Contacts of the helix formed by residues 71 - 88 (chain A) in PDB entry 3HS3
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 ASN 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP* 3.2 27.8 + - - +
69A LEU 4.0 0.9 - - - +
70A ASN* 1.3 79.0 - - - +
72A ARG* 1.3 64.9 + - - +
73A PHE* 2.9 36.1 + - - +
74A TYR* 3.0 27.4 + - + -
75A ALA* 3.1 10.7 + - - +
179A TRP* 6.0 3.0 - - - -
235A ASN* 5.5 6.1 - - - +
263A ASP* 4.7 9.6 + - - +
265A ASN* 4.9 6.2 + - - -
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Residues in contact with ARG 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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70A ASN 3.6 5.3 + - - +
71A ASN* 1.3 73.5 + - - +
73A PHE* 1.3 61.0 + - - +
74A TYR 3.4 0.2 - - - -
75A ALA* 3.7 8.5 - - - -
76A GLN* 3.0 44.0 + - - +
265A ASN* 4.0 23.1 - - - +
266A ILE* 3.6 40.6 - - - +
70B ASN* 3.4 43.8 + - - +
71B ASN* 3.8 25.7 + - - +
72B ARG 4.4 1.4 - - - +
237B LEU* 4.4 16.0 - - - +
265B ASN* 4.3 9.7 + - - +
266B ILE* 5.5 9.4 - - - +
267B LEU* 6.1 0.8 - - - +
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Residues in contact with PHE 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 ASN* 2.9 20.9 + - - +
72A ARG* 1.3 79.5 - - - +
74A TYR* 1.3 86.8 + + - +
76A GLN* 3.4 5.9 + - - +
77A ILE* 3.2 47.4 + - + +
141A ASP* 3.6 23.8 - - + -
154A SER* 5.9 0.2 - - - -
263A ASP* 5.0 13.7 - - + +
265A ASN* 5.5 0.4 - - - +
280A GLN* 3.7 51.4 - - + -
282A PRO* 3.5 24.1 - - + +
285A ILE* 4.0 11.2 - - + -
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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
----------------------------------------------------------
66A ILE* 3.6 17.7 - - + -
67A PRO* 3.5 27.0 - - + +
68A ASP* 3.3 45.1 - - + +
71A ASN* 3.0 17.9 + - + -
73A PHE* 1.3 98.8 - + - +
75A ALA* 1.3 66.1 + - - +
77A ILE* 3.2 5.3 + - + +
78A ILE* 3.0 28.4 + - - +
123A SER* 5.0 0.4 - - - -
140A TYR* 3.9 29.6 - + - +
141A ASP* 3.5 22.2 + - - -
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Residues in contact with ALA 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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66A ILE* 4.8 1.0 - - - +
69A LEU 4.7 3.6 + - - +
71A ASN 3.1 13.0 + - - +
72A ARG* 3.6 11.4 - - - +
74A TYR* 1.3 79.4 - - - +
76A GLN* 1.3 57.3 + - - +
78A ILE* 3.5 4.8 + - - +
79A ASP* 3.0 26.6 + - - +
69B LEU* 3.1 49.8 + - + +
70B ASN* 3.8 13.1 + - - +
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Residues in contact with GLN 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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72A ARG* 3.0 32.6 + - - +
73A PHE* 4.5 1.2 - - - +
75A ALA* 1.3 75.7 - - - +
77A ILE* 1.3 63.2 + - - +
79A ASP* 3.4 8.4 + - - +
80A GLY 3.0 17.2 + - - -
264A ASN 5.4 5.1 + - - -
265A ASN* 5.7 4.2 - - - +
266A ILE 5.9 0.8 - - - +
282A PRO* 3.6 34.1 - - + +
283A LYS* 3.5 19.7 + - + +
70B ASN* 3.2 21.5 - - - +
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Residues in contact with ILE 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 PHE* 3.2 48.8 + - + +
74A TYR* 3.2 10.3 + - + +
76A GLN* 1.3 75.6 - - - +
78A ILE* 1.3 64.7 + - + +
80A GLY 3.1 2.3 + - - -
81A ILE* 2.9 32.7 + - + +
140A TYR* 3.8 42.2 - - + -
141A ASP* 5.2 0.2 - - + -
282A PRO* 3.5 23.8 - - + +
285A ILE* 4.0 11.2 - - + -
286A GLY* 3.3 18.5 - - - +
289A ALA* 5.9 0.2 - - + -
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Residues in contact with ILE 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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64A ILE* 4.8 17.9 - - + -
66A ILE* 3.3 46.2 - - + -
74A TYR* 3.0 14.8 + - + +
75A ALA 3.8 4.9 - - - +
77A ILE* 1.3 76.1 - - + +
79A ASP* 1.3 65.9 + - - +
81A ILE* 3.1 9.5 + - + +
82A GLN* 2.9 23.8 + - + +
94A ILE* 4.5 14.6 - - + -
140A TYR* 5.8 2.0 - - - +
69B LEU* 3.6 21.1 - - + +
96B PHE* 3.7 32.8 - - + -
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Residues in contact with ASP 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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75A ALA 3.0 17.8 + - - +
