Contacts of the strand formed by residues 85 - 92 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29I PHE 3.5 0.3 - - - +
30I ARG* 3.2 4.0 - - - -
31I VAL* 2.6 38.8 + - - +
33I PRO* 4.5 4.5 - - + +
39I ILE* 3.5 55.1 - - + +
40I GLU* 5.9 0.4 - - - -
77I PHE* 4.2 17.9 - - + -
78I HIS 3.3 12.8 - - - -
79I ASP* 3.3 57.0 + - + -
80I MET* 4.4 1.3 - - - -
83I GLY* 4.3 9.3 + - - -
84I SER* 1.3 83.9 - - - +
86I ILE* 1.3 64.5 + - - +
87I VAL* 3.8 4.4 + - + -
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Residues in contact with ILE 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I VAL* 3.7 22.7 - - + -
29I PHE 3.3 2.0 - - - +
30I ARG* 4.0 25.8 - - + +
76I ASP* 3.5 3.2 - - - +
77I PHE* 3.5 4.7 - - - -
78I HIS* 2.8 45.7 + - + +
80I MET* 3.7 23.6 - - - -
85I TRP* 1.3 71.9 - - - +
87I VAL* 1.3 62.6 + - - +
88I ARG* 4.2 7.5 - - + +
124I GLU* 4.6 2.0 - - + +
349I VAL* 3.2 26.7 - - + +
350I PHE* 3.8 31.9 - - + -
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Residues in contact with VAL 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ALA 3.5 3.3 - - - +
28I VAL* 4.6 0.4 - - - -
29I PHE* 2.7 39.8 + - + +
31I VAL* 4.0 17.5 - - + -
39I ILE* 3.9 23.3 - - + -
43I ALA* 3.8 20.4 - - + -
74I ALA* 4.0 18.8 - - + -
76I ASP 3.3 8.3 - - - +
77I PHE* 3.9 22.7 - - + -
85I TRP* 4.3 2.7 - - + -
86I ILE* 1.3 78.2 - - - +
88I ARG* 1.3 64.4 + - - +
89I ILE* 3.9 11.0 + - + +
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Residues in contact with ARG 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE* 4.1 3.8 - - + -
27I ALA 3.5 5.2 - - - -
28I VAL* 4.4 17.3 - - + +
74I ALA* 3.5 3.8 - - - -
75I TYR* 3.0 60.5 + - + +
76I ASP* 3.1 44.8 + - + +
78I HIS* 6.3 0.6 - - - +
86I ILE* 5.2 5.8 - - + +
87I VAL* 1.3 75.0 - - - +
89I ILE* 1.3 60.4 + - - +
348I ASP 5.5 2.4 + - - -
349I VAL* 5.0 16.6 + - - +
352I LEU* 3.8 31.8 - - - +
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Residues in contact with ILE 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE* 3.2 3.3 - - - -
27I ALA* 2.8 42.1 + - + +
29I PHE* 3.9 11.7 - - + -
43I ALA 4.3 4.9 - - - +
46I VAL* 3.6 32.1 - - + -
47I ALA* 4.0 16.8 - - + +
72I ALA* 3.8 11.7 - - + -
73I LYS 3.4 17.5 - - - +
74I ALA* 4.0 4.9 - - + +
75I TYR* 4.1 2.7 - - - -
87I VAL* 4.1 17.7 - - + +
88I ARG* 1.3 79.6 - - - +
90I ALA* 1.3 63.1 + - - +
91I TYR* 3.4 28.5 - - + +
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Residues in contact with ALA 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I TYR* 4.0 26.2 - - + -
19I PRO* 4.4 4.3 - - + -
24I ASP* 4.2 13.0 - - + +
25I ILE 3.3 6.3 - - - +
26I ILE* 4.5 1.6 - - + +
71I SER 4.6 0.2 - - - +
72I ALA* 3.2 6.8 - - - +
73I LYS* 2.9 33.3 + - + +
75I TYR* 3.9 19.7 - - + -
89I ILE* 1.3 74.0 - - - +
91I TYR* 1.3 61.6 + - - +
92I PRO* 4.4 1.3 - - - +
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Residues in contact with TYR 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ASP* 3.5 6.2 - - - -
25I ILE* 2.7 56.6 + - + +
27I ALA* 3.7 17.3 - - + -
29I PHE* 4.0 11.4 - - - -
50I SER* 2.8 41.7 + - - -
51I SER* 4.5 3.8 - - - -
70I LEU 5.8 0.7 - - - -
72I ALA* 3.2 26.5 - - + -
89I ILE* 3.4 33.3 - - + +
90I ALA* 1.3 73.0 - - - +
92I PRO* 1.3 68.3 - - + +
93I PHE 3.4 0.2 + - - -
95I ALA* 5.6 0.4 - - + -
96I PHE* 3.7 32.3 - + + -
108I ILE* 3.7 17.9 - - + +
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Residues in contact with PRO 92 (chain I).
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* 3.8 11.2 - - - +
23I ARG* 3.9 1.8 - - + +
24I ASP* 3.9 11.6 - - - +
69I ASP 3.7 13.0 - - - +
70I LEU* 3.3 31.9 - - - +
71I SER 3.9 11.4 - - - +
90I ALA 4.4 1.1 - - - +
91I TYR* 1.3 85.7 - - + +
93I PHE* 1.3 65.4 + - - +
94I HIS* 3.2 25.8 - - + -
95I ALA* 3.0 22.2 + - + +
96I PHE* 3.9 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