Contacts of the helix formed by residues 47 - 67 (chain D) in PDB entry 2QXU
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 THR 47 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASP* 2.7 17.7 + - - +
45D THR* 3.5 22.2 - - - +
46D GLY* 1.3 75.6 - - - +
48D ASN* 1.3 63.9 + - - +
49D TYR* 4.1 7.7 - - - +
50D ASN* 3.2 21.5 + - - +
51D ASN* 3.0 23.2 + - - +
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLY 3.7 0.6 + - - +
47D THR* 1.3 72.7 - - - +
49D TYR* 1.3 59.0 + - - +
52D GLY* 2.8 31.6 + - - +
78D MET* 5.5 1.0 - - - +
81D ALA* 3.3 7.7 - - - +
82D ASN* 2.9 35.1 + - - +
85D TYR* 3.4 41.1 - - + +
108D LEU* 4.3 8.9 + - - +
109D THR* 2.8 25.9 + - - +
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.2 8.2 - - - +
48D ASN* 1.3 79.3 - - - +
50D ASN* 1.3 70.7 + - - +
53D PRO* 3.2 23.3 - - + +
85D TYR* 4.5 16.3 - - - -
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Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TRP* 3.3 39.3 + - + -
43D ASP* 2.9 33.1 + - + +
47D THR* 3.2 13.8 + - - +
48D ASN 3.3 0.2 - - - -
49D TYR* 1.3 94.3 - - - +
51D ASN* 1.3 65.2 + - - +
53D PRO* 3.7 7.4 - - - +
54D VAL* 3.4 21.4 + - - +
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Residues in contact with ASN 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D HIS* 5.4 0.6 - - - -
11D GLY 6.2 0.6 - - - -
41D PHE* 3.1 51.3 - - + +
42D TRP* 5.1 1.0 + - - -
43D ASP* 3.6 18.6 + - - +
46D GLY* 3.3 20.0 - - - -
47D THR 3.0 15.7 + - - +
50D ASN* 1.3 78.0 - - - +
52D GLY* 1.3 65.5 + - - +
53D PRO 3.4 0.2 - - - -
54D VAL* 3.3 1.2 + - - +
55D LEU* 2.9 22.8 + - - +
82D ASN* 2.9 36.3 - - - +
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Residues in contact with GLY 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASN* 2.8 22.4 + - - +
51D ASN* 1.3 73.1 - - - +
53D PRO* 1.3 61.0 - - - +
55D LEU* 3.3 5.3 + - - +
56D SER 2.9 23.9 + - - -
82D ASN* 4.8 9.4 - - - +
85D TYR* 3.9 8.5 - - - -
86D TYR* 4.5 2.1 - - - -
90D LEU* 3.3 23.4 - - - +
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Residues in contact with PRO 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASN 3.8 1.8 - - - +
49D TYR* 3.2 25.8 - - + +
50D ASN 3.7 6.5 - - - +
52D GLY* 1.3 85.6 - - - +
54D VAL* 1.3 63.4 + - - +
56D SER* 3.3 8.4 + - - -
57D ARG* 3.0 51.3 + - - +
85D TYR* 4.9 2.5 - - + -
90D LEU* 4.2 13.5 - - + -
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 4.0 13.5 - - + -
40D ASP 5.0 5.8 - - - +
41D PHE* 3.8 22.4 - - + -
42D TRP* 3.7 27.6 - - + +
50D ASN 3.4 17.0 - - - +
51D ASN* 3.3 9.1 + - - +
53D PRO* 1.3 78.1 - - - +
55D LEU* 1.3 58.9 + - - +
57D ARG* 3.4 24.1 + - - +
58D PHE* 2.9 27.2 + - + +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.0 10.3 - - + -
9D VAL* 3.9 27.6 - - + -
39D VAL* 4.8 5.2 - - + -
41D PHE* 4.1 12.3 - - + -
51D ASN 2.9 18.1 + - - +
52D GLY* 3.6 4.0 - - - +
54D VAL* 1.3 73.7 - - - +
56D SER* 1.3 67.4 + - - +
58D PHE* 3.2 6.8 + - + +
59D VAL* 2.9 47.0 + - + +
73D ILE* 5.0 3.4 - - + -
82D ASN* 4.1 6.3 - - + +
83D THR* 3.9 35.4 - - - +
86D TYR* 3.9 20.9 - - + -
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLY 2.9 14.6 + - - -
53D PRO* 3.5 12.8 - - - -
54D VAL 3.2 0.4 - - - -
55D LEU* 1.3 77.6 - - - +
57D ARG* 1.3 64.4 + - - +
59D VAL* 3.4 2.3 + - - +
60D GLN* 3.1 23.7 + - - +
86D TYR* 3.5 19.3 + - - -
90D LEU* 4.4 4.7 - - - -
91D ASP* 2.6 32.2 + - - +
95D LYS* 5.9 0.2 - - - +
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TRP* 5.5 1.4 - - - +
53D PRO* 3.0 35.5 + - - +
54D VAL* 3.6 34.5 - - - +
56D SER* 1.3 77.1 - - - +
58D PHE* 1.3 62.3 + - - +
60D GLN* 3.4 6.7 + - - +
