Contacts of the strand formed by residues 36 - 43 (chain C) in PDB entry 3K2M
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 TYR 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B TYR* 4.3 2.9 - + - -
193B TYR* 2.7 33.8 + - - -
227B GLY 2.6 29.9 + - - -
228B LEU 4.1 1.8 - - - -
229B ILE* 3.6 44.6 - - + -
34C VAL* 3.6 6.0 - - - +
35C TYR* 1.3 87.3 - - + +
37C TYR* 1.3 69.7 + - - +
38C ARG* 4.9 1.8 - - + -
54C THR* 4.2 16.8 - - + -
55C VAL 3.3 15.3 - - - +
56C PRO* 4.6 0.9 - - + -
57C TYR 3.9 2.7 - - - +
79C ALA* 3.7 0.2 - - - -
80C TRP* 3.0 51.4 + + + +
88C MET* 3.7 19.7 - - + -
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 4.5 3.6 - - + +
8C PRO* 4.1 7.6 - - + -
25C TRP* 3.4 35.7 + + + -
26C ASP 4.2 4.9 + - - -
27C ALA* 5.0 0.2 - - - -
28C PRO* 3.6 28.4 - - - +
34C VAL* 3.6 13.5 - - + +
36C TYR* 1.3 77.2 - - - +
38C ARG* 1.3 60.3 + - - +
39C ILE* 3.8 9.1 - - + +
54C THR* 3.1 5.4 - - - -
55C VAL* 2.8 43.2 + - + +
56C PRO 3.9 8.7 - - - -
57C TYR* 3.7 21.3 + - - -
59C SER 3.6 15.9 - - - -
77C VAL* 4.0 13.9 - - + -
78C TYR 3.1 9.0 - - - +
79C ALA* 3.6 30.1 - - + -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA* 6.4 0.2 - - - -
226B ASP* 3.7 19.2 + - - -
227B GLY* 3.8 29.5 - - - +
228B LEU 5.6 0.2 - - - -
36C TYR* 4.6 2.4 - - + -
37C TYR* 1.3 73.6 - - - +
39C ILE* 1.3 61.7 + - - +
40C THR* 3.6 19.1 - - + +
50C VAL* 4.9 4.4 - - - +
52C GLU* 2.9 42.8 + - + +
53C PHE 3.5 8.3 - - - +
54C THR* 4.0 15.3 - - + -
77C VAL* 3.4 3.5 - - - -
78C TYR* 2.8 80.6 + - + +
80C TRP* 4.7 10.9 - - + +
90C MET* 5.9 1.4 - - - -
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 4.1 14.8 - - + -
25C TRP* 4.0 11.2 - - + -
37C TYR* 3.8 17.9 - - + +
38C ARG* 1.3 77.5 - - - +
40C THR* 1.3 67.4 + - - +
41C TYR* 4.8 0.2 - - - -
52C GLU* 3.1 5.7 - - - +
53C PHE* 2.7 75.3 + - + +
55C VAL* 3.8 22.2 - - + -
62C ALA* 4.8 0.4 - - + -
64C ILE* 3.9 23.3 - - + -
75C ILE* 4.3 1.3 - - + -
76C THR 3.4 7.0 - - - +
77C VAL* 4.1 15.7 - - + -
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Residues in contact with THR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.6 38.8 + - + +
39C ILE* 1.3 79.3 - - - +
41C TYR* 1.3 66.5 + - - +
50C VAL* 3.6 20.6 - - + +
51C GLN 3.2 7.4 - - - -
52C GLU* 3.8 7.0 - - + -
74C THR 4.5 0.8 + - - -
75C ILE* 3.3 5.0 - - - +
76C THR* 2.8 51.9 + - - +
78C TYR* 3.9 13.8 + - + +
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Residues in contact with TYR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 4.8 0.4 - - + -
40C THR* 1.3 80.7 - - - +
42C GLY* 1.3 60.3 + - - +
50C VAL* 3.5 6.2 - - - -
51C GLN* 2.8 83.2 + - + +
52C GLU 4.4 0.4 - - - -
53C PHE* 4.0 24.1 - + - -
64C ILE* 3.6 49.1 - - + -
65C SER 4.1 10.6 + - - -
67C LEU* 3.7 21.3 - - + -
73C TYR* 4.8 6.7 - + + -
74C THR 3.3 10.1 - - - +
75C ILE* 4.3 7.6 - - + -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 1.3 77.4 - - - +
43C GLU* 1.3 64.7 + - - -
48C SER 5.6 3.6 - - - -
49C PRO 5.6 0.9 - - - -
50C VAL* 4.4 15.6 - - - +
73C TYR* 3.4 12.5 - - - -
74C THR* 2.9 32.0 + - - +
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLY* 1.3 71.4 - - - -
44C THR* 1.3 68.3 + - - +
45C GLY 3.3 0.7 + - - -
46C GLY* 3.0 25.3 + - - +
48C SER 5.7 1.5 + - - +
68C SER* 5.1 5.2 + - - -
71C VAL* 3.9 21.0 - - + +
72C ASP 3.4 9.0 - - - +
73C TYR* 3.6 25.3 + - + -
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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