Contacts of the helix formed by residues 53 - 68 (chain D) in PDB entry 2OQH
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 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.7 13.0 - - - -
32D THR* 3.6 15.6 - - - +
34D THR* 3.5 6.4 + - - -
52D TRP* 1.3 79.7 - - - +
54D ALA* 1.3 66.4 + - - -
55D PRO* 3.4 4.1 - - - +
56D VAL 2.9 4.7 + - - -
57D ALA* 2.8 21.5 + - - +
374D ASP* 3.5 11.5 + - - -
376D THR 4.5 1.8 + - - -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.0 8.9 - - - +
53D GLY* 1.3 69.9 - - - +
55D PRO* 1.3 64.1 - - + +
57D ALA* 3.4 2.6 + - - +
58D ALA* 2.9 31.5 + - - +
374D ASP* 3.0 21.1 + - - +
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Residues in contact with PRO 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 6.5 1.3 - - + -
62B ARG* 6.2 3.4 - - - +
89B TYR* 4.2 15.7 - - + +
52D TRP* 3.8 28.7 - - + -
53D GLY* 3.5 4.5 - - - +
54D ALA* 1.3 95.3 - - + +
56D VAL* 1.3 63.0 + - + +
58D ALA* 3.5 6.8 - - + +
59D ILE* 3.2 28.5 + - - +
89D TYR* 5.6 0.2 - - - -
92D LEU* 3.7 16.6 - - + -
374D ASP* 4.1 5.8 - - - +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D THR* 3.9 6.7 - - + +
50D THR* 3.6 30.7 - - + -
51D MSE 3.3 20.6 - - + +
52D TRP* 3.6 16.8 - - + -
53D GLY 2.9 7.2 + - - +
55D PRO* 1.3 71.6 - - - +
57D ALA* 1.3 68.2 + - - +
58D ALA 3.1 1.3 - - - -
59D ILE* 3.0 11.2 + - - +
60D VAL* 3.0 21.2 + - + +
92D LEU* 4.0 27.4 - - + +
95D ALA* 4.8 2.0 - - + -
96D ALA* 4.0 19.7 - - + +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.6 24.6 - - + +
12D VAL* 3.6 31.4 - - + -
34D THR* 4.0 5.5 + - + -
53D GLY 2.8 11.2 + - - +
54D ALA* 3.9 3.6 - - - +
56D VAL* 1.3 73.4 - - - +
58D ALA* 1.3 57.2 + - - +
60D VAL* 3.2 3.6 + - - +
61D ARG* 2.9 47.2 + - - +
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 6.5 1.6 - - + -
54D ALA 2.9 18.0 + - - +
55D PRO* 3.5 9.9 - - + +
57D ALA* 1.3 78.2 - - - +
59D ILE* 1.3 61.7 + - + +
61D ARG* 3.4 11.1 + - - +
62D ARG* 3.2 29.5 + - - +
89D TYR* 6.5 0.2 - - + -
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D PRO 3.2 16.4 + - - +
56D VAL* 3.0 7.7 + - - +
58D ALA* 1.3 78.1 - - + +
60D VAL* 1.3 62.4 + - - +
62D ARG* 3.1 16.0 + - - +
63D MSE 3.3 19.7 + - + +
85D VAL* 3.8 25.1 - - + -
89D TYR* 3.4 51.6 - - + -
92D LEU* 3.7 34.3 - - + +
96D ALA* 3.6 15.9 - - + -
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.6 5.6 - - + -
10D VAL* 3.4 25.8 - - + -
34D THR* 4.9 2.0 - - + -
36D VAL* 3.9 24.9 - - + -
56D VAL* 3.0 24.3 + - + +
57D ALA* 3.6 8.5 - - - +
59D ILE* 1.3 77.0 - - - +
61D ARG* 1.3 57.9 + - - +
63D MSE 3.2 10.8 + - + +
64D ALA* 3.0 25.5 + - - +
67D LEU* 5.7 0.2 - - - +
96D ALA* 3.7 29.8 - - + +
99D ALA* 5.0 1.1 - - + -
100D VAL* 4.2 14.8 - - + +
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.1 49.5 + - + +
11D TRP* 4.5 4.8 - - - +
12D VAL* 5.3 3.8 - - - +
57D ALA* 2.9 32.5 + - - +
58D ALA* 3.8 8.4 - - - +
59D ILE 3.3 0.2 - - - -
60D VAL* 1.3 76.1 - - - +
62D ARG* 1.3 62.3 + - + +
64D ALA* 3.7 9.2 - - + +
