Contacts of the helix formed by residues 51 - 63 (chain B) in PDB entry 3Q02
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 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B THR* 1.3 75.8 - - - +
52B GLY* 1.3 68.1 + - - -
54B THR 3.2 5.9 + - - -
55B GLN* 3.1 19.8 + - - -
305B ASP* 3.0 32.3 + - - +
307B THR* 4.4 3.6 - - - -
308B SER* 4.0 6.3 + - - -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLY* 1.3 71.6 - - - +
53B GLU* 1.3 61.9 + - - -
55B GLN* 3.7 5.9 + - - +
56B GLN* 3.2 24.2 + - - +
305B ASP* 3.4 10.9 + - - -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY* 1.3 70.1 - - - -
54B THR* 1.3 66.0 + - - +
56B GLN* 3.7 17.3 - - - +
57B GLN* 3.1 42.4 + - - +
297B ASP* 3.5 19.3 - - - +
305B ASP* 4.8 2.6 + - - +
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 3.6 20.0 - - + -
51B GLY 3.2 2.5 + - - -
53B GLU* 1.3 80.6 - - - +
55B GLN* 1.3 62.1 + - - +
57B GLN* 3.6 4.1 + - - +
58B ILE* 3.4 21.7 + - + +
297B ASP* 3.3 25.1 + - - +
298B MET* 4.0 27.3 - - + +
303B GLN 4.0 0.2 + - - -
304B ALA* 3.6 1.7 - - - -
305B ASP* 2.8 45.8 + - - +
306B PHE* 4.5 2.5 - - + -
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 3.2 23.0 + - - +
50B THR* 3.4 30.3 + - - +
51B GLY* 3.1 18.3 + - - -
52B GLY 3.7 9.8 + - - +
54B THR* 1.3 78.5 - - - +
56B GLN* 1.3 61.7 + - + +
58B ILE* 3.3 5.0 + - - +
59B GLN* 3.1 53.7 + - + +
66B ILE* 5.9 1.4 - - - +
67B ASP* 5.6 4.6 + - - +
308B SER* 5.1 0.8 + - - -
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 3.2 14.2 + - - +
53B GLU* 3.7 24.9 - - - +
54B THR 3.3 0.2 - - - -
55B GLN* 1.3 78.2 - - + +
57B GLN* 1.3 65.2 + - - +
59B GLN* 4.6 13.1 + - - +
60B ALA* 3.0 33.0 + - - +
65B LYS* 6.2 1.2 - - - +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 3.1 29.2 + - - +
54B THR 3.9 4.5 - - - +
55B GLN 3.5 0.2 - - - -
56B GLN* 1.3 74.5 - - - +
58B ILE* 1.3 62.5 + - + +
60B ALA* 3.7 4.9 + - - +
61B ALA* 3.2 24.4 + - - +
293B LEU 5.0 0.7 - - - +
294B GLY 3.2 24.0 + - - +
295B MET* 3.5 10.2 - - + +
296B THR* 3.0 17.6 + - - -
297B ASP* 2.8 56.4 + - - +
298B MET* 4.5 1.8 + - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.0 9.0 - - + +
46B LEU* 4.2 16.6 - - + -
47B GLN* 3.7 24.5 - - + +
50B THR* 4.0 27.8 - - + +
54B THR* 3.4 12.3 + - + +
55B GLN 3.3 7.1 + - - +
56B GLN 3.2 0.8 - - - -
57B GLN* 1.3 76.5 - - - +
59B GLN* 1.3 57.6 + - - +
61B ALA* 3.3 2.6 + - - +
62B MET* 3.0 45.1 + - + +
295B MET* 3.8 12.1 - - + -
298B MET* 3.2 35.0 - - + -
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 3.1 33.7 + - - +
55B GLN* 3.1 48.1 + - + +
56B GLN* 3.3 15.9 + - - +
58B ILE* 1.3 73.4 - - - +
60B ALA* 1.3 60.3 + - - +
63B GLY* 2.9 28.8 + - - -
64B PHE 3.7 15.2 + - - +
65B LYS* 3.3 39.8 - - + +
66B ILE* 4.5 1.2 - - - +
67B ASP* 5.6 1.6 - - - +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 5.4 0.3 + - - -
56B GLN* 3.0 23.5 + - - +
57B GLN* 3.9 5.4 - - - +
59B GLN* 1.3 78.5 - - - +
61B ALA* 1.3 61.6 + - - +
62B MET 3.5 0.2 + - - -
63B GLY* 3.8 7.0 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.3 9.5 - - + -
18B ARG* 2.8 36.1 + - - +
57B GLN 3.2 12.6 + - - +
58B ILE 3.8 3.1 - - - +
60B ALA* 1.3 82.2 - - - +
62B MET* 1.3 55.5 + - - +
293B LEU* 3.9 16.4 - - + +
295B MET* 3.5 32.5 - - + -
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.1 16.3 - - - +
15B PHE* 3.9 28.4 - - + +
18B ARG* 4.6 5.4 + - - -
40B ALA* 3.4 31.9 - - + +
43B LEU* 3.7 28.7 - - - +
44B ALA 4.1 2.9 - - - +
47B GLN* 3.6 22.0 - - - +
58B ILE* 3.0 23.1 + - + +
59B GLN 4.4 0.9 - - - +
61B ALA* 1.3 76.4 - - - +
63B GLY* 1.3 61.7 + - - +
64B PHE* 3.2 48.1 - - + +
295B MET* 5.4 0.2 - - - -
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TYR* 5.3 1.0 + - - -
11B LEU* 4.1 14.2 - - - +
18B ARG* 5.8 0.2 - - - -
59B GLN 2.9 12.1 + - - -
60B ALA 3.8 5.1 + - - -
61B ALA 3.5 2.0 - - - -
62B MET* 1.3 76.8 - - - +
64B PHE* 1.3 62.2 + - - +
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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