Contacts of the strand formed by residues 68 - 77 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B CYS* 4.4 1.4 + - - -
19D ILE 5.9 1.8 - - - +
20D CYS* 6.4 2.0 - - + -
64D CYS* 3.2 3.5 - - - -
65D LEU* 2.7 51.4 + - + +
66D ASP 2.9 9.3 + - - -
67D ASP* 1.3 80.8 + - - +
69D THR* 1.3 68.6 + - - +
70D VAL* 4.9 5.4 - - + -
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B THR 5.8 0.2 + - - -
63B VAL* 5.7 0.7 - - - -
64B CYS* 2.8 27.2 + - - -
19D ILE* 3.8 24.1 + - + +
20D CYS* 3.7 17.5 + - - +
62D THR* 3.6 30.3 - - + -
63D VAL 4.2 1.8 - - - +
64D CYS* 3.5 5.2 - - + -
68D THR* 1.3 75.6 - - - +
70D VAL* 1.3 69.5 + - - +
71D LYS* 5.7 1.3 - - + -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D CYS* 3.5 7.6 - - + +
22D PHE* 3.6 31.2 - - + -
62D THR* 3.9 1.6 - - - -
63D VAL* 2.8 56.9 + - + +
65D LEU* 4.1 26.0 - - + -
68D THR* 3.9 6.9 + - + +
69D THR* 1.3 82.7 - - - +
71D LYS* 1.3 61.2 + - - +
72D PHE* 4.1 9.2 - - + -
176D MET* 6.4 0.2 - - + -
179D ALA* 4.4 18.2 - - + +
182D LEU* 6.2 1.3 - - + -
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C GLU* 2.3 38.2 + - - -
466C ASP* 3.8 9.9 + - - +
473C TYR* 3.8 6.0 + - - -
19D ILE* 5.4 10.3 - - + -
20D CYS 2.9 9.8 + - - +
21D GLN* 3.3 43.7 - - + +
22D PHE 3.1 24.8 + - - +
60D THR* 3.6 29.4 - - + -
61D GLN 4.0 2.5 - - - -
62D THR* 4.2 16.8 - - + +
69D THR* 5.7 0.9 - - + -
70D VAL* 1.3 73.6 - - - +
72D PHE* 1.3 65.8 + - - +
73D GLU* 3.8 3.0 + - + -
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Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE* 3.6 30.5 - + + -
24D LEU* 4.2 21.3 - - + -
41D PHE* 4.2 13.7 - + - -
60D THR* 3.4 30.7 - - - +
61D GLN 3.1 15.0 + - - +
63D VAL* 4.1 20.0 - - + -
70D VAL* 4.7 7.6 - - + -
71D LYS* 1.3 75.5 - - - +
73D GLU* 1.3 60.6 + - - +
74D ILE* 3.5 17.0 - - + -
96D ALA* 5.9 1.1 - - + -
175D PHE* 3.8 51.1 - + + -
178D ILE* 5.0 4.0 - - + -
179D ALA* 4.3 18.6 - - + -
182D LEU* 5.1 5.6 - - + -
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472C ASN* 2.9 26.6 + - - -
473C TYR* 3.7 17.5 - - + +
476C GLN* 3.1 26.5 + - - +
21D GLN* 3.2 19.8 - - + +
22D PHE 2.9 19.1 + - - +
23D LYS* 4.0 14.9 - - - +
24D LEU 3.0 19.5 + - - +
58D PHE* 4.0 19.9 - - + -
59D LEU 4.3 0.9 - - - -
60D THR* 4.4 2.2 - - - +
71D LYS* 4.6 7.6 - - + +
72D PHE* 1.3 72.9 - - - +
74D ILE* 1.3 58.8 + - - +
75D TRP* 3.1 18.5 + - - +
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.6 13.2 - - + -
26D LEU* 3.6 24.9 - - + -
38D VAL* 3.7 28.5 - - + -
41D PHE* 3.7 36.6 - - + -
42D VAL* 4.6 6.7 - - + -
57D ALA 3.8 0.4 - - - +
58D PHE* 3.1 8.7 - - - -
59D LEU* 3.1 37.4 + - + +
61D GLN* 4.7 5.2 - - + +
72D PHE* 3.5 20.3 - - + +
73D GLU* 1.3 70.3 - - - +
75D TRP* 1.3 62.0 + - - +
76D ASP* 4.3 4.7 - - + +
175D PHE* 4.2 9.0 - - + -
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Residues in contact with TRP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C ALA* 4.0 40.4 - - + -
453C HIS* 4.4 5.2 - - + -
454C LEU* 3.8 22.4 - - + -
476C GLN* 4.7 5.5 + - - -
23D LYS* 3.8 31.7 - - - +
24D LEU 2.8 17.6 + - - +
25D VAL* 3.6 8.7 - - + -
26D LEU* 3.2 23.8 + - - -
56D ALA* 4.4 11.0 - - + -
57D ALA 3.8 2.5 - - - -
58D PHE* 3.3 48.0 - + + -
73D GLU* 3.1 29.7 + - - +
74D ILE* 1.3 72.6 - - - +
76D ASP* 1.3 63.2 + - - +
77D THR* 3.4 6.0 + - + +
90D TYR* 4.3 29.2 - + + -
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Residues in contact with ASP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.5 9.3 - - - +
34D LYS* 3.7 22.6 - - - +
35D SER* 2.7 37.8 + - - -
38D VAL* 4.2 17.1 - - + +
53D THR* 4.0 7.2 + - - +
56D ALA* 3.2 3.4 - - - +
57D ALA* 2.7 53.4 + - + +
59D LEU* 6.0 1.6 - - + -
74D ILE* 3.9 4.1 - - + +
75D TRP* 1.3 69.4 - - - +
77D THR* 1.3 74.1 + - - +
302D MG 3.8 0.2 - - - -
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 4.0 5.6 - - + -
26D LEU 2.4 28.6 + - - +
27D LEU* 3.5 19.9 - - + +
28D GLY 4.9 0.3 + - - -
34D LYS* 3.6 11.1 - - - -
53D THR* 4.0 9.4 + - - -
55D GLY 3.9 8.3 - - - -
56D ALA* 4.4 1.6 - - + +
75D TRP 3.4 11.6 + - - +
76D ASP* 1.3 89.9 + - - +
78D ALA* 1.3 67.0 + - - +
90D TYR* 3.5 41.1 - - + -
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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