22B PHE* 4.2 17.3 - - + -
61B GLN 4.4 0.3 - - - +
62B THR* 3.4 6.6 - - - +
63B VAL* 2.9 54.7 + - + +
65B LEU* 3.7 27.8 - - + +
68B THR* 3.9 4.0 + - + -
69B THR* 1.3 81.7 - - - +
71B LYS* 1.3 60.5 + - - +
72B PHE* 4.3 7.4 - - + -
179B ALA* 4.5 19.1 - - + +
182B LEU* 5.8 2.0 - - + -
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Residues in contact with LYS 71 (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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461A GLU* 4.8 8.3 - - - +
466A ASP* 5.2 6.7 - - - -
469A SER* 4.4 2.2 + - - -
473A TYR* 4.0 14.6 + - - -
19B ILE* 4.5 13.7 - - + -
20B CYS 3.0 8.5 + - - +
21B GLN* 2.5 53.9 + - + +
22B PHE* 2.7 33.5 + - - +
60B THR* 3.6 30.2 - - + +
61B GLN 4.0 2.5 - - - -
62B THR* 3.9 17.5 - - + +
70B VAL* 1.3 76.7 - - - +
72B PHE* 1.3 61.4 + - - +
73B GLU* 4.3 8.1 + - - +
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Residues in contact with PHE 72 (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* 3.3 10.3 - + + -
24B LEU* 3.9 34.5 - - + -
41B PHE* 4.5 20.6 - + - -
60B THR* 3.4 31.4 + - - +
61B GLN 3.1 20.1 + - - +
63B VAL* 4.1 23.3 - - + -
70B VAL* 4.6 7.9 - - + -
71B LYS* 1.3 77.2 - - - +
73B GLU* 1.3 60.8 + - - +
74B ILE* 3.6 21.2 + - + -
96B ALA* 5.5 1.1 - - + -
175B PHE* 4.1 23.1 - + - -
176B MET* 5.8 0.4 - - + -
178B ILE* 5.1 2.2 - - + -
179B ALA* 4.2 16.4 - - + -
182B LEU* 3.9 21.1 - - + -
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Residues in contact with GLU 73 (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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472A ASN* 2.9 27.1 + - - -
473A TYR* 4.0 18.3 - - + +
476A GLN* 3.5 20.3 + - - +
21B GLN* 4.1 14.7 - - - +
22B PHE* 2.5 24.0 + - - +
23B LYS* 3.5 21.1 + - + +
24B LEU 2.8 22.1 + - - +
58B PHE* 4.3 14.1 - - + -
59B LEU 4.0 4.5 - - - -
60B THR* 4.5 3.4 - - - +
71B LYS* 4.3 10.3 + - - +
72B PHE* 1.3 73.8 - - - +
74B ILE* 1.3 61.7 + - - +
75B TRP* 3.5 9.3 - - - +
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Residues in contact with ILE 74 (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* 3.4 14.1 - - + -
26B LEU* 3.7 27.6 - - + -
38B VAL* 4.4 17.5 - - + -
41B PHE* 4.0 32.3 - - + -
42B VAL* 4.7 7.2 - - + -
57B ALA 3.9 0.7 - - - +
58B PHE* 3.5 10.6 - - - -
59B LEU* 3.1 39.9 + - + +
61B GLN* 4.3 13.0 - - + +
72B PHE* 3.7 23.8 - - + +
73B GLU* 1.3 72.5 - - - +
75B TRP* 1.3 63.0 + - - +
76B ASP 4.0 1.6 - - - +
175B PHE* 4.5 5.4 - - + -
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Residues in contact with TRP 75 (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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449A GLN* 6.2 0.2 - - + -
450A ALA* 3.8 38.4 - - + -
453A HIS* 4.1 16.8 - + + -
454A LEU* 4.3 10.8 - - + -
476A GLN* 4.9 1.6 + - - -
23B LYS* 3.9 20.0 - - + +
24B LEU 2.7 13.5 + - - +
25B VAL* 3.5 12.4 - - + +
26B LEU 3.1 21.9 + - - -
56B ALA* 4.2 9.2 - - + -
57B ALA 3.8 6.1 - - - -
58B PHE* 3.2 34.9 - + - -
73B GLU* 3.5 17.5 + - - +
74B ILE* 1.3 76.1 - - - +
76B ASP* 1.3 62.8 + - - +
77B THR* 3.3 2.6 + - - +
90B TYR* 3.4 44.0 - + + -
303B EDO 3.1 30.4 + - - -
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Residues in contact with ASP 76 (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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26B LEU* 4.1 8.6 - - - +
34B LYS* 3.3 30.7 - - - +
35B SER* 2.4 32.9 + - - -
38B VAL* 4.3 11.2 - - + -
53B THR* 3.2 6.8 + - - +
56B ALA* 3.2 5.6 - - - -
57B ALA 3.1 33.3 + - - +
74B ILE* 4.0 3.4 - - + +
75B TRP* 1.3 68.7 - - - +
77B THR* 1.3 65.4 + - - +
302B EDO 2.4 29.6 + - - +
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Residues in contact with THR 77 (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* 3.8 15.3 - - + -
26B LEU 2.6 27.8 + - - +
27B LEU* 3.7 18.4 - - + +
28B GLY 5.0 0.5 + - - -
34B LYS* 3.7 12.1 - - - -
53B THR* 4.1 2.1 - - - -
55B GLY 3.8 5.8 - - - -
56B ALA* 4.2 1.3 - - - -
75B TRP 3.3 10.9 + - - +
76B ASP* 1.3 85.7 + - - +
78B ALA* 1.3 68.9 + - - +
90B TYR* 3.9 33.4 - - + -
301B GNP 3.7 4.0 + - - -
304B MG 3.9 3.8 - - - -
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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