Contacts of the helix formed by residues 42 - 54 (chain C) in PDB entry 3B1D
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 MET 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C GLU 3.8 1.2 + - - -
41C VAL* 1.3 77.6 - - + +
43C PRO* 1.3 74.2 - - + +
44C GLU* 3.1 27.4 + - + +
45C VAL* 3.2 26.3 + - + -
46C LYS* 3.6 6.8 + - - +
236C PHE* 3.6 23.1 + - + -
279C THR 3.8 12.3 - - - +
280C ALA* 3.8 12.8 - - - -
283C TYR 3.6 7.9 - - - +
284C GLY* 3.5 39.3 - - - +
287C TRP* 3.7 32.6 - - + +
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Residues in contact with PRO 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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3C LYS 5.9 0.4 - - - +
4C TYR* 3.5 34.8 - - + -
41C VAL 3.4 5.1 - - - +
42C MET* 1.3 83.5 - - + +
44C GLU* 1.3 72.2 + - - +
46C LYS* 3.3 22.3 + - + +
47C GLN* 3.0 28.5 + - - +
287C TRP* 4.8 0.2 - - + -
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Residues in contact with GLU 44 (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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4C TYR* 4.7 10.3 + - - -
42C MET* 3.1 23.0 + - + +
43C PRO* 1.3 93.7 - - - +
45C VAL* 1.3 57.3 + - - +
47C GLN* 3.5 7.5 + - - +
48C ALA* 2.9 22.5 + - - +
279C THR* 3.4 17.9 - - + +
283C TYR* 4.0 28.3 - - + +
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Residues in contact with VAL 45 (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 VAL* 3.7 9.9 - - + -
42C MET* 3.2 32.5 + - + +
44C GLU* 1.3 75.3 - - - +
46C LYS* 1.3 65.9 + - - +
48C ALA* 3.0 12.3 + - + +
49C ILE* 3.1 18.9 + - + +
238C ILE* 4.1 11.7 - - + -
241C THR* 5.7 0.2 - - + -
276C ALA* 4.1 29.2 - - + +
279C THR* 3.8 18.6 - - + -
280C ALA* 4.1 6.1 - - + +
58D TYR* 3.9 23.3 - - + -
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Residues in contact with LYS 46 (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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40C GLU* 4.8 7.5 + - - -
41C VAL 5.4 2.9 - - - +
42C MET 3.6 3.7 + - - +
43C PRO* 3.3 26.6 + - + +
45C VAL* 1.3 76.4 - - - +
47C GLN* 1.3 63.6 + - - +
49C ILE* 3.2 7.3 + - - +
50C HIS* 3.2 28.7 + - + -
53D ALA* 3.6 7.1 - - - +
54D GLU* 3.6 22.5 + - - +
56D LEU* 3.6 34.6 - - + +
58D TYR* 3.3 25.4 + - + +
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Residues in contact with GLN 47 (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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43C PRO 3.0 15.3 + - - +
44C GLU* 3.7 8.5 - - - +
46C LYS* 1.3 75.8 - - - +
48C ALA* 1.3 57.5 + - - +
50C HIS* 3.2 24.1 + - - +
51C ASP* 2.9 60.5 + - - +
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Residues in contact with ALA 48 (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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44C GLU 2.9 15.5 + - - +
45C VAL* 3.0 10.5 + - + +
47C GLN* 1.3 75.9 - - - +
49C ILE* 1.3 58.6 + - + +
51C ASP* 3.4 11.5 + - - +
52C TYR* 2.8 27.5 + - - +
275C ILE* 3.7 20.8 - - + +
276C ALA* 5.6 0.7 - - - -
279C THR* 3.5 26.2 - - + +
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Residues in contact with ILE 49 (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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45C VAL* 3.1 15.4 + - + +
46C LYS 3.5 5.4 - - - +
47C GLN 3.2 0.2 - - - -
48C ALA* 1.3 75.0 - - + +
50C HIS* 1.3 66.2 + - - +
52C TYR* 3.2 7.4 + - - +
53C ALA 3.1 18.0 + - - -
241C THR* 5.5 2.0 - - + -
272C LEU* 3.7 25.4 - - + -
49D ILE* 3.5 26.3 - - + +
52D TYR* 4.1 17.0 - - + -
53D ALA* 3.5 20.0 - - + +
58D TYR* 3.5 50.3 - - + +
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Residues in contact with HIS 50 (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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46C LYS* 3.2 25.7 + - + -
47C GLN* 3.2 27.5 + - - +
49C ILE* 1.3 77.8 - - - +
51C ASP* 1.3 61.0 + - - +
53C ALA* 3.2 6.8 + - - +
54C GLU* 3.1 19.4 + - - +
50D HIS* 2.6 65.0 + + + +
53D ALA* 3.5 7.0 - - + +
54D GLU* 2.8 33.2 + - + -
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Residues in contact with ASP 51 (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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47C GLN* 2.9 45.6 + - - +
48C ALA* 3.6 12.4 + - - +
49C ILE 3.2 0.2 - - - -
50C HIS* 1.3 74.3 - - - +
52C TYR* 1.3 63.4 + - - +
54C GLU* 3.0 18.1 + - - +
55C GLN* 3.2 13.8 + - - +
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Residues in contact with TYR 52 (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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48C ALA 2.8 14.5 + - - +
49C ILE* 3.4 11.0 - - - +
51C ASP* 1.3 75.7 - - - +
53C ALA* 1.3 63.6 - - - +
55C GLN* 2.9 47.1 + - - +
58C TYR* 3.4 43.6 - + - +
61C THR* 5.9 0.9 - - + -
271C SER* 3.3 35.2 + - - -
272C LEU* 4.6 13.7 - - + -
275C ILE* 3.5 24.5 - - + -
49D ILE* 4.1 11.2 - - + -
240D GLY 4.0 9.7 - - - -
241D THR* 4.2 2.4 - - + +
272D LEU* 3.8 29.8 - - + -
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Residues in contact with ALA 53 (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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49C ILE 3.1 6.9 + - - +
50C HIS 3.4 9.9 - - - +
52C TYR* 1.3 75.9 - - - +
54C GLU* 1.3 57.7 + - - +
56C LEU 3.2 9.0 + - - -
58C TYR* 2.6 28.1 + - - -
46D LYS* 3.6 16.4 - - + +
49D ILE* 3.4 32.0 - - + +
50D HIS* 3.6 23.3 - - + +
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Residues in contact with GLU 54 (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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50C HIS 3.1 12.4 + - - +
51C ASP* 3.0 14.2 + - - +
53C ALA* 1.3 74.7 - - - +
55C GLN* 1.3 62.0 + - - +
56C LEU* 3.2 22.9 + - - +
46D LYS* 3.6 21.1 + - - +
50D HIS* 2.8 29.2 + - + +
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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