65D PRO* 3.5 16.3 - - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 4.6 7.3 - - - -
54B ALA* 4.3 5.7 - - - +
55B PRO* 4.1 20.8 - - - +
374B ASP* 3.6 29.9 + - - +
376B THR 5.6 6.1 + - - -
58D ALA* 3.2 16.4 + - - +
59D ILE* 3.1 11.2 + - + +
61D ARG* 1.3 77.9 - - - +
63D MSE 1.3 61.5 + - + +
64D ALA 3.5 0.2 - - - -
65D PRO* 3.5 11.0 - - - +
66D ASP* 4.5 5.4 - - - +
89D TYR* 3.2 28.1 + - + -
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Residues in contact with MSE 63 (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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59D ILE* 3.3 10.7 + - + +
60D VAL* 3.2 17.8 + - - +
62D ARG* 1.3 79.4 - - + +
64D ALA* 1.3 65.7 + - - +
65D PRO* 3.3 1.8 - - - -
66D ASP* 2.9 29.0 + - - +
67D LEU* 3.6 12.3 + - + +
78D PHE* 4.4 4.5 - - + -
82D GLN* 3.2 37.5 - - - +
85D VAL* 4.0 15.5 - - + -
96D ALA* 4.0 18.6 - - + +
97D ILE* 3.8 29.4 - - - +
100D VAL* 3.9 26.7 - - + -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.9 27.6 - - + +
10D VAL* 6.0 0.7 - - + -
60D VAL 3.0 16.1 + - - +
61D ARG* 3.7 11.2 - - + +
63D MSE 1.3 74.8 - - - +
65D PRO* 1.3 69.5 - - + +
67D LEU* 2.9 29.7 + - - +
68D ILE* 3.5 13.6 + - + +
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Residues in contact with PRO 65 (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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61D ARG 3.5 9.4 - - - +
62D ARG* 3.5 14.1 - - - +
63D MSE 3.3 4.9 - - - -
64D ALA* 1.3 95.1 - - + +
66D ASP* 1.3 62.3 + - - +
67D LEU 3.2 0.7 + - - -
68D ILE* 3.5 23.5 + - + +
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Residues in contact with ASP 66 (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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62D ARG 4.5 4.0 - - - +
63D MSE 2.9 20.3 + - - +
65D PRO* 1.3 78.3 - - - +
67D LEU* 1.3 59.4 + - + +
68D ILE 3.8 2.1 + - - +
70D THR* 3.4 19.9 - - - +
78D PHE* 5.9 1.1 - - + -
81D LYS* 2.8 35.8 + - + +
82D GLN* 3.5 26.0 + - - +
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Residues in contact with LEU 67 (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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5D ILE* 3.3 27.2 - - + +
8D VAL* 3.8 30.1 - - + -
38D VAL* 5.7 0.9 - - + -
60D VAL 5.7 0.2 - - - +
63D MSE 4.1 6.1 - - + +
64D ALA* 2.9 21.6 + - - +
66D ASP* 1.3 79.1 - - - +
68D ILE* 1.3 66.2 + - - +
69D GLY 3.3 0.5 + - - -
70D THR* 2.6 27.9 + - + +
78D PHE* 3.7 37.5 - - + -
100D VAL* 3.7 32.5 - - + -
104D CYS* 5.1 4.3 - - - -
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Residues in contact with ILE 68 (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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5D ILE* 3.4 9.9 - - + +
6D THR* 3.5 33.4 - - - +
7D ASP* 3.8 10.5 - - - +
8D VAL* 4.0 13.2 - - + +
64D ALA* 3.6 15.3 - - + +
65D PRO* 3.5 18.1 + - + +
66D ASP 4.2 3.5 - - - +
67D LEU* 1.3 75.9 - - - +
69D GLY* 1.3 61.8 + - - +
70D THR* 3.2 4.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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