Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 4HSZ
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 PHE 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 5.6 0.7 - - + -
13A VAL* 4.0 28.7 - - + -
16A PHE* 3.4 53.3 - + + -
17A HIS* 4.8 0.2 - - - -
27A PHE 4.1 2.1 + - - +
71A ASP* 1.3 72.4 - - - +
73A GLN* 1.3 66.9 + - - +
75A TYR* 3.0 21.3 + + - +
76A CYS* 3.0 34.8 + - - -
83B ALA* 3.7 27.8 - - + -
84B MET* 3.9 16.4 - - + -
87B ASN* 3.3 34.8 - - + +
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Residues in contact with GLN 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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71A ASP* 3.1 12.9 + - - +
72A PHE* 1.3 81.0 - - - +
74A GLU* 1.3 67.6 + - + +
76A CYS* 3.2 10.9 + - - +
77A VAL* 3.3 31.5 + - + +
84B MET* 2.6 45.0 - - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.9 20.4 - - - +
63A ASP* 4.2 1.0 - - - -
64A SER* 3.5 16.6 + - - +
65A ASN* 2.6 28.1 + - - +
69A GLU 3.2 0.6 - - - +
70A VAL* 3.2 16.4 - - + +
71A ASP* 2.7 40.6 + - - +
73A GLN* 1.3 79.7 - - + +
75A TYR* 1.3 60.6 + - - +
77A VAL* 3.5 9.7 + - - +
78A PHE* 3.2 21.8 + - - +
102A CA 2.5 30.8 - - - -
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Residues in contact with TYR 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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12A MET* 2.6 36.0 + - + -
15A THR* 3.7 14.9 - - - -
16A PHE* 3.4 35.4 - + + -
29A LEU* 4.2 9.9 - - + -
34A LEU* 6.0 2.5 - - + -
37A LEU* 3.9 25.1 - - + -
70A VAL* 4.2 9.0 - - + -
71A ASP 3.0 13.3 + - - +
72A PHE* 3.0 21.3 + + - +
74A GLU* 1.3 75.2 - - - +
76A CYS* 1.3 62.3 + - - +
78A PHE* 3.4 12.7 - + - +
79A LEU* 3.0 58.7 + - + +
5B LEU* 3.9 6.0 - - + +
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Residues in contact with CYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 3.6 30.9 - - + +
72A PHE* 3.0 43.9 + - - -
73A GLN 3.2 7.6 + - - +
75A TYR* 1.3 75.4 - - - +
77A VAL* 1.3 56.8 + - + +
79A LEU* 3.2 2.3 + - - +
80A SER* 2.8 38.8 + - - -
80B SER* 4.6 12.5 + - - +
83B ALA* 4.4 5.8 - - - -
84B MET* 3.9 17.7 - - + -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 6.5 0.2 - - + -
73A GLN* 3.3 30.7 + - + +
74A GLU* 3.6 10.8 - - - +
76A CYS* 1.3 76.5 - - - +
78A PHE* 1.3 58.1 + - - +
80A SER* 3.2 7.7 + - - -
81A CYS* 2.8 41.9 + - - -
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Residues in contact with PHE 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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34A LEU* 5.7 2.2 - - + -
38A LEU* 3.9 28.3 - - + -
42A LEU* 4.5 3.8 - - + -
58A LEU* 4.6 18.6 - - + -
62A LEU* 3.3 45.8 - - + -
74A GLU 3.2 10.7 + - - +
75A TYR* 3.4 17.3 - + - +
76A CYS 3.3 0.2 - - - -
77A VAL* 1.3 80.5 - - - +
79A LEU* 1.3 65.2 + - + +
81A CYS* 3.2 10.3 + - + +
82A ILE* 2.9 56.0 + - + +
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Residues in contact with LEU 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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12A MET* 3.4 46.9 - - + -
42A LEU* 4.8 2.5 - - + -
75A TYR* 3.0 39.1 + - + +
76A CYS 3.2 7.4 + - - +
78A PHE* 1.3 82.2 - - + +
80A SER* 1.3 57.4 + - - +
82A ILE* 3.1 22.9 + - + +
83A ALA* 2.8 27.8 + - - +
5B LEU* 4.3 19.1 - - + -
9B LEU* 3.8 27.2 - - + +
12B MET* 5.7 3.4 - - + -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 5.8 1.2 - - - +
76A CYS 2.8 21.3 + - - -
77A VAL* 3.6 7.6 - - - -
79A LEU* 1.3 68.1 - - - +
81A CYS* 1.3 61.2 + - - +
83A ALA* 3.2 7.9 + - - +
84A MET* 2.9 51.3 + - - +
12B MET* 5.7 5.8 - - - +
76B CYS* 4.2 14.9 + - - +
80B SER* 3.2 20.6 + - - -
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Residues in contact with CYS 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 VAL* 2.8 31.0 + - - +
78A PHE* 3.5 14.8 - - + +
80A SER* 1.3 72.9 - - - +
82A ILE* 1.3 67.7 + - - +
84A MET* 3.4 14.1 + - - +
85A MET* 3.0 24.4 + - - +
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Residues in contact with ILE 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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42A LEU* 4.0 20.0 - - + -
45A PHE* 3.6 38.1 - - + -
78A PHE* 2.9 56.6 + - + +
79A LEU* 3.4 14.8 - - + +
81A CYS* 1.3 77.2 - - - +
83A ALA* 1.3 65.0 + - - +
85A MET* 3.2 11.0 + - + +
86A CYS* 3.0 24.3 + - - -
9B LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 83 (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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79A LEU 2.8 14.2 + - - +
80A SER* 3.2 12.5 + - - +
82A ILE* 1.3 76.4 - - - +
84A MET* 1.3 61.5 + - - +
86A CYS* 3.5 3.3 + - - -
87A ASN* 3.3 17.2 + - - +
9B LEU* 4.5 12.6 - - + -
12B MET* 4.6 13.7 - - + -
13B VAL* 3.5 31.8 - - + +
72B PHE* 3.7 8.6 - - + -
76B CYS* 4.6 5.6 - - - -
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Residues in contact with MET 84 (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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80A SER* 2.9 47.3 + - - +
81A CYS* 3.8 15.0 - - - +
83A ALA* 1.3 74.2 - - - +
85A MET* 1.3 56.9 + - - +
87A ASN* 2.8 27.3 + - - +
88A GLU* 3.2 18.7 - - - +
72B PHE* 3.6 27.6 - - + -
73B GLN* 3.1 40.6 - - - +
76B CYS* 4.4 4.3 - - + -
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Residues in contact with MET 85 (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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45A PHE* 5.5 13.7 - - + -
81A CYS 3.0 13.7 + - - +
82A ILE* 3.4 15.3 - - - +
84A MET* 1.3 76.2 - - - +
86A CYS* 1.3 58.7 + - - +
87A ASN 2.9 5.2 + - - -
88A GLU* 3.2 24.9 + - - +
91A GLU* 3.5 32.3 - - + +
92A GLY* 3.5 37.0 - - - +
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Residues in contact with CYS 86 (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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45A PHE* 4.0 27.1 - - - -
82A ILE* 3.0 20.3 + - - +
83A ALA* 3.7 10.1 - - - +
84A MET 3.2 0.2 - - - -
85A MET* 1.3 77.3 - - - +
87A ASN* 1.3 59.2 + - - +
88A GLU 3.4 6.6 + - - +
91A GLU* 2.9 35.6 - - - +
9B LEU* 6.0 3.8 - - - -
13B VAL* 4.5 18.0 - - + +
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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