Contacts of the strand formed by residues 69 - 77 (chain H) 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 69 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F THR 5.4 2.8 + - - -
64F CYS* 2.7 26.5 - - - -
19H ILE* 2.8 46.5 + - + +
20H CYS 3.5 1.9 + - - -
62H THR* 4.0 29.2 - - + -
63H VAL 3.7 5.8 - - - +
68H THR* 1.3 76.8 - - - +
70H VAL* 1.3 65.4 + - - +
71H LYS* 5.0 0.9 - - + +
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Residues in contact with VAL 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H CYS* 3.8 16.4 - - + +
22H PHE* 4.4 16.4 - - + -
61H GLN 4.0 0.7 - - - +
62H THR* 3.4 2.8 - - - -
63H VAL* 3.0 56.0 + - + +
65H LEU* 4.4 23.8 - - + -
68H THR* 4.0 6.0 + - + -
69H THR* 1.3 79.0 - - - +
71H LYS* 1.3 61.7 + - - +
72H PHE* 5.0 6.2 - - + -
179H ALA* 4.1 23.3 - - + +
182H LEU* 6.0 0.2 - - + -
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Residues in contact with LYS 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461G GLU* 2.7 36.6 + - - -
466G ASP* 4.0 11.3 + - - -
473G TYR* 4.5 2.7 + - - +
19H ILE* 4.8 10.0 - - + +
20H CYS 3.3 8.4 + - - +
21H GLN* 3.4 41.4 + - + +
22H PHE* 2.7 33.7 + - - +
60H THR* 3.6 25.6 - - + -
61H GLN 3.8 2.2 - - - -
62H THR* 3.6 24.2 - - + -
69H THR* 4.1 1.7 + - + -
70H VAL* 1.3 73.7 - - - +
72H PHE* 1.3 63.6 + - - +
73H GLU* 5.8 1.6 - - + -
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Residues in contact with PHE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H PHE* 4.1 16.2 - + + -
24H LEU* 4.1 26.9 - - + -
41H PHE* 4.4 13.9 - + - -
60H THR* 3.5 10.1 - - - +
61H GLN 3.0 36.5 + - - +
63H VAL* 4.0 23.1 - - + -
70H VAL* 5.0 4.9 - - + -
71H LYS* 1.3 78.9 - - - +
73H GLU* 1.3 61.8 + - - +
74H ILE* 3.3 22.6 + - + +
96H ALA* 5.4 0.9 - - + -
175H PHE* 3.4 36.1 - + + -
178H ILE* 5.0 3.1 - - + -
179H ALA* 4.2 19.1 - - + -
182H LEU* 4.2 19.3 - - + -
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Residues in contact with GLU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454G LEU* 5.4 0.2 - - - +
472G ASN* 3.2 22.5 + - - -
473G TYR* 4.0 18.8 - - + +
476G GLN* 2.6 32.1 + - - +
21H GLN* 3.7 20.1 + - + +
22H PHE 2.5 20.1 + - - +
23H LYS* 3.4 18.7 + - + +
24H LEU* 2.5 33.8 + - - +
58H PHE* 4.0 21.8 - - + -
59H LEU 4.3 1.3 - - - -
60H THR* 5.2 2.9 - - + +
71H LYS* 4.0 2.2 + - + -
72H PHE* 1.3 69.6 - - - +
74H ILE* 1.3 56.9 + - - +
75H TRP* 3.7 4.5 + - - -
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Residues in contact with ILE 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 3.6 13.5 - - + -
26H LEU* 3.6 27.1 - - + -
38H VAL* 4.3 22.4 - - + -
41H PHE* 4.1 31.0 - - + -
42H VAL* 4.8 2.9 - - + -
57H ALA 3.6 0.5 - - - +
58H PHE* 3.3 9.9 - - - -
59H LEU* 3.1 41.7 + - + +
61H GLN* 4.5 9.4 - - + +
72H PHE* 3.6 27.6 - - + +
73H GLU* 1.3 71.4 - - - +
75H TRP* 1.3 63.8 + - - +
76H ASP 4.0 0.9 - - - +
175H PHE* 4.8 7.4 - - + -
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Residues in contact with TRP 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G ALA* 3.6 46.7 - - + -
453G HIS* 3.9 16.6 - + + -
454G LEU* 4.2 18.2 - - + -
476G GLN* 4.4 7.6 + - - -
480G ILE* 5.4 2.2 - - + -
23H LYS* 3.3 45.3 - - + +
24H LEU 2.7 15.2 + - - +
25H VAL* 3.6 12.4 - - + +
26H LEU* 3.2 27.1 + - - +
56H ALA* 4.2 10.8 - - + -
57H ALA 3.5 5.2 - - - -
58H PHE* 3.3 31.2 - + - -
73H GLU* 3.7 6.8 + - - +
74H ILE* 1.3 73.7 - - - +
76H ASP* 1.3 59.8 + - - +
77H THR* 3.4 5.1 + - + -
90H TYR* 4.1 28.0 - + + -
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Residues in contact with ASP 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H LEU* 4.3 10.2 - - + +
34H LYS* 3.4 28.5 - - - +
35H SER* 2.5 39.0 + - - -
38H VAL* 4.7 5.2 - - + +
53H THR* 3.8 5.7 + - - +
56H ALA* 3.2 5.0 - - - -
57H ALA* 2.7 55.7 + - + +
59H LEU* 4.7 9.9 - - + +
74H ILE* 4.0 1.2 - - + -
75H TRP* 1.3 68.0 - - - +
77H THR* 1.3 64.7 + - - +
302H MG 3.6 2.0 - - - -
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Residues in contact with THR 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H VAL* 3.6 20.0 - - + -
26H LEU 2.2 35.0 + - - +
27H LEU* 3.8 16.1 - - + +
28H GLY 5.0 0.2 + - - -
34H LYS* 3.2 23.2 - - - +
53H THR* 4.1 8.7 - - - -
55H GLY 3.9 5.4 - - - -
56H ALA* 4.4 1.6 - - + -
75H TRP 3.4 4.8 + - - +
76H ASP* 1.3 82.6 + - - +
78H ALA* 1.3 65.8 + - - +
79H GLY* 5.5 0.3 - - - -
90H TYR* 3.5 33.7 - - + -
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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