Contacts of the strand formed by residues 20 - 28 (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 CYS 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ILE* 1.3 79.5 - - - +
21D GLN* 1.3 61.6 + - - +
22D PHE* 3.9 28.7 - - + -
68D THR* 6.4 2.7 - - + -
69D THR 3.7 7.8 + - - +
70D VAL* 3.5 7.0 - - + -
71D LYS 2.9 23.9 + - - -
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Residues in contact with GLN 21 (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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466C ASP* 5.0 0.2 + - - -
468C SER* 4.2 9.3 + - - -
469C SER* 3.3 27.5 + - - +
472C ASN* 3.1 26.4 + - - +
473C TYR* 4.4 0.8 + - - -
19D ILE* 4.0 14.5 + - + +
20D CYS* 1.3 77.1 - - - +
22D PHE* 1.3 65.4 + - - +
23D LYS 4.3 0.2 + - - -
71D LYS* 3.3 47.3 - - + +
73D GLU* 3.2 17.0 - - + +
95D GLN* 3.6 10.9 + - - -
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Residues in contact with PHE 22 (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* 3.9 28.9 - - + -
21D GLN* 1.3 78.4 - - - +
23D LYS* 1.3 61.7 + - - +
24D LEU* 3.6 0.7 + - + -
70D VAL* 3.6 34.3 - - + -
71D LYS 3.1 8.3 + - - +
72D PHE* 3.6 18.4 - + + -
73D GLU* 2.9 26.1 + - - -
95D GLN* 3.6 28.0 - - + +
96D ALA* 5.7 1.3 - - + +
179D ALA* 6.5 0.7 - - - -
182D LEU* 3.7 51.4 - - + -
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Residues in contact with LYS 23 (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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476C GLN* 5.1 9.8 + - - +
22D PHE* 1.3 72.0 - - - +
24D LEU* 1.3 61.3 + - - +
73D GLU* 3.8 18.3 + - - +
75D TRP* 3.8 34.7 - - + +
89D MET 3.6 16.2 + - - -
90D TYR* 3.2 26.8 + - - +
92D ARG* 4.7 2.4 - - - +
93D GLY* 3.5 44.5 - - - +
94D ALA* 3.6 5.8 - - + -
95D GLN* 3.0 28.1 + - - +
96D ALA* 3.1 11.5 + - - +
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Residues in contact with LEU 24 (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 3.9 + - - +
23D LYS* 1.3 74.8 - - - +
25D VAL* 1.3 79.8 + - - +
26D LEU* 3.6 24.7 - - + -
72D PHE* 4.2 26.7 - - + -
73D GLU 3.0 14.4 + - - +
74D ILE* 4.3 10.3 - - + -
75D TRP* 2.8 30.4 + - - +
96D ALA* 3.8 17.3 - - + -
98D ILE* 3.7 22.7 - - + +
175D PHE* 3.6 31.0 - - + -
178D ILE* 4.6 9.0 - - + -
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Residues in contact with VAL 25 (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* 1.3 78.0 - - - +
26D LEU* 1.3 66.9 + - - +
27D LEU* 4.1 16.7 + - + -
75D TRP* 3.6 11.9 - - + +
77D THR* 4.0 8.3 - - + -
90D TYR* 3.9 35.9 - - + +
91D TYR* 3.9 20.6 - - + +
94D ALA* 4.0 5.4 - - + -
96D ALA 3.4 18.0 + - - +
97D ALA* 3.5 13.2 - - + -
98D ILE 2.8 26.5 + - - -
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Residues in contact with LEU 26 (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 16.4 - - + -
25D VAL* 1.3 73.6 - - - +
27D LEU* 1.3 56.8 + - - +
34D LYS* 4.0 20.9 - - + +
37D LEU* 4.7 9.0 - - + -
38D VAL* 3.7 24.0 - - + -
74D ILE* 3.6 30.5 - - + -
75D TRP 3.2 16.2 + - - +
76D ASP* 4.5 8.7 - - - +
77D THR* 2.4 33.8 + - - -
98D ILE* 3.5 27.6 - - + +
100D VAL* 4.6 11.0 - - + -
175D PHE* 4.9 5.4 - - + -
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Residues in contact with LEU 27 (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* 4.1 14.9 + - + +
26D LEU* 1.3 76.0 - - - +
28D GLY* 1.3 58.4 + - - +
34D LYS* 3.7 4.0 - - - -
77D THR* 3.5 27.4 - - + +
78D ALA 5.9 1.1 - - - +
87D ALA* 4.8 8.7 - - + +
90D TYR* 5.6 0.2 - - + -
91D TYR* 4.1 21.1 - - + -
98D ILE 3.0 9.5 + - - +
99D VAL* 3.5 4.7 - - + -
100D VAL* 2.8 29.6 + - - +
115D TRP* 3.6 56.1 - - + -
119D LEU* 4.3 21.1 - - + -
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Residues in contact with GLY 28 (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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27D LEU* 1.3 77.5 - - - +
29D GLU* 1.3 62.4 + - - +
34D LYS* 3.8 9.0 + - - +
77D THR* 4.9 0.6 + - - -
78D ALA 4.7 0.7 - - - +
79D GLY* 3.3 20.6 - - - -
99D VAL* 5.4 0.4 - - - -
100D VAL 3.6 14.4 - - - -
111D ARG* 5.4 0.2 - - - -
115D TRP* 3.5 30.6 + - - +
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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