Contacts of the helix formed by residues 52 - 71 (chain A) in PDB entry 2HBF
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 SER 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 2.5 45.1 + - - +
49A SER* 2.9 15.5 + - - -
50A HIS 3.4 0.8 + - - -
51A GLY* 1.3 77.7 - - - +
53A ALA* 1.3 62.4 + - - +
54A GLN* 2.9 20.3 + - - +
55A VAL* 3.2 14.5 + - - +
56A LYS* 3.2 22.0 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 2.9 6.6 + - - +
52A SER* 1.3 69.6 + - - +
54A GLN* 1.3 60.5 + - - +
56A LYS* 3.6 9.1 - - + +
57A GLY* 2.9 26.0 + - - -
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 3.1 26.1 + - - +
46A PHE* 3.6 31.3 - - + +
47A ASP* 2.7 36.4 + - - +
52A SER* 2.9 6.4 + - - +
53A ALA* 1.3 78.9 - - - +
55A VAL* 1.3 62.2 + - - +
57A GLY* 3.2 1.3 + - - -
58A HIS* 2.9 24.6 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.7 24.1 - - + +
29A LEU* 3.9 17.5 - - + -
30A GLU* 4.3 11.0 - - + +
33A PHE* 4.6 6.5 - - + -
46A PHE* 4.7 2.5 - - + -
47A ASP 3.7 8.7 - - - +
48A LEU* 3.8 29.2 - - + +
49A SER 4.7 2.5 - - - +
50A HIS 6.0 1.6 - - - +
52A SER* 3.2 25.1 + - - +
54A GLN* 1.3 76.8 - - - +
56A LYS* 1.3 58.6 + - + +
58A HIS* 3.0 5.0 + - - +
59A GLY* 2.7 29.8 + - - -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 4.9 0.3 - - - +
26A ALA* 3.9 20.9 - - + +
50A HIS* 4.8 11.9 - - - +
51A GLY* 4.3 15.7 + - - +
52A SER 3.2 19.2 + - - +
53A ALA* 3.6 12.3 - - + +
55A VAL* 1.3 79.4 - - + +
57A GLY* 1.3 63.1 + - - +
58A HIS 3.1 0.5 + - - -
59A GLY* 3.4 1.6 + - - -
60A LYS* 3.2 35.5 + - - +
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 2.9 16.2 + - - -
54A GLN* 3.8 1.6 - - - -
56A LYS* 1.3 78.0 - - - +
58A HIS* 1.3 60.9 + - - +
60A LYS* 3.7 11.4 + - - +
61A LYS* 3.3 28.8 + - - +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.6 6.5 - - + -
43A PHE* 4.3 3.5 - + - -
46A PHE* 4.0 21.9 - + + -
54A GLN 2.9 16.4 + - - +
55A VAL* 3.7 3.1 - - - +
57A GLY* 1.3 78.0 - - - +
59A GLY* 1.3 60.3 + - - +
61A LYS* 3.1 17.9 + - + +
62A VAL* 3.0 26.8 + - + +
142A HEM 3.4 51.0 + + + +
143A NPN 2.9 51.1 - - - -
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.9 7.4 - - - -
25A GLY* 3.6 5.1 - - - -
26A ALA* 3.5 22.9 - - - -
29A LEU* 3.1 18.8 - - - +
55A VAL 2.7 15.3 + - - -
56A LYS 3.7 0.9 - - - -
58A HIS* 1.3 66.9 - - - +
60A LYS* 1.3 63.5 + - - +
62A VAL* 3.2 3.3 + - - +
63A ALA* 2.9 23.6 + - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 3.9 30.4 + - - +
23A GLU* 4.7 8.3 - - - +
56A LYS* 3.2 25.7 + - - +
57A GLY* 4.0 11.9 - - - +
58A HIS 3.3 0.2 - - - -
59A GLY* 1.3 74.3 - - - +
61A LYS* 1.3 59.8 + - + +
63A ALA* 3.6 0.5 - - - +
64A ASP* 2.9 41.7 + - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY 3.3 18.9 + - - +
58A HIS* 3.1 27.9 + - + +
60A LYS* 1.3 77.1 - - + +
62A VAL* 1.3 62.2 + - - +
64A ASP* 3.5 6.3 + - - +
65A ALA 3.1 17.5 + - - -
142A HEM 3.4 57.1 + - + +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 5.2 5.4 - - - +
29A LEU* 4.5 10.3 - - + -
58A HIS* 3.0 18.8 + - + +
