Contacts of the helix formed by residues 56 - 72 (chain A) in PDB entry 1HYH
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 GLU 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 3.2 10.1 + - - +
55A ASN* 1.3 70.1 + - - +
57A ALA* 1.3 66.7 + - - +
58A LYS 3.2 0.3 + - - -
59A VAL* 3.3 11.1 - - - +
60A LYS* 3.1 25.4 + - - +
81A ILE* 5.3 0.6 - - - +
82A ASN* 3.1 26.1 + - - +
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Residues in contact with ALA 57 (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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55A ASN* 3.5 8.5 + - - +
56A GLU* 1.3 78.5 - - - +
58A LYS* 1.3 57.5 + - - +
60A LYS* 3.6 6.0 + - - +
61A ALA* 3.0 28.6 + - - +
240C THR* 4.8 3.1 - - - +
243C ASN* 4.5 13.7 - - - +
244C GLY* 3.5 18.8 - - - +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 3.0 23.8 + - - +
30A GLY* 4.5 6.4 + - - -
34A ALA* 4.4 8.5 - - - +
53A ASP* 5.2 2.9 - - - -
55A ASN* 3.3 34.9 + - + +
57A ALA* 1.3 78.6 - - - +
59A VAL* 1.3 63.6 + - - +
61A ALA* 3.1 3.3 + - - +
62A ASP* 2.6 47.8 + - - +
330A NAD 4.9 6.1 - - - +
244C GLY 3.7 18.8 + - - +
245C LYS* 4.6 17.9 - - + +
247C TYR* 5.5 3.7 + - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.2 10.8 - - + -
51A PHE* 3.5 39.9 - - + -
53A ASP* 3.7 22.2 - - + +
55A ASN 3.4 6.8 + - - +
56A GLU* 3.3 11.0 - - - +
58A LYS* 1.3 79.2 - - - +
60A LYS* 1.3 60.2 + - - +
62A ASP* 3.3 7.6 + - - +
63A GLN* 2.9 28.3 + - - +
81A ILE* 4.1 16.4 - - + -
82A ASN* 4.0 24.9 - - - +
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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
----------------------------------------------------------
56A GLU 3.1 14.9 + - - +
57A ALA* 3.9 4.9 - - - +
59A VAL* 1.3 81.2 - - - +
61A ALA* 1.3 61.0 + - - +
63A GLN* 2.6 28.2 + - - +
64A ILE* 3.1 39.9 + - + +
81A ILE* 3.8 24.7 - - + +
240C THR* 4.0 18.8 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 3.0 14.7 + - - +
58A LYS 3.1 9.4 + - - +
60A LYS* 1.3 77.1 - - - +
62A ASP* 1.3 57.4 + - - +
64A ILE* 4.9 0.2 - - - -
65A ASP* 3.0 29.8 + - - +
240C THR* 3.9 6.0 + - - +
241C VAL* 3.6 42.1 - - - +
244C GLY 3.9 1.1 - - - -
245C LYS* 3.8 19.1 - - + +
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 15.3 - - + +
34A ALA* 4.2 7.8 - - - +
51A PHE* 4.7 8.1 - - + -
58A LYS* 2.6 43.9 + - - +
59A VAL* 3.3 8.5 + - - +
61A ALA* 1.3 74.6 - - - +
63A GLN* 1.3 64.4 + - - +
65A ASP* 3.9 3.9 - - - +
66A PHE* 3.0 40.6 + - + -
245C LYS* 3.2 29.0 + - - +
250C TYR* 3.7 11.1 + - - -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 4.6 4.4 - - + -
59A VAL 2.9 17.6 + - - +
60A LYS* 2.6 38.1 + - - +
61A ALA 3.4 0.2 - - - -
62A ASP* 1.3 76.7 - - - +
64A ILE* 1.3 58.6 - - - +
66A PHE* 3.6 2.9 - - - +
67A GLN* 2.9 54.2 + - - +
79A ILE* 3.0 44.0 + - + +
80A VAL* 4.1 3.8 - - - +
81A ILE* 3.7 25.2 - - + +
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Residues in contact with ILE 64 (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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60A LYS* 3.1 40.2 + - + +
61A ALA 3.9 3.1 - - - +
63A GLN* 1.3 77.4 - - - +
65A ASP* 1.3 60.4 + - - +
67A GLN* 3.1 22.4 + - - +
68A ASP* 2.8 42.1 + - - +
177C ARG* 4.0 26.0 - - - +
181C GLU* 5.4 0.2 - - - +
233C GLU* 5.4 4.3 - - - +
237C GLY* 3.8 21.5 - - - +
240C THR* 4.7 11.9 - - + -
241C VAL* 3.9 5.8 - - + -
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Residues in contact with ASP 65 (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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61A ALA 3.0 19.3 + - - +
62A ASP 3.9 3.4 - - - +
