Contacts of the helix formed by residues 73 - 90 (chain A) in PDB entry 2HSG
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 ILE 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 1.3 100.1 - - - +
74A PHE* 1.3 81.4 + - + +
75A TYR 2.9 7.1 - - - +
76A ALA* 2.6 25.7 + - + +
77A GLU* 3.0 18.3 + - + +
276A ASN 5.5 3.6 - - - +
277A THR* 5.2 1.8 - - - -
278A ARG* 4.7 27.4 - - + +
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Residues in contact with PHE 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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72A ASN* 4.7 3.1 - - - +
73A ILE* 1.3 88.0 - - + +
75A TYR* 1.3 105.3 + + - +
77A GLU* 3.9 3.9 + - - +
78A LEU 3.5 11.1 + - - -
275A ASP* 4.0 26.2 - - + -
276A ASN 5.2 6.7 - - - +
277A THR* 3.5 37.2 - - + -
294A MET* 3.2 51.2 - - + +
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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
----------------------------------------------------------
67A ILE* 3.4 39.5 - - + +
68A PRO* 3.6 39.8 - - + +
71A SER* 3.9 13.2 - - - -
72A ASN* 3.9 26.2 - - + +
73A ILE 4.6 0.2 - - - -
74A PHE* 1.3 111.4 - + - +
76A ALA* 1.3 63.5 + - - +
78A LEU* 3.3 7.2 + - + +
79A ALA* 3.0 17.8 + - - +
123A MET* 5.5 7.4 - - + -
125A GLY* 5.5 6.1 + - - -
294A MET* 5.3 4.0 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 4.3 9.6 + - - +
72A ASN 3.8 16.8 + - - +
73A ILE* 2.6 20.1 + - + +
75A TYR* 1.3 74.9 - - - +
77A GLU* 1.3 59.7 + - - +
79A ALA* 2.8 11.9 + - - +
80A ARG* 2.8 48.6 + - - +
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Residues in contact with GLU 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 ILE* 3.0 17.2 + - + +
74A PHE* 4.2 5.8 - - - +
76A ALA* 1.3 75.6 - - + +
78A LEU* 1.3 64.4 + - - +
80A ARG* 3.4 21.3 - - - +
81A GLY 3.0 17.3 + - - -
294A MET* 4.3 4.9 - - + -
295A TYR* 3.3 44.1 - - + +
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Residues in contact with LEU 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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65A VAL* 5.9 1.6 - - + -
67A ILE* 4.9 10.3 - - + -
74A PHE 3.5 11.3 + - - +
75A TYR* 3.3 14.3 + - + +
76A ALA 3.2 0.6 - - - -
77A GLU* 1.3 78.4 - - - +
79A ALA* 1.3 63.5 + - - +
81A GLY* 3.3 1.6 + - - -
82A ILE* 3.1 42.8 + - + +
121A ILE* 5.2 1.1 - - + -
123A MET* 5.0 8.5 - - + -
145A ALA* 4.1 25.6 - - + +
146A ALA* 4.3 6.7 - - + -
294A MET* 3.1 40.5 + - + +
297A ILE* 4.1 11.4 - - + -
298A GLY* 3.8 9.3 - - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 6.1 2.7 - - + -
67A ILE* 4.9 6.7 - - + -
71A SER* 5.8 1.8 - - - +
75A TYR 3.0 12.4 + - - +
76A ALA* 2.8 16.5 + - - +
78A LEU* 1.3 76.6 - - - +
80A ARG* 1.3 58.7 + - - +
81A GLY 2.9 2.4 + - - -
82A ILE* 3.0 8.4 + - - +
83A GLU* 2.7 56.0 + - - +
95A LEU* 4.2 15.0 - - + -
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Residues in contact with ARG 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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71A SER* 5.2 3.8 + - - -
76A ALA* 2.8 40.6 + - - +
77A GLU* 3.2 28.0 + - - +
79A ALA* 1.3 75.0 - - - +
81A GLY* 1.3 53.0 + - - +
83A GLU* 2.6 43.6 + - - -
84A ASP* 2.8 45.5 + - - +
95A LEU* 5.9 0.8 - - - +
295A TYR* 3.7 15.7 - - + -
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Residues in contact with GLY 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 GLU 3.0 9.3 + - - -
78A LEU 3.7 1.1 - - - -
79A ALA 2.9 1.0 - - - -
80A ARG* 1.3 75.3 - - - +
82A ILE* 1.3 64.3 - - - +
84A ASP* 3.5 2.4 + - - +
85A ILE* 3.4 25.1 + - - +
