Contacts of the helix formed by residues 47 - 67 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ASP* 2.8 18.4 + - - +
45H THR* 3.3 22.2 + - - +
46H GLY* 1.3 75.7 - - - +
48H ASN* 1.3 63.4 + - - +
49H TYR* 3.8 8.2 + - - +
50H ASN* 3.1 22.2 + - - +
51H ASN* 3.0 20.4 + - - +
78H MET* 6.0 0.2 - - - -
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Residues in contact with ASN 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLY 3.5 0.8 + - - -
47H THR* 1.3 71.7 - - - +
49H TYR* 1.3 62.4 + - - +
52H GLY* 2.8 31.8 + - - +
78H MET* 5.6 0.8 - - - +
81H ALA* 3.2 19.8 - - - +
82H ASN* 2.9 29.6 + - - +
85H TYR* 3.5 40.5 - - + -
108H LEU* 4.2 11.3 + - - +
109H THR* 2.9 23.0 + - - +
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H THR* 3.2 8.7 - - - +
48H ASN* 1.3 78.5 - - - +
50H ASN* 1.3 86.2 + - - +
53H PRO* 3.2 22.0 - - - +
85H TYR* 4.6 13.5 + - - -
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Residues in contact with ASN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H TRP* 3.2 41.1 + - + -
43H ASP* 2.9 32.4 + - + +
47H THR* 3.1 10.5 + - - +
48H ASN 3.2 0.4 - - - -
49H TYR* 1.3 103.5 - - - +
51H ASN* 1.3 63.8 + - - +
53H PRO* 3.5 8.8 - - - +
54H VAL* 3.3 20.0 - - - +
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Residues in contact with ASN 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H HIS* 5.3 0.8 - - - -
11H GLY 6.3 0.2 - - - -
41H PHE* 3.2 44.8 - - + +
42H TRP* 5.1 0.9 + - - -
43H ASP* 3.4 22.6 + - - +
46H GLY* 3.3 19.8 - - - -
47H THR 3.0 14.9 + - - +
50H ASN* 1.3 76.4 - - - +
52H GLY* 1.3 66.5 + - - +
54H VAL* 3.2 2.2 + - - +
55H LEU* 2.9 27.3 + - - +
82H ASN* 3.1 35.0 - - - +
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Residues in contact with GLY 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ASN* 2.8 21.9 + - - +
51H ASN* 1.3 73.7 - - - +
53H PRO* 1.3 60.4 - - - +
55H LEU* 3.3 6.3 + - - +
56H SER 2.9 23.2 + - - -
82H ASN* 4.8 9.4 - - - +
85H TYR* 3.9 10.5 - - - -
86H TYR* 4.5 2.3 - - - -
90H LEU* 3.1 22.7 - - - +
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Residues in contact with PRO 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ASN 3.8 1.3 - - - +
49H TYR 3.2 23.8 - - - +
50H ASN* 3.5 8.5 - - - +
52H GLY* 1.3 86.5 - - - +
54H VAL* 1.3 64.3 + - - +
56H SER* 3.2 4.3 + - - -
57H ARG* 3.0 47.5 + - - +
85H TYR* 4.8 3.1 - - + -
90H LEU* 4.0 15.7 - - + -
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Residues in contact with VAL 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H VAL* 4.2 11.4 - - + -
40H ASP 4.3 8.3 - - - +
41H PHE* 3.6 24.5 - - + -
42H TRP* 3.9 25.6 - - + +
50H ASN 3.3 18.1 + - - +
51H ASN* 3.2 8.0 + - - +
53H PRO* 1.3 77.7 - - + +
55H LEU* 1.3 57.7 + - - +
57H ARG* 3.4 25.0 + - - +
58H PHE* 3.0 27.0 + - + +
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.2 9.9 - - + -
9H VAL* 4.0 26.7 - - + -
39H VAL* 4.9 4.5 - - + -
41H PHE* 4.0 12.5 - - + -
51H ASN 2.9 17.4 + - - +
52H GLY 3.6 3.8 - - - +
54H VAL* 1.3 77.8 - - - +
56H SER* 1.3 56.7 + - - +
58H PHE* 3.1 5.4 + - + +
59H VAL* 2.9 49.0 + - + +
73H ILE* 4.9 4.5 - - + -
82H ASN* 4.0 7.0 - - + +
83H THR* 3.9 35.2 - - - +
86H TYR* 3.9 24.9 - - + -
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Residues in contact with SER 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLY 2.9 14.3 + - - -
53H PRO* 3.2 10.5 + - - -
55H LEU* 1.3 76.5 - - - +
57H ARG* 1.3 64.4 + - - +
59H VAL* 3.4 2.3 + - - +
60H GLN* 3.1 23.2 + - - +
86H TYR* 3.5 21.0 + - - -
90H LEU* 4.1 8.3 - - - -
91H ASP* 2.6 30.7 + - - +
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Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H TRP* 5.5 1.8 - - - +