59A GLY* 3.2 6.9 + - - +
61A LYS* 1.3 73.1 - - - +
63A ALA* 1.3 63.7 + - - +
65A ALA* 3.1 6.1 + - - +
66A LEU* 3.1 39.9 + - + +
101A LEU* 4.6 13.9 - - + -
105A LEU* 5.1 9.0 - - + -
142A HEM 3.9 24.6 - - + +
143A NPN 3.3 42.6 - - + +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 4.0 4.5 - - + -
21A ALA* 3.2 44.4 - - + +
22A GLY* 3.6 4.3 - - - +
25A GLY* 4.8 3.3 - - - +
59A GLY 2.9 16.5 + - - +
60A LYS 3.6 4.5 - - - +
62A VAL* 1.3 76.9 - - - +
64A ASP* 1.3 58.9 + - - +
66A LEU* 3.1 12.5 + - - +
67A THR* 2.9 32.5 + - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 5.8 1.4 - - - +
22A GLY* 5.8 0.5 + - - -
60A LYS* 2.9 26.7 + - - +
61A LYS* 3.9 6.0 - - - +
63A ALA* 1.3 75.6 - - - +
65A ALA* 1.3 62.9 + - - +
67A THR* 3.1 8.5 + - - -
68A ASN* 2.8 30.4 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS 3.1 11.1 + - - +
62A VAL 3.1 9.9 + - - +
64A ASP* 1.3 78.8 - - - +
66A LEU* 1.3 63.6 + - - +
68A ASN* 3.4 9.1 - - - +
69A ALA* 3.1 19.9 + - - +
80A LEU* 3.8 8.9 - - + +
83A LEU* 3.6 31.9 - - + -
142A HEM 3.7 19.1 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 4.0 27.1 - - + -
62A VAL* 3.1 28.7 + - + +
63A ALA* 3.1 7.8 + - - +
65A ALA* 1.3 74.6 - - - +
67A THR* 1.3 60.4 + - - +
69A ALA* 3.0 6.5 + - + +
70A VAL* 2.9 33.3 + - - +
105A LEU* 4.0 30.3 - - + -
128A PHE* 4.0 7.7 - - + -
129A LEU* 4.3 17.7 - - + -
132A VAL* 4.2 24.5 - - + -
142A HEM 3.9 22.7 - - + -
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 2.7 35.5 + - + +
21A ALA* 4.5 6.9 - - - +
63A ALA 2.9 16.5 + - - -
64A ASP* 3.4 12.2 + - - -
66A LEU* 1.3 76.8 - - - +
68A ASN* 1.3 56.8 + - - +
69A ALA 3.4 0.2 + - - -
70A VAL* 3.4 3.3 + - + +
71A ALA* 2.9 31.8 + - + +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP 2.8 13.3 + - - +
65A ALA* 3.4 13.9 - - - +
67A THR* 1.3 76.3 - - - +
69A ALA* 1.3 56.8 + - - +
71A ALA* 3.4 3.2 + - - +
72A HIS* 3.0 63.5 + - - +
79A ALA* 3.6 27.5 - - - +
80A LEU* 4.3 5.4 - - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 3.1 12.8 + - - +
66A LEU* 3.0 12.3 + - + +
68A ASN* 1.3 71.8 + - - +
70A VAL* 1.3 63.0 + - - +
72A HIS* 3.1 2.8 - - - +
73A VAL* 2.9 32.6 + - - +
76A MET* 3.9 17.1 - - + +
79A ALA* 5.2 1.3 - - - -
80A LEU* 4.3 13.0 - - + +
128A PHE* 3.9 17.7 - - + -
132A VAL* 4.1 15.5 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.8 17.9 - - + -
11A LYS* 3.5 43.6 - - + -
14A TRP* 3.9 36.8 - - + -
66A LEU 2.9 14.3 + - - +
67A THR* 3.6 7.4 - - + +
69A ALA* 1.3 74.8 - - - +
71A ALA* 1.3 64.6 + - - +
72A HIS 3.4 0.2 + - - -
73A VAL* 3.7 6.9 - - - +
128A PHE* 3.5 28.3 - - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.2 4.9 + - - +
67A THR* 2.9 20.5 + - + +
68A ASN* 3.7 7.4 - - - +
70A VAL* 1.3 78.7 - - - +
72A HIS* 1.3 77.0 + - + +
73A VAL 3.6 1.1 + - - -
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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
------------------------------------------------------------
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