Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 4HI7
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 ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 5.8 0.8 + - - -
56A PRO 3.9 7.7 + - - -
66A ALA* 1.3 79.0 - - - +
68A SER* 1.3 62.0 + - - +
69A HIS* 2.7 41.9 + - - +
70A ALA* 3.4 7.7 + - + -
71A ILE* 2.8 30.2 + - - +
301A GSH 2.8 35.9 + - - -
98B ASN* 3.6 16.2 + - - +
101B TYR* 3.3 27.0 - - - +
102B PHE* 4.5 1.4 + - - -
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Residues in contact with SER 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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14A PRO* 3.3 38.1 - - - +
17A ALA* 4.7 1.4 - - - +
18A VAL* 3.8 13.9 - - - -
56A PRO* 3.9 4.6 - - - +
67A ASP* 1.3 71.1 + - - +
69A HIS* 1.3 70.5 + - - +
71A ILE* 3.4 1.8 + - - +
72A MET* 2.9 43.7 + - - +
103A GLU* 5.3 0.2 + - - -
163A SER* 5.0 0.7 + - - -
301A GSH 2.6 31.3 + - - -
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Residues in contact with HIS 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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14A PRO* 5.9 0.2 - - + -
67A ASP* 2.7 21.7 + - - +
68A SER* 1.3 78.2 + - - +
70A ALA* 1.3 66.7 + - - +
72A MET* 3.9 8.6 - - + +
73A ALA* 3.1 24.8 + - - +
100A MET* 3.6 33.3 + - + +
103A GLU* 2.7 29.2 + - - -
104A SER* 3.6 19.5 - - - -
108A PHE* 6.0 0.9 - + + -
163A SER* 3.1 21.5 + - - -
301A GSH 3.2 22.9 - - - -
101B TYR* 3.3 34.5 - + + +
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Residues in contact with ALA 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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65A ILE* 4.0 4.7 - - + +
66A ALA 3.4 22.2 - - - +
67A ASP* 3.1 5.4 + - + +
69A HIS* 1.3 80.6 - - - +
71A ILE* 1.3 61.4 + - - +
73A ALA* 3.9 1.7 - - - +
74A TYR* 3.1 24.8 + - - +
94B ALA* 3.6 26.1 - - - +
97B ASP* 4.0 15.6 - - + +
98B ASN* 3.7 15.0 - - - +
101B TYR* 4.3 1.6 - - - -
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Residues in contact with ILE 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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6A LEU* 5.0 0.9 - - + -
18A VAL* 3.7 16.6 - - + -
56A PRO* 3.9 36.8 - - + +
58A LEU* 3.9 24.9 - - + +
65A ILE* 3.4 38.6 - - + +
67A ASP 2.8 28.0 + - - +
68A SER 3.7 3.8 - - - +
70A ALA* 1.3 72.2 - - - +
72A MET* 1.3 57.8 + - - +
74A TYR* 3.3 4.9 + - - +
75A LEU* 2.8 50.6 + - + +
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Residues in contact with MET 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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17A ALA* 3.5 34.1 - - + +
18A VAL* 4.2 9.2 - - + -
21A THR* 3.1 36.8 - - - +
68A SER* 2.9 32.0 + - - +
69A HIS* 3.9 9.0 - - - +
71A ILE* 1.3 77.1 - - - +
73A ALA* 1.3 63.4 + - - +
75A LEU* 3.3 2.6 + - - +
76A VAL* 3.1 29.3 + - - +
100A MET* 4.1 4.5 - - - -
159A ILE* 3.8 31.4 - - + +
162A PHE* 4.1 2.5 - - - -
163A SER* 3.9 22.2 - - - +
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Residues in contact with ALA 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 HIS 3.1 18.4 + - - +
70A ALA 3.9 3.4 - - - +
72A MET* 1.3 76.2 - - - +
74A TYR* 1.3 61.5 + - - +
76A VAL* 3.6 0.3 + - - -
77A SER* 2.9 30.6 + - - -
86A TYR* 3.5 34.2 - - + +
