Contacts of the strand formed by residues 85 - 92 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H PHE 3.4 0.7 - - - +
30H ARG* 3.2 4.2 - - - -
31H VAL* 2.6 38.4 + - - +
33H PRO* 4.5 6.7 - - + +
39H ILE* 3.6 57.8 - - + +
40H GLU* 5.9 1.1 - - - -
77H PHE* 4.3 12.3 - - + -
78H HIS 3.3 11.4 - - - -
79H ASP* 3.4 53.3 - - + -
80H MET* 4.2 0.4 - - - -
83H GLY* 4.3 9.9 + - - -
84H SER* 1.3 84.3 + - - +
86H ILE* 1.3 65.6 + - - +
87H VAL* 3.7 6.6 + - + -
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Residues in contact with ILE 86 (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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28H VAL* 3.6 22.2 - - + -
29H PHE 3.4 0.9 - - - +
30H ARG* 4.0 30.7 - - + +
76H ASP* 3.6 3.1 - - - +
77H PHE* 3.5 3.3 - - - -
78H HIS* 2.8 40.4 + - + +
80H MET* 3.3 31.6 - - - -
85H TRP* 1.3 71.0 - - - +
87H VAL* 1.3 61.7 + - - +
88H ARG* 4.2 7.5 + - + +
124H GLU* 4.9 2.7 - - + -
349H VAL* 3.2 36.1 - - + +
350H PHE* 4.0 20.6 - - + -
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Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ALA 3.5 2.9 - - - +
28H VAL* 4.6 0.4 - - - -
29H PHE* 2.7 42.2 + - + +
31H VAL* 4.0 22.9 - - + -
39H ILE* 4.1 15.3 - - + -
43H ALA* 3.8 20.9 - - + -
74H ALA* 4.1 6.7 - - + -
76H ASP 3.2 8.7 - - - +
77H PHE* 3.9 22.7 - - + -
85H TRP* 4.2 4.7 - - + -
86H ILE* 1.3 77.9 - - - +
88H ARG* 1.3 66.5 + - - +
89H ILE* 3.9 19.7 + - + +
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Residues in contact with ARG 88 (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 ILE* 4.2 4.3 - - + -
27H ALA 3.6 3.8 - - - -
28H VAL* 4.2 21.5 - - + +
74H ALA* 3.5 3.5 - - - -
75H TYR* 3.1 59.2 + - + +
76H ASP* 3.0 44.3 + - + +
86H ILE* 5.2 5.0 - - + +
87H VAL* 1.3 75.7 - - - +
89H ILE* 1.3 59.4 + - - +
348H ASP 5.4 2.4 + - - -
349H VAL* 4.9 21.8 + - - +
351H HIS 5.6 1.2 + - - -
352H LEU* 3.9 27.5 - - - +
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Residues in contact with ILE 89 (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 ILE* 3.4 3.1 - - - -
27H ALA 2.9 36.0 + - - +
29H PHE* 3.9 13.2 - - + -
43H ALA* 4.4 3.8 - - - +
46H VAL* 3.8 30.5 - - + -
47H ALA* 3.7 26.2 - - + +
72H ALA* 3.9 5.4 - - + -
73H LYS 3.2 17.0 - - - +
74H ALA* 4.1 3.8 - - + -
75H TYR* 4.1 2.9 - - - -
87H VAL* 4.0 18.4 - - + +
88H ARG* 1.3 81.5 - - - +
90H ALA* 1.3 60.8 + - - +
91H TYR* 3.4 29.4 - - + +
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Residues in contact with ALA 90 (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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17H TYR* 3.8 29.8 - - + -
19H PRO* 4.5 2.7 - - + -
24H ASP* 4.1 15.3 - - + +
25H ILE 3.3 5.4 - - - +
26H ILE* 4.7 1.3 - - + +
71H SER 4.6 0.2 - - - +
72H ALA* 3.2 8.7 - - - +
73H LYS* 2.8 35.4 + - + +
75H TYR* 3.9 16.0 - - + -
89H ILE* 1.3 72.7 - - - +
91H TYR* 1.3 62.6 + - - +
92H PRO* 4.3 1.7 - - - +
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Residues in contact with TYR 91 (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 ASP* 3.3 4.9 - - - -
25H ILE* 2.6 52.4 + - + +
27H ALA* 3.9 15.3 - - + -
29H PHE* 4.1 12.1 - - - -
50H SER* 2.7 44.8 + - - -
51H SER* 4.5 3.8 - - - -
70H LEU 5.9 0.4 - - - -
72H ALA* 3.4 23.8 - - + -
89H ILE* 3.4 36.9 - - + +
90H ALA* 1.3 75.4 - - - +
92H PRO* 1.3 68.3 - - + +
95H ALA* 6.3 0.2 - - + -
96H PHE* 3.6 34.1 - + + -
108H ILE* 4.0 20.5 - - + +
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Residues in contact with PRO 92 (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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23E ARG* 3.7 13.2 - - - +
23H ARG 3.7 7.0 - - - +
24H ASP* 3.9 8.0 - - - +
25H ILE* 4.5 0.4 - - - -
69H ASP 3.7 19.1 - - - +
70H LEU* 3.9 21.1 - - - +
71H SER 4.2 11.2 - - - +
72H ALA* 4.9 0.2 - - - -
90H ALA 4.3 1.6 - - - +
91H TYR* 1.3 86.9 - - + +
93H PHE* 1.3 65.7 + - - +
94H HIS* 3.2 24.2 - - + +
95H ALA* 3.0 28.0 + - + +
96H PHE* 3.7 4.0 - - - -
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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