61D LYS* 3.0 24.3 + - - +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 3.9 25.1 - - + -
37D TYR* 3.7 38.1 - + + -
38D ALA 3.8 16.2 - - - -
39D VAL* 4.0 33.4 - - + -
54D VAL* 2.9 18.4 + - + +
55D LEU* 3.5 8.5 - - + +
57D ARG* 1.3 78.1 - - - +
59D VAL* 1.3 60.4 + - - +
61D LYS* 3.2 20.8 - - + +
62D VAL* 3.0 33.3 + - + +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.4 15.5 - - + -
55D LEU* 2.9 37.1 + - + +
56D SER 3.8 0.4 - - - +
58D PHE* 1.3 73.2 - - - +
60D GLN* 1.3 67.5 + - - +
62D VAL* 3.1 9.0 + - - +
63D LEU* 2.9 34.6 + - + +
71D VAL* 4.0 28.5 - - + -
73D ILE* 4.8 2.9 - - + -
86D TYR* 3.3 35.4 - - + +
95D LYS* 4.3 3.8 - - + -
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Residues in contact with GLN 60 (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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56D SER* 3.1 17.2 + - - +
57D ARG* 3.7 7.4 - - - +
59D VAL* 1.3 76.8 - - - +
61D LYS* 1.3 56.4 + - - +
63D LEU* 3.4 14.3 + - - +
64D ASP* 2.9 64.3 + - - +
86D TYR* 5.1 0.2 + - - -
91D ASP* 4.5 3.5 + - - +
95D LYS* 3.3 32.1 - - + +
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Residues in contact with LYS 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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57D ARG 3.0 13.9 + - - +
58D PHE* 3.2 26.2 - - + +
60D GLN* 1.3 77.5 - - - +
62D VAL* 1.3 58.8 + - + +
64D ASP* 3.1 7.5 + - - +
65D GLU* 2.7 73.2 + - + +
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Residues in contact with VAL 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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5D PRO* 3.6 30.3 - - + -
7D VAL* 4.1 8.7 - - + -
37D TYR* 3.9 40.4 - - + -
58D PHE* 3.0 29.0 + - + +
59D VAL* 3.5 8.5 - - - +
61D LYS* 1.3 78.5 - - + +
63D LEU* 1.3 51.8 + - - +
65D GLU* 4.7 5.2 - - - +
66D THR* 2.7 43.5 + - + +
71D VAL* 3.9 13.0 - - + -
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Residues in contact with LEU 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 VAL* 2.9 21.0 + - + +
60D GLN* 3.7 17.3 - - - +
62D VAL* 1.3 75.2 - - - +
64D ASP* 1.3 57.3 + - - +
66D THR* 3.8 2.7 - - - -
67D GLY* 2.8 32.9 + - - -
68D ALA* 3.3 25.5 + - + +
69D LYS 3.8 14.8 - - - +
70D LYS* 3.8 9.9 - - - +
71D VAL* 3.5 24.9 - - + -
95D LYS* 3.8 40.8 - - + -
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Residues in contact with ASP 64 (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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60D GLN* 2.9 49.3 + - - +
61D LYS* 3.5 6.7 - - - +
63D LEU* 1.3 79.3 - - - +
65D GLU* 1.3 64.2 + - + +
66D THR 3.6 0.2 + - - -
67D GLY* 4.0 5.0 + - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D TYR* 4.7 16.9 + - - +
61D LYS* 2.7 64.0 + - + +
62D VAL* 4.2 3.5 + - - +
64D ASP* 1.3 80.4 - - + +
66D THR* 1.3 63.2 + - + +
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Residues in contact with THR 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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5D PRO* 3.5 22.9 - - + +
35D LYS* 5.2 12.3 - - + -
37D TYR* 3.4 30.1 - - + +
62D VAL* 2.7 27.3 + - + +
63D LEU* 3.6 0.9 + - - -
65D GLU* 1.3 78.6 - - - +
67D GLY* 1.3 62.9 + - - +
68D ALA* 3.2 21.6 + - - +
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Residues in contact with GLY 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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63D LEU 2.8 17.3 + - - -
64D ASP 4.0 3.9 + - - -
65D GLU 3.7 1.2 - - - -
66D THR* 1.3 74.2 - - - +
68D ALA* 1.3 64.8 + - - +
69D LYS* 3.8 3.6 + - - +
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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