Contacts of the helix formed by residues 52 - 62 (chain D) in PDB entry 1B3K
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 GLY 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D GLY* 1.3 71.8 - - - -
53D GLU* 1.3 67.8 + - - +
55D GLN* 2.7 33.1 + - - +
56D GLN* 3.3 8.1 + - - -
305D ASP* 4.2 5.2 - - - -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLY 3.6 0.4 + - - -
52D GLY* 1.3 69.1 - - - +
54D THR* 1.3 68.2 + - - +
56D GLN* 2.9 23.5 + - - +
57D GLN* 3.5 10.7 + - - +
297D ASP* 3.8 17.5 - - - +
303D GLN 4.9 4.5 - - - +
305D ASP* 4.5 10.7 + - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 3.4 17.7 - - - +
51D GLY 4.1 0.6 + - - -
52D GLY 3.2 1.4 + - - -
53D GLU* 1.3 77.9 - - - +
55D GLN* 1.3 64.1 + - - +
57D GLN* 3.1 23.8 + - - +
58D ILE* 3.4 6.8 + - + +
297D ASP* 3.2 21.8 + - + +
298D MET* 3.3 44.4 - - + +
303D GLN 3.6 1.2 + - - -
304D ALA* 3.5 1.2 - - - -
305D ASP* 2.8 31.9 + - - +
306D PHE* 4.7 2.2 - - + -
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Residues in contact with GLN 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN* 4.2 6.2 + - - +
48D LEU* 5.9 0.2 - - - +
50D THR* 3.0 43.3 + - + +
51D GLY* 3.5 13.1 + - - -
52D GLY* 2.7 31.7 + - - +
54D THR* 1.3 70.9 - - - +
56D GLN* 1.3 65.2 + - - +
58D ILE* 3.2 5.9 + - - +
59D GLN* 3.0 48.1 + - + +
308D SER* 5.1 1.2 + - - -
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLY 4.5 8.3 - - - +
53D GLU* 2.9 17.2 + - - +
55D GLN* 1.3 80.4 - - - +
57D GLN* 1.3 58.8 + - - +
59D GLN* 4.0 18.4 - - - +
60D ALA* 2.7 39.0 + - + +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU 3.8 9.2 - - - +
54D THR* 3.1 11.2 + - - +
56D GLN* 1.3 77.2 - - + +
58D ILE* 1.3 65.2 + - - +
60D ALA* 3.8 4.1 - - - +
61D ALA* 2.9 25.8 + - - +
293D LEU 5.1 0.3 - - - +
294D GLY 3.2 20.4 + - - +
295D MET* 3.6 16.8 + - + +
296D THR* 2.9 11.7 + - - -
297D ASP* 2.7 54.2 + - - +
298D MET 4.1 2.1 + - - -
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.1 6.5 - - + +
46D LEU* 4.3 15.5 - - + +
47D GLN* 3.4 24.9 - - + -
50D THR* 3.7 28.7 - - + +
54D THR* 3.8 9.4 - - + +
55D GLN 3.2 6.2 + - - +
57D GLN* 1.3 75.8 - - - +
59D GLN* 1.3 57.6 + - - +
61D ALA* 3.2 1.4 + - - +
62D MET* 2.8 51.3 + - + +
295D MET* 3.6 17.5 - - + -
298D MET* 3.1 35.9 - - + -
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Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN* 3.4 24.5 - - - +
55D GLN* 3.0 42.7 + - + +
56D GLN* 3.6 24.8 - - - +
58D ILE* 1.3 76.1 - - - +
60D ALA* 1.3 58.9 + - - +
62D MET* 2.9 2.1 + - - -
63D GLY* 2.7 33.1 + - - -
64D PHE 3.6 11.4 + - - +
65D LYS* 3.2 47.1 - - + +
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Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ARG* 5.3 0.7 + - - -
56D GLN* 2.7 23.4 + - + +
57D GLN* 3.8 4.0 - - - +
59D GLN* 1.3 74.0 - - - +
61D ALA* 1.3 62.6 + - - +
63D GLY* 3.2 11.2 + - - +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 3.2 15.6 - - + -
18D ARG* 2.9 28.9 + - - +
57D GLN 2.9 19.1 + - - +
58D ILE 3.4 4.0 - - - +
60D ALA* 1.3 79.3 - - - +
62D MET* 1.3 55.6 + - - +
293D LEU* 3.7 25.1 - - + +
295D MET* 3.9 18.6 - - + -
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.2 14.7 - - - +
15D PHE* 3.7 37.3 - - + +
18D ARG* 5.0 3.0 + - - -
40D ALA* 3.3 28.9 - - + +
43D LEU* 3.7 18.4 - - - -
44D ALA* 4.1 4.0 - - - +
47D GLN* 3.4 22.7 - - - +
58D ILE* 2.8 35.6 + - + +
59D GLN 3.8 2.5 - - - +
61D ALA* 1.3 74.5 - - - +
63D GLY* 1.3 61.5 + - - +
64D PHE* 3.2 45.8 - - + +
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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