Contacts of the strand formed by residues 36 - 43 (chain C) in PDB entry 3RIK
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 THR 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PRO* 4.0 24.1 - - + +
33C ALA* 3.0 26.0 + - - +
34C LEU 4.8 0.3 + - - -
35C GLY* 1.3 83.1 + - - +
37C PHE* 1.3 70.8 + - - +
53C MET* 4.1 16.6 - - + -
54C GLY* 3.3 13.2 - - - +
55C PRO* 5.5 0.3 - - - +
56C ILE* 4.1 2.1 - - - +
494C TRP* 3.7 15.8 - - - +
495C HIS 4.7 2.4 + - - -
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Residues in contact with PHE 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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32C PRO* 5.4 0.9 - - - -
36C THR* 1.3 74.7 - - - +
38C SER* 1.3 73.9 + - - +
39C ARG* 3.7 43.7 - - + -
53C MET* 3.2 11.2 - - - +
54C GLY* 2.9 67.8 + - - -
55C PRO* 3.3 27.6 - - + -
56C ILE* 4.0 3.4 - - + -
480C LEU* 3.5 38.8 - - + -
481C GLU 4.8 5.8 - - - -
492C TYR* 3.9 12.8 - + - -
493C LEU 3.3 12.6 - - - +
494C TRP* 3.9 8.1 - - + -
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Residues in contact with SER 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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30C THR* 5.4 0.5 + - - +
32C PRO* 3.6 14.8 - - - +
37C PHE* 1.3 77.9 - - - +
39C ARG* 1.3 59.2 + - - +
40C TYR* 4.6 2.2 - - - -
51C LEU* 4.0 15.5 - - - -
52C SER 3.5 5.2 - - - -
53C MET* 3.5 23.2 - - - +
491C THR 4.4 0.4 - - - -
492C TYR* 3.3 5.7 - - - -
493C LEU* 2.8 54.6 + - - +
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Residues in contact with ARG 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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37C PHE* 3.7 30.9 - - + -
38C SER* 1.3 73.4 - - - +
40C TYR* 1.3 69.2 + - - +
41C GLU* 4.3 14.1 - - - -
50C GLU 3.3 1.6 - - - +
51C LEU* 3.3 5.0 - - - +
52C SER* 2.7 69.9 + - - +
53C MET 5.1 2.4 + - - +
481C GLU 4.4 2.4 + - - -
482C THR* 2.9 28.3 + - - +
490C HIS* 3.8 25.4 - - + +
491C THR 3.5 3.8 - - - +
492C TYR* 3.4 23.6 + - + -
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Residues in contact with TYR 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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26C PHE* 4.0 23.6 - + - -
27C ASP 5.8 0.2 + - - -
29C PRO* 5.5 7.6 - - - +
38C SER* 4.6 1.8 - - - -
39C ARG* 1.3 77.7 - - - +
41C GLU* 1.3 59.3 + - - +
49C MET* 3.6 23.8 - - + -
50C GLU 3.1 4.5 - - - +
51C LEU* 3.9 39.9 - - + +
422C HIS* 3.2 16.6 - - + +
425C LYS* 4.7 5.4 - - - -
426C PHE* 3.5 46.0 - + + -
490C HIS* 3.2 4.7 - - - +
491C THR 3.0 36.6 + - - +
493C LEU* 3.7 19.1 - - + +
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Residues in contact with GLU 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 ARG* 4.3 11.3 - - - -
40C TYR* 1.3 74.6 - - - +
42C SER* 1.3 65.1 + - - +
43C THR* 3.6 21.0 - - + +
47C ARG* 3.1 28.6 + - - -
48C ARG 3.6 1.2 - - - -
49C MET 2.8 20.1 + - - -
50C GLU* 2.9 28.0 + - + +
485C PRO* 3.4 21.0 - - - +
489C ILE 3.6 3.1 - - - -
490C HIS* 2.9 33.4 + - + +
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Residues in contact with SER 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 GLU* 1.3 70.6 - - - +
43C THR* 1.3 65.4 + - - +
47C ARG 3.1 11.4 - - - -
48C ARG* 3.9 2.6 - - - -
49C MET* 2.8 20.7 + - - +
357C TRP* 3.5 12.4 - - - -
418C TYR* 4.2 9.3 - - - +
419C HIS* 5.5 0.2 - - - -
422C HIS* 2.7 29.1 + - - -
488C SER* 3.2 4.0 - - - -
489C ILE* 2.8 45.2 + - - +
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Residues in contact with THR 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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41C GLU* 3.6 30.7 - - + +
42C SER* 1.3 80.9 - - - +
44C ARG* 1.3 58.0 + - - +
45C SER* 3.0 22.5 + - - +
46C GLY 3.1 5.2 + - - -
47C ARG* 3.0 31.1 + - - +
48C ARG* 2.8 25.6 + - - -
357C TRP* 3.3 5.2 - - - -
485C PRO* 4.8 7.4 - - + -
486C GLY 5.4 0.9 - - - -
487C TYR 3.6 7.9 - - - -
488C SER* 4.1 9.6 - - - -
508C SO4 5.7 0.9 - - - +
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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