100A MET* 4.8 2.2 - - + -
159A ILE* 3.6 12.2 - - + +
97B ASP* 4.4 13.9 - - - +
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Residues in contact with TYR 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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58A LEU* 3.9 18.2 - - + -
60A ASP* 2.7 33.6 + - - +
63A ALA* 4.8 1.6 - - - +
65A ILE* 3.8 28.7 - - + +
70A ALA 3.1 18.4 + - - +
71A ILE* 3.4 5.4 - - - +
73A ALA* 1.3 78.0 - - - +
75A LEU* 1.3 61.2 + - - +
77A SER* 3.3 4.1 + - - -
78A LYS* 2.8 58.0 + - + +
79A TYR* 4.4 7.9 - + - -
90B LEU* 3.8 34.3 - - + +
91B VAL* 3.8 26.3 - - + +
94B ALA* 4.3 10.5 - - + -
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Residues in contact with LEU 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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4A PRO* 5.3 1.1 - - + -
18A VAL* 4.1 7.6 - - + -
21A THR* 4.3 11.4 - - + -
22A LEU* 3.7 30.1 - - + -
25A LEU* 3.7 14.8 - - + +
27A LEU* 3.9 24.9 - - + -
58A LEU* 3.7 24.0 - - + -
71A ILE* 2.8 41.8 + - + +
72A MET* 3.7 4.0 - - - +
74A TYR* 1.3 76.5 - - + +
76A VAL* 1.3 57.2 + - - +
79A TYR* 2.9 44.5 + - + +
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Residues in contact with VAL 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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21A THR* 4.1 11.0 - - + -
25A LEU* 4.2 7.4 - - + -
72A MET 3.1 17.3 + - - +
73A ALA 4.2 0.4 - - - +
75A LEU* 1.3 75.3 - - - +
77A SER* 1.3 60.0 + - - +
80A GLY* 2.8 30.7 + - - +
82A ASP 4.4 15.3 - - - +
83A ASP* 4.8 3.1 - - - -
85A LEU* 3.9 19.7 - - + -
86A TYR* 3.8 35.9 - - + +
159A ILE* 3.7 23.6 - - + -
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Residues in contact with SER 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 ALA 2.9 20.2 + - - -
74A TYR 3.9 1.6 - - - -
76A VAL* 1.3 76.7 - - - +
78A LYS* 1.3 59.1 + - - +
80A GLY 4.8 0.4 - - - +
86A TYR* 3.7 18.5 + - - -
93A ARG* 4.0 13.2 + - - +
90B LEU* 3.7 31.7 - - - +
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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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60A ASP* 5.1 0.2 - - - -
74A TYR* 2.8 41.5 + - + +
77A SER* 1.3 80.1 - - - +
79A TYR* 1.3 94.5 + - + +
80A GLY 3.8 0.8 - - - +
90B LEU* 3.7 21.3 - - + +
91B VAL* 5.8 4.0 - - - +
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Residues in contact with TYR 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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4A PRO* 4.3 5.9 - - + +
25A LEU* 4.5 13.1 - - + +
27A LEU* 3.6 45.5 - - + -
60A ASP* 2.6 38.3 + - - -
74A TYR* 4.4 1.6 - + - -
75A LEU* 2.9 26.5 + - + +
78A LYS* 1.3 106.9 - - + +
80A GLY* 1.3 64.6 + - - +
81A LYS* 3.5 9.7 + - - +
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Residues in contact with GLY 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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25A LEU* 3.7 19.7 - - - +
75A LEU 3.7 1.8 + - - -
76A VAL* 2.8 21.5 + - - +
77A SER 5.7 0.5 - - - +
78A LYS 5.4 0.5 - - - +
79A TYR* 1.3 78.8 - - - +
81A LYS* 1.3 67.8 + - - +
82A ASP* 3.2 13.4 + - - +
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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