295A TYR* 3.4 39.4 - - - -
299A ALA* 3.6 9.3 - - - +
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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
----------------------------------------------------------
65A VAL* 4.1 20.4 - - + -
78A LEU* 3.1 36.2 + - + +
79A ALA* 3.0 8.2 + - - +
81A GLY* 1.3 73.3 - - - +
83A GLU* 1.3 68.1 + - + +
85A ILE* 3.1 3.3 + - - -
86A ALA* 3.0 19.8 + - - +
93A ILE* 3.7 26.7 - - + -
121A ILE* 3.7 34.5 - - + -
298A GLY* 3.3 23.6 - - - +
302A MET* 3.7 14.8 - - + +
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Residues in contact with GLU 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 ALA* 2.7 41.7 + - - +
80A ARG* 2.6 41.4 + - - +
82A ILE* 1.3 74.3 - - + +
84A ASP* 1.3 61.4 + - - +
86A ALA* 3.2 3.5 + - - +
87A THR* 2.9 35.6 + - - +
93A ILE* 4.3 28.0 - - + -
95A LEU* 3.6 14.9 - - - +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 2.8 23.2 + - - +
81A GLY 3.8 3.4 - - - +
82A ILE 3.1 0.4 - - - -
83A GLU* 1.3 81.8 - - - +
85A ILE* 1.3 63.1 + - + +
87A THR* 3.4 13.8 + - - -
88A MET* 3.4 18.3 + - - +
295A TYR* 2.5 37.0 + - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY 3.4 15.3 - - - +
82A ILE 3.1 2.5 + - - +
84A ASP* 1.3 77.5 - - + +
86A ALA* 1.3 66.9 + - - +
87A THR 3.0 1.3 - - - -
88A MET* 3.8 13.9 - - + -
89A TYR* 2.8 60.0 + - + +
295A TYR* 6.0 1.1 - - + +
299A ALA* 3.9 21.3 - - + +
302A MET* 3.6 24.2 - - + -
303A ARG* 3.3 37.2 - - + +
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Residues in contact with ALA 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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82A ILE 3.0 8.4 + - - +
83A GLU 3.5 8.3 - - - +
85A ILE* 1.3 76.6 - - - +
87A THR* 1.3 58.9 + - - +
89A TYR* 4.4 0.9 - - - -
90A LYS* 2.7 25.6 + - - -
91A TYR* 2.7 34.6 + - - +
93A ILE* 3.8 19.1 - - + -
302A MET* 3.5 26.2 - - + +
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Residues in contact with THR 87 (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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83A GLU* 2.9 22.2 + - - +
84A ASP* 3.6 9.6 + - - -
85A ILE 3.0 0.8 - - - -
86A ALA* 1.3 77.2 - - - +
88A MET* 1.3 58.0 + - + +
90A LYS* 3.2 23.6 + - - +
91A TYR 5.0 0.9 - - - -
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Residues in contact with MET 88 (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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84A ASP 3.4 16.8 - - - +
85A ILE* 3.7 16.8 - - + +
87A THR* 1.3 76.0 - - + +
89A TYR* 1.3 92.2 + - + +
90A LYS* 3.0 12.3 + - - +
303A ARG* 3.6 24.7 - - - +
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Residues in contact with TYR 89 (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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85A ILE* 2.8 38.2 + - + +
86A ALA 4.0 0.9 - - - +
88A MET* 1.3 99.6 - - + +
90A LYS* 1.3 69.3 + - - +
91A TYR* 3.3 40.3 - + + -
302A MET* 5.2 0.4 - - + -
303A ARG* 3.4 30.0 + - + +
306A THR* 3.8 35.7 - - + -
307A LYS* 5.2 3.8 + - - -
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Residues in contact with LYS 90 (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 THR* 3.7 13.9 - - - +
86A ALA 2.7 9.1 + - - -
87A THR* 3.2 12.4 + - - +
88A MET 3.0 12.9 - - - +
89A TYR* 1.3 82.1 - - - +
91A TYR* 1.3 63.1 + - - +
92A ASN* 5.4 1.7 + - - -
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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
------------------------------------------------------------
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