76A GLN* 3.6 10.1 - - - +
77A ILE 3.2 0.2 - - - -
78A ILE* 1.3 76.2 - - - +
80A GLY* 1.3 62.6 + - - +
82A GLN* 3.1 44.8 + - - +
83A GLU* 3.1 11.4 + - - +
283A LYS* 4.5 19.9 + - - +
67B PRO 5.4 0.5 - - - +
68B ASP* 4.6 16.8 - - + +
70B ASN* 4.6 13.6 + - - +
96B PHE* 6.4 0.4 - - - -
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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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76A GLN 3.0 12.0 + - - -
77A ILE 3.1 3.8 + - - -
79A ASP* 1.3 78.9 - - - +
81A ILE* 1.3 61.4 + - - +
83A GLU* 3.6 3.2 + - - +
84A VAL* 3.5 25.3 + - - +
283A LYS* 3.6 27.6 - - - +
287A GLN* 3.6 17.1 - - - +
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Residues in contact with ILE 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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62A ILE* 5.5 0.2 - - + -
64A ILE* 3.7 37.7 - - + -
77A ILE* 2.9 32.4 + - + +
78A ILE* 3.1 11.4 + - + +
80A GLY* 1.3 76.1 - - - +
82A GLN* 1.3 63.8 + - - +
84A VAL* 3.1 4.5 + - - +
85A ILE* 3.0 35.2 + - + +
121A ILE* 3.8 44.6 - - + -
140A TYR* 4.9 1.8 - - + -
286A GLY* 3.4 21.1 - - - +
289A ALA* 4.7 0.9 - - + -
290A ALA* 4.2 2.7 - - + -
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Residues in contact with GLN 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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64A ILE* 5.7 1.1 - - + +
78A ILE* 2.9 19.8 + - + +
79A ASP* 3.1 39.0 + - - +
81A ILE* 1.3 70.4 - - - +
83A GLU* 1.3 84.6 + - - +
85A ILE* 3.8 12.1 - - + -
86A GLN* 2.9 55.6 + - + +
92A ALA* 5.7 2.0 - - + -
67B PRO 5.6 1.6 + - - -
96B PHE* 3.5 45.5 - - + +
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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 ASP* 3.1 17.5 + - - +
80A GLY 3.7 4.0 - - - +
81A ILE 3.2 0.2 - - - -
82A GLN* 1.3 94.8 - - - +
84A VAL* 1.3 64.4 + - + +
86A GLN* 4.7 1.1 - - - +
87A LYS* 3.7 18.9 + - - +
283A LYS* 3.5 22.7 + - - -
287A GLN* 2.7 32.4 + - - +
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Residues in contact with VAL 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 GLY 3.5 14.1 + - - +
81A ILE 3.1 1.6 + - - +
83A GLU* 1.3 79.3 - - + +
85A ILE* 1.3 65.1 + - - +
87A LYS* 3.5 16.1 + - - +
88A GLU* 3.7 11.2 - - + +
287A GLN* 3.8 23.3 - - + +
290A ALA* 3.5 23.1 - - + -
291A HIS* 3.6 41.7 - - + +
294A LEU* 4.0 14.4 - - + -
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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
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62A ILE* 4.0 35.0 - - + -
64A ILE* 4.7 0.7 - - + -
81A ILE* 3.0 34.4 + - + +
82A GLN* 3.8 8.5 - - - -
84A VAL* 1.3 75.9 - - + +
86A GLN* 1.3 71.9 + - + +
88A GLU* 3.0 11.5 + - - -
90A TYR* 3.0 41.4 + - + +
91A THR 4.5 0.2 - - - -
92A ALA* 4.3 25.1 - - + +
121A ILE* 5.3 0.9 - - + -
290A ALA* 3.9 22.0 - - + +
293A LEU* 5.6 2.2 - - + -
294A LEU* 5.2 8.3 - - + -
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Residues in contact with GLN 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 GLN* 2.9 40.2 + - + +
83A GLU* 4.7 1.3 - - - +
85A ILE* 1.3 75.3 - - + +
87A LYS* 1.3 62.3 + - - +
89A GLY* 3.0 13.3 + - - -
90A TYR 3.6 18.1 + - - +
91A THR* 5.5 1.8 - - - +
92A ALA* 5.4 3.4 - - + +
94B ILE 4.2 2.8 + - - -
95B SER* 3.7 9.2 - - - +
96B PHE* 2.9 59.8 - - - +
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Residues in contact with LYS 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 3.7 13.2 + - - +
84A VAL* 3.5 12.3 + - - +
85A ILE 3.2 0.4 - - - -
86A GLN* 1.3 78.6 - - - +
88A GLU* 1.3 73.1 + - - +
89A GLY 3.3 0.8 + - - -
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Residues in contact with GLU 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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60A LYS* 3.3 18.9 + - - -
84A VAL* 3.7 14.0 - - + +
85A ILE 3.0 8.7 + - - +
87A LYS* 1.3 99.7 - - - +
89A GLY* 1.3 58.4 + - - +
90A TYR* 3.4 19.9 + - + -
294A LEU* 4.3 20.0 - - + -
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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