63A GLN 3.3 0.2 - - - -
64A ILE* 1.3 76.7 - - - +
66A PHE* 1.3 61.0 + - - +
68A ASP* 3.4 8.7 + - - +
69A ALA 3.4 14.6 + - - -
170C LEU* 5.8 0.2 - - - +
174C ARG* 5.3 2.1 + - - -
241C VAL* 4.0 14.8 - - + +
245C LYS* 2.3 35.8 + - - +
248C THR* 4.0 6.8 - - - -
249C SER 2.9 19.3 + - - -
250C TYR* 3.1 13.3 + - + +
251C GLY* 2.9 31.5 + - - -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 5.3 0.4 - - + -
34A ALA* 4.1 3.6 - - - -
37A ALA* 3.9 9.9 - - + -
38A HIS* 3.7 37.7 - + + -
41A ILE* 3.7 24.0 - - + -
51A PHE* 3.6 27.1 - + - -
62A ASP* 3.0 30.0 + - + +
63A GLN 3.6 0.4 - - - +
65A ASP* 1.3 73.6 - - - +
67A GLN* 1.3 58.5 + - - +
68A ASP 3.2 0.4 - - - -
69A ALA* 3.0 25.9 + - + +
70A MET* 3.2 14.6 + - + +
73A LEU* 4.7 0.2 - - - +
79A ILE* 3.6 20.0 - - + -
250C TYR* 3.6 50.0 - + + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 2.9 45.4 + - + +
64A ILE* 3.6 26.7 - - - +
66A PHE* 1.3 76.3 - - - +
68A ASP* 1.3 59.6 + - - +
69A ALA 3.6 0.2 + - - -
70A MET* 3.6 24.5 + - + +
71A ALA 4.6 1.4 + - - -
79A ILE* 3.9 19.8 + - + +
173C ALA 4.9 0.7 - - - +
177C ARG* 3.5 27.7 - - + +
181C GLU* 3.6 21.8 + - - +
187C PRO* 5.0 2.6 - - - +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 2.8 28.7 + - - +
65A ASP* 3.5 11.3 - - - +
66A PHE 3.2 0.2 - - - -
67A GLN* 1.3 75.2 - - - +
69A ALA* 1.3 60.1 + - - +
70A MET 3.4 0.4 + - - -
71A ALA 4.2 1.7 + - - -
72A ASN* 4.8 0.9 + - - -
170C LEU* 4.4 3.8 - - + +
173C ALA* 3.2 31.8 - - - +
174C ARG* 3.1 45.9 + - + +
177C ARG* 2.7 33.2 + - - -
237C GLY 5.1 1.2 - - - -
241C VAL* 4.7 2.4 - - - +
251C GLY* 4.3 13.1 - - - +
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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 ASP 3.4 7.2 + - - +
66A PHE* 3.0 16.0 + - + +
68A ASP* 1.3 79.9 - - - +
70A MET* 1.4 56.5 + - - +
71A ALA 3.3 0.2 - - - -
72A ASN* 2.8 23.8 + - - -
73A LEU* 3.0 23.0 + - + +
250C TYR* 3.9 12.6 - - + +
251C GLY* 4.2 6.1 - - - -
254C THR* 3.5 26.6 - - - +
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Residues in contact with MET 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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41A ILE* 4.4 13.7 - - + -
66A PHE 3.2 14.6 + - - +
67A GLN* 3.6 18.6 - - + +
68A ASP 3.4 0.8 - - - -
69A ALA* 1.4 76.7 - - - +
71A ALA* 1.3 63.9 + - - +
72A ASN 2.9 1.2 + - - -
73A LEU* 3.0 39.1 + - + +
75A ALA 4.1 10.2 - - - +
76A HIS* 4.2 11.0 - - + +
77A GLY* 3.3 46.2 - - - +
79A ILE* 4.3 19.3 - - + -
187C PRO* 4.0 18.2 - - + -
188C ARG* 3.8 8.3 - - - +
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Residues in contact with ALA 71 (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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67A GLN 4.6 1.4 + - - -
68A ASP 4.2 2.0 + - - -
69A ALA 3.3 1.4 - - - -
70A MET* 1.3 77.7 - - - +
72A ASN* 1.3 63.5 + - - +
73A LEU 3.5 0.7 - - - +
173C ALA* 3.9 17.9 - - + +
176C GLN* 3.1 44.9 + - + +
187C PRO* 4.2 9.5 - - + +
188C ARG* 3.9 22.5 - - - +
258C ARG* 3.7 9.4 + - - -
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Residues in contact with ASN 72 (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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68A ASP 4.8 1.2 + - - -
69A ALA* 2.8 9.9 + - - +
71A ALA* 1.3 80.0 - - - +
73A LEU* 1.3 61.6 + - - +
74A GLU* 4.8 4.3 - - - +
169C LEU* 3.7 24.2 + - - +
173C ALA* 3.6 25.8 - - - +
176C GLN* 5.1 2.1 - - - +
251C GLY 5.0 2.6 + - - -
254C THR* 3.5 25.7 - - + +
255C SER* 3.9 16.6 + - - +
258C ARG* 2.6 58.3 + - - +
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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