Contacts of the helix formed by residues 50 - 63 (chain B) in PDB entry 1Q6H
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 ASP 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASP* 3.2 27.7 + - + +
21A GLN* 3.6 25.6 + - + +
24A ALA* 3.3 5.8 - - - +
48B LYS 3.8 0.6 + - - -
49B LEU* 1.3 72.6 - - - +
51B LYS* 1.3 56.4 + - - +
52B ASP* 3.1 15.2 + - - +
53B GLN* 3.0 26.4 + - + +
54B LEU* 2.9 22.0 + - - +
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Residues in contact with LYS 51 (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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62A PHE* 3.9 20.1 - - + -
39B LEU* 3.9 29.5 - - + +
43B GLU* 4.4 14.9 + - - -
49B LEU 3.8 12.1 - - - +
50B ASP* 1.3 69.5 + - - +
52B ASP* 1.3 67.3 + - - +
54B LEU* 3.2 9.8 + - - +
55B ILE* 3.0 23.2 + - - +
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Residues in contact with ASP 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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50B ASP* 3.1 10.4 + - - +
51B LYS* 1.3 79.2 - - - +
53B GLN* 1.3 60.2 + - + +
55B ILE* 3.4 7.7 + - - +
56B ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 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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15A ALA 5.9 0.4 + - - -
16A PHE* 3.4 33.3 - - - -
21A GLN* 3.6 38.4 + - + +
24A ALA* 4.0 1.6 - - + -
25A TYR* 3.4 23.5 - - - +
50B ASP* 3.0 33.1 + - - +
52B ASP* 1.3 76.6 - - + +
54B LEU* 1.3 67.1 + - - +
56B ALA* 4.3 5.6 - - - +
57B GLY 3.0 19.1 + - - -
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Residues in contact with LEU 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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24A ALA* 3.4 27.9 - - + +
27A LEU* 4.0 17.5 - - + -
28A GLY* 3.4 22.6 - - - +
31A LEU* 4.9 3.8 - - + -
62A PHE* 3.6 27.1 - - + -
35B MSE 3.7 25.1 - - + +
39B LEU* 4.2 20.6 - - + -
49B LEU* 5.5 4.3 - - + -
50B ASP 2.9 12.0 + - - +
51B LYS* 3.2 9.8 + - - +
53B GLN* 1.3 79.5 - - - +
55B ILE* 1.3 62.6 + - - +
57B GLY 3.4 0.5 + - - -
58B VAL* 3.3 24.3 + - - +
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Residues in contact with ILE 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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55A ILE* 6.3 0.2 - - + -
58A VAL* 4.1 25.8 - - + -
59A GLN* 4.1 24.9 - - + -
62A PHE* 3.5 32.5 - - + -
35B MSE 4.1 7.4 - - + -
51B LYS 3.0 12.6 + - - +
52B ASP* 3.8 6.5 - - - +
54B LEU* 1.3 77.7 - - - +
56B ALA* 1.3 61.0 + - + +
58B VAL* 3.2 6.1 + - + +
59B GLN* 2.9 50.6 + - + +
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Residues in contact with ALA 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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25A TYR* 3.8 12.1 - - + -
52B ASP 2.9 17.6 + - - +
53B GLN* 3.3 12.1 + - - +
55B ILE* 1.3 77.7 - - + +
57B GLY* 1.3 57.7 + - - +
59B GLN* 3.7 12.7 - - - +
60B ASP* 2.7 40.5 + - - +
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Residues in contact with GLY 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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25A TYR* 3.5 38.9 - - - -
28A GLY 3.5 6.7 - - - -
29A ALA* 3.4 3.9 - - - +
53B GLN 3.0 10.3 + - - -
54B LEU 3.9 2.0 - - - -
56B ALA* 1.3 76.3 - - - +
58B VAL* 1.3 63.9 + - - +
60B ASP* 4.0 0.3 - - - +
61B ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 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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28A GLY* 3.4 25.1 - - - +
31A LEU* 4.5 7.4 - - + -
32A GLY* 4.0 9.4 - - - -
35A MSE 6.3 0.4 - - + -
55A ILE* 4.5 16.6 - - + -
58A VAL* 4.5 11.7 - - + -
31B LEU* 4.2 19.5 - - + -
35B MSE 4.0 25.4 - - + -
54B LEU* 3.3 14.9 + - + +
55B ILE* 3.2 8.7 + - + +
57B GLY* 1.3 77.1 - - - +
59B GLN* 1.3 63.6 + - + +
61B ALA* 3.9 1.4 - - - +
62B PHE* 3.0 27.1 + - + +
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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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55A ILE* 4.1 22.0 - - + -
59A GLN* 2.8 30.7 + - - +
55B ILE* 2.9 41.3 + - + +
56B ALA* 3.8 10.7 - - - +
58B VAL* 1.3 79.6 - - + +
60B ASP* 1.3 65.7 + - - +
62B PHE* 3.3 7.1 + - - +
63B ALA* 3.1 24.1 + - - +
65B LYS* 4.5 3.9 + - - +
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Residues in contact with ASP 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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25A TYR* 2.6 36.8 + - + +
56B ALA* 2.7 29.6 + - - +
57B GLY 4.0 1.6 - - - +
59B GLN* 1.3 71.8 - - - +
61B ALA* 1.3 63.4 - - - +
63B ALA* 3.0 3.8 + - - -
64B ASP 2.9 5.0 + - - -
65B LYS* 2.7 66.5 + - - +
66B SER* 4.1 1.8 - - - -
67B LYS* 3.8 19.4 + - - -
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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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29A ALA* 3.3 31.4 - - + +
32A GLY* 3.9 3.4 - - - -
33A ARG* 3.8 15.6 - - + +
36A GLU* 4.1 7.3 - - - +
57B GLY 3.0 19.5 + - - +
58B VAL 3.9 2.5 - - - +
60B ASP* 1.3 76.3 - - - +
62B PHE* 1.3 57.7 + - - +
64B ASP* 2.8 25.7 + - - +
65B LYS 4.7 1.6 - - - +
66B SER* 4.7 9.3 - - - +
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Residues in contact with PHE 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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32A GLY* 3.8 19.5 + - - +
35A MSE 4.1 14.6 - - + -
36A GLU* 3.9 34.8 - - + +
39A LEU* 3.9 24.9 - - + -
51A LYS* 3.7 53.7 + - + +
54A LEU* 4.0 13.0 - - + -
55A ILE* 3.2 33.2 - - + -
58B VAL* 3.0 19.2 + - + +
59B GLN 3.7 4.3 - - - +
60B ASP 3.1 0.2 - - - -
61B ALA* 1.3 76.6 - - - +
63B ALA* 1.3 58.0 + - - +
64B ASP* 3.3 2.6 + - - +
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Residues in contact with ALA 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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59B GLN 3.1 13.9 + - - +
60B ASP 3.0 5.4 + - - +
62B PHE* 1.3 78.6 - - - +
64B ASP* 1.3 72.4 + - - +
65B LYS* 3.3 30.5 + - + +
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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