Contacts of the strand formed by residues 85 - 92 (chain D) in PDB entry 3KDO
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 TRP 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D LYS* 6.2 0.7 - - - -
29D PHE 3.4 0.9 - - - +
30D ARG* 3.3 3.3 - - - +
31D VAL* 2.6 39.3 + - - -
33D PRO* 4.7 4.3 - - + +
39D ILE* 3.6 52.5 - - + +
40D GLU* 6.0 0.2 - - - -
77D PHE* 4.2 17.9 - - + -
78D HIS 3.2 12.6 - - - -
79D ASP* 3.3 57.3 + - + -
80D MET* 4.2 0.4 - - - -
83D GLY* 4.4 8.1 + - - -
84D SER* 1.3 85.8 - - - +
86D ILE* 1.3 64.5 + - - +
87D VAL* 3.8 5.0 + - + -
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Residues in contact with ILE 86 (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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28D VAL* 3.5 26.7 - - + -
29D PHE 3.3 2.2 - - - +
30D ARG* 3.9 24.9 - - + +
76D ASP* 3.4 7.8 - - - +
77D PHE* 3.5 1.0 - - - -
78D HIS* 2.8 50.1 + - + +
80D MET* 3.6 25.1 - - - -
85D TRP* 1.3 74.1 - - - +
87D VAL* 1.3 61.1 + - - +
88D ARG* 5.2 6.5 - - + +
124D GLU* 4.8 0.9 - - + -
349D VAL* 3.3 26.5 - - + +
350D PHE* 3.9 29.6 - - + -
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Residues in contact with VAL 87 (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 ALA 3.6 2.4 - - - +
28D VAL* 3.6 1.0 - - - -
29D PHE* 2.8 41.7 + - + +
31D VAL* 3.9 18.6 - - + -
39D ILE* 3.8 22.4 - - + -
43D ALA* 3.9 11.4 - - + -
74D ALA* 3.8 28.7 - - + -
76D ASP 3.2 7.6 - - - +
77D PHE* 3.8 24.2 - - + -
85D TRP* 4.4 2.5 - - + -
86D ILE* 1.3 77.1 - - - +
88D ARG* 1.3 66.8 + - - +
89D ILE* 4.0 8.2 + - + -
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Residues in contact with ARG 88 (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 ILE* 4.2 3.4 - - + -
27D ALA 3.6 3.6 - - - -
28D VAL* 4.2 22.0 - - + +
74D ALA* 3.4 3.5 - - - -
75D TYR* 2.9 61.8 + - + +
76D ASP* 2.9 44.9 + - + +
86D ILE* 5.2 4.0 - - + +
87D VAL* 1.3 75.4 - - - +
89D ILE* 1.3 61.3 + - - +
348D ASP 5.3 6.1 + - - -
349D VAL* 4.9 13.7 + - - +
351D HIS 5.5 1.6 + - - -
352D LEU* 3.9 28.4 - - - +
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Residues in contact with ILE 89 (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 ILE* 3.2 4.7 - - - +
27D ALA 3.0 33.9 + - - +
29D PHE* 3.9 15.5 - - + -
43D ALA* 4.4 5.2 - - - +
46D VAL* 3.8 29.4 - - + -
47D ALA* 3.9 17.9 - - + +
72D ALA* 3.8 15.3 - - + -
73D LYS 3.4 11.9 - - - +
74D ALA* 4.0 10.8 - - + -
75D TYR* 4.1 2.7 - - - -
87D VAL* 4.2 9.4 - - + -
88D ARG* 1.3 79.4 - - - +
90D ALA* 1.3 61.7 + - - +
91D TYR* 3.4 36.0 - - + +
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Residues in contact with ALA 90 (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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17D TYR* 3.8 28.7 - - + -
19D PRO* 4.3 4.5 - - + -
24D ASP* 4.1 13.0 - - + +
25D ILE 3.3 4.9 - - - +
26D ILE* 4.6 1.3 - - + +
71D SER 4.6 0.3 - - - +
72D ALA* 3.2 7.3 - - - +
73D LYS* 2.9 34.4 + - + +
75D TYR* 3.9 17.8 - - + -
89D ILE* 1.3 73.0 - - - +
91D TYR* 1.3 59.8 + - - +
92D PRO* 4.4 1.3 - - - +
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Residues in contact with TYR 91 (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 ASP* 3.3 6.4 - - - -
25D ILE* 2.7 56.8 + - + +
27D ALA* 4.0 9.0 - - + -
29D PHE* 4.1 7.4 - - - -
50D SER* 2.7 42.5 + - - -
51D SER* 4.5 4.5 - - - -
70D LEU 5.9 0.4 - - - -
72D ALA* 3.3 24.5 - - + -
89D ILE* 3.4 40.7 - - + +
90D ALA* 1.3 74.6 - - - +
92D PRO* 1.3 69.1 - - + +
95D ALA* 5.6 0.2 - - + -
96D PHE* 3.7 32.8 - + + -
108D ILE* 3.7 24.3 - - + +
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Residues in contact with PRO 92 (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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23D ARG* 3.9 1.6 - - + +
24D ASP* 3.7 12.7 - - - +
69D ASP 3.7 14.4 - - - +
70D LEU* 3.6 29.4 - - - +
71D SER 3.9 12.6 - - - +
72D ALA* 4.8 0.2 - - - -
90D ALA 4.4 0.9 - - - +
91D TYR* 1.3 86.0 - - + +
93D PHE* 1.3 66.4 + - - +
94D HIS* 3.6 23.6 - - + -
95D ALA* 3.0 21.5 + - + +
96D PHE* 3.8 4.5 - - - -
23I ARG* 3.8 13.2 - - - +
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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