Contacts of the helix formed by residues 67 - 82 (chain A) in PDB entry 1HS7
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LYS* 2.7 56.6 + - + +
66A THR* 1.3 80.1 - - - +
68A LEU* 1.3 68.6 + - + +
70A PRO* 3.1 4.2 - - - +
71A ASN* 2.7 46.0 + - - +
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Residues in contact with LEU 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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40A GLN* 4.0 11.2 - - - +
43A VAL* 3.1 31.0 - - + -
44A LEU* 3.6 14.1 - - + -
47A GLU* 3.1 38.4 - - + -
63A LYS* 2.7 24.9 + - - +
64A ILE* 3.0 27.2 + - + +
67A GLU* 1.3 81.0 - - + +
69A ILE* 1.3 58.4 + - - +
71A ASN* 2.6 27.4 + - - +
72A CYS* 2.7 18.2 + - - -
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Residues in contact with ILE 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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44A LEU* 3.8 12.6 - - + -
64A ILE* 2.7 38.9 + - + +
65A GLU* 4.4 12.8 - - + +
68A LEU* 1.3 72.5 - - - +
70A PRO* 1.3 64.8 - - + +
72A CYS* 2.9 6.7 + - - -
73A THR* 2.7 41.1 + - + +
102A TYR* 2.7 39.9 - - + +
106A GLN* 4.4 12.3 - - + +
109A TYR* 3.9 15.0 - - + -
110A ASN* 5.7 0.4 - - - +
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Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE 3.2 4.7 - - - +
65A GLU 2.9 30.1 - - - +
66A THR* 3.2 6.7 - - - +
67A GLU* 3.1 27.4 - - - +
69A ILE* 1.3 97.4 - - + +
71A ASN* 1.3 53.0 + - - +
73A THR* 3.6 7.6 - - + +
74A SER* 2.5 41.8 + - - -
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Residues in contact with ASN 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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40A GLN* 4.3 19.3 + - - +
66A THR 5.5 0.2 - - - +
67A GLU* 2.7 35.3 + - - +
68A LEU 2.6 9.5 + - - +
70A PRO* 1.3 77.2 - - - +
72A CYS* 1.3 58.2 + - - +
74A SER* 3.7 5.6 - - - -
75A VAL* 2.8 34.7 + - + +
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Residues in contact with CYS 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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37A PHE* 3.0 36.2 - - + -
40A GLN* 3.6 37.2 - - + -
44A LEU* 4.3 6.7 - - - -
68A LEU* 2.7 44.8 + - - -
69A ILE* 3.5 7.0 - - - +
71A ASN* 1.3 72.4 - - - +
73A THR* 1.3 63.1 + - - +
75A VAL* 3.0 18.8 + - - +
76A ARG 3.2 2.4 + - - -
102A TYR* 4.0 13.9 - - + -
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Residues in contact with THR 73 (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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69A ILE* 2.7 27.7 + - + +
70A PRO* 3.6 11.0 - - + +
72A CYS* 1.3 69.8 - - - +
74A SER* 1.3 64.4 + - - +
75A VAL 2.9 1.6 - - - -
76A ARG* 2.6 55.9 + - - +
77A ASP* 3.1 8.6 + - - +
102A TYR* 4.1 14.0 + - - -
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Residues in contact with SER 74 (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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70A PRO 2.5 22.5 + - - -
71A ASN* 3.7 8.5 + - - -
73A THR* 1.3 84.3 - - - +
75A VAL* 1.3 61.1 + - - +
77A ASP* 3.5 9.6 + - - +
78A LYS* 3.3 25.6 + - - +
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Residues in contact with VAL 75 (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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33A LEU* 3.8 13.0 - - + +
36A THR* 3.1 29.6 - - + -
37A PHE* 3.2 39.7 - - + -
40A GLN* 5.2 2.2 - - + +
71A ASN 2.8 16.9 + - - +
72A CYS* 3.0 15.9 - - - +
74A SER* 1.3 76.4 - - - +
76A ARG* 1.3 61.2 + - - +
78A LYS* 3.4 16.0 - - - +
79A ILE* 3.1 24.4 + - + +
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Residues in contact with ARG 76 (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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37A PHE* 3.1 39.5 - - + -
72A CYS 3.2 1.7 + - - +
73A THR* 2.6 39.3 + - - +
75A VAL* 1.3 67.3 - - - +
77A ASP* 1.3 51.4 + - - +
78A LYS 2.9 1.3 - - - -
79A ILE* 2.6 7.3 + - - -
80A GLU* 2.5 56.3 + - - +
95A PHE* 3.5 17.8 - - + -
99A LYS* 3.3 34.2 - - - +
102A TYR* 4.2 15.4 - - - -
103A GLN* 4.2 19.0 + - - +
106A GLN* 5.7 0.2 - - - +
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Residues in contact with ASP 77 (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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73A THR* 3.1 7.9 + - - +
74A SER* 3.7 11.8 - - - +
76A ARG* 1.3 79.7 - - - +
78A LYS* 1.3 53.2 + - + +
80A GLU* 4.0 15.0 + - - +
81A SER* 2.7 37.3 + - - -
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Residues in contact with LYS 78 (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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33A LEU* 3.6 42.6 - - + +
74A SER 3.3 13.6 + - - +
75A VAL* 3.4 19.3 - - - +
76A ARG 2.9 0.6 - - - -
77A ASP* 1.3 80.5 - - + +
79A ILE* 1.3 61.4 + - - +
81A SER* 3.5 7.1 + - - -
82A ASN* 3.3 17.2 + - - +
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Residues in contact with ILE 79 (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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30A LEU* 3.2 23.1 - - + -
33A LEU* 3.6 14.1 - - + -
34A ILE* 3.2 36.6 - - + +
37A PHE* 4.2 3.1 - - + -
75A VAL* 3.1 24.8 + - + +
76A ARG 2.6 10.8 + - - +
78A LYS* 1.3 69.4 - - - +
80A GLU* 1.3 63.5 + - - +
82A ASN* 3.1 14.2 + - - +
85A ILE* 3.0 49.7 - - + +
95A PHE* 3.3 27.1 - - + -
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Residues in contact with GLU 80 (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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76A ARG* 2.5 37.0 + - - +
77A ASP* 4.0 17.8 + - - +
79A ILE* 1.3 70.2 - - - +
81A SER* 1.3 64.3 + - - +
82A ASN 3.3 1.9 + - - -
83A ILE* 4.3 1.2 + - - +
85A ILE* 3.8 15.7 - - - +
86A HIS* 4.3 14.9 + - - +
95A PHE* 3.1 40.1 - - + -
99A LYS* 5.1 0.3 - - - +
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Residues in contact with SER 81 (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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77A ASP* 2.7 26.0 + - - -
78A LYS* 3.5 9.4 - - - -
80A GLU* 1.3 75.0 - - - +
82A ASN* 1.3 57.9 + - - +
83A ILE* 3.0 9.2 + - - +
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Residues in contact with ASN 82 (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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26A LYS* 3.9 9.0 + - - +
30A LEU* 3.3 34.4 - - + +
33A LEU* 5.3 2.5 - - + -
78A LYS 3.3 9.4 + - - +
79A ILE 3.1 9.8 + - - +
80A GLU 3.1 0.8 - - - -
81A SER* 1.3 74.5 - - - +
83A ILE* 1.3 53.8 + - - +
84A LEU* 2.9 43.1 - - - +
85A ILE* 2.7 40.8 + - - +
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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
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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