53H PRO* 3.0 40.0 + - - +
54H VAL* 3.7 30.1 - - - +
56H SER* 1.3 78.4 - - - +
58H PHE* 1.3 62.5 + - - +
60H GLN* 3.4 6.9 + - - +
61H LYS* 3.0 22.9 + - - +
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Residues in contact with PHE 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 3.8 26.2 - - + -
37H TYR* 3.6 31.0 - + + -
38H ALA 3.7 20.4 - - - -
39H VAL* 3.9 33.4 - - + -
40H ASP 5.2 0.2 - - - -
54H VAL* 3.0 18.0 + - + +
55H LEU* 3.1 6.5 + - + +
57H ARG* 1.3 77.8 - - - +
59H VAL* 1.3 61.0 + - - +
61H LYS* 3.3 33.7 + - + +
62H VAL* 3.1 28.8 + - + +
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.5 10.3 - - + -
55H LEU* 2.9 37.8 + - + +
56H SER 3.8 0.9 - - - +
57H ARG 3.4 0.2 - - - -
58H PHE* 1.3 72.8 - - - +
60H GLN* 1.3 66.1 + - - +
62H VAL* 3.2 8.4 + - - +
63H LEU* 2.9 34.4 + - + +
71H VAL* 3.8 34.3 - - + -
73H ILE* 5.0 2.5 - - + -
86H TYR* 3.2 35.2 - - + +
95H LYS* 4.5 3.1 - - + -
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Residues in contact with GLN 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H SER 3.1 16.8 + - - +
57H ARG* 3.7 7.6 - - - +
58H PHE 3.3 0.2 - - - -
59H VAL* 1.3 77.7 - - - +
61H LYS* 1.3 57.7 + - - +
63H LEU* 3.3 13.9 + - - +
64H ASP* 2.8 63.8 + - - +
91H ASP* 4.2 5.4 + - - +
95H LYS* 3.3 32.7 - - + +
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Residues in contact with LYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H TYR* 4.6 7.8 - - - -
57H ARG 3.0 14.4 + - - +
58H PHE* 3.4 38.4 - - + +
60H GLN* 1.3 77.2 - - - +
62H VAL* 1.3 65.4 + - - +
64H ASP* 3.3 7.6 + - + +
65H GLU* 2.8 71.7 + - + +
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Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO* 3.6 32.5 - - + -
7H VAL* 4.2 7.9 - - + -
37H TYR* 3.6 45.3 - - + -
58H PHE* 3.1 22.5 + - + +
59H VAL* 3.2 8.3 + - - +
61H LYS* 1.3 80.2 - - - +
63H LEU* 1.3 56.9 + - - +
65H GLU* 3.4 5.8 + - - -
66H THR* 2.8 36.2 + - - +
71H VAL* 3.7 14.1 - - + -
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H VAL* 2.9 22.5 + - + +
60H GLN* 3.7 16.8 - - - +
62H VAL* 1.3 75.4 - - - +
64H ASP* 1.3 59.4 + - - +
66H THR* 3.9 2.9 - - - -
67H GLY* 2.8 32.2 + - - -
68H ALA* 3.4 25.8 + - + +
69H LYS 4.2 6.5 - - - +
70H LYS* 3.7 19.3 - - - +
71H VAL* 3.6 25.1 - - + +
95H LYS* 3.9 39.3 - - + -
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Residues in contact with ASP 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H GLN* 2.8 51.5 + - - +
61H LYS* 3.6 7.5 - - - +
63H LEU* 1.3 79.3 - - - +
65H GLU* 1.3 62.7 + - + +
66H THR 3.5 0.2 + - - -
67H GLY* 3.9 5.5 + - - -
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Residues in contact with GLU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H TYR* 4.0 18.0 + - - +
61H LYS* 2.8 68.6 + - + +
62H VAL 4.1 2.5 - - - +
64H ASP* 1.3 75.2 - - + +
66H THR* 1.3 63.4 + - + +
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Residues in contact with THR 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO* 3.6 21.2 - - + +
35H LYS* 4.9 21.4 + - + +
37H TYR* 3.4 28.0 - - + +
62H VAL 2.8 22.4 + - - +
63H LEU 3.6 0.5 + - - -
65H GLU* 1.3 79.3 - - - +
67H GLY* 1.3 62.8 + - - +
68H ALA* 3.1 22.6 + - - +
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Residues in contact with GLY 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU 2.8 11.9 + - - -
64H ASP 3.9 4.5 + - - -
65H GLU 3.7 1.2 - - - -
66H THR* 1.3 79.1 - - - +
68H ALA* 1.3 64.9 + - - +
69H LYS 3.8 0.5 + - - -
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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
------------------------------------------------------------
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