Contacts of the helix formed by residues 71 - 88 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.8 12.4 + - - +
68B ASP* 4.3 2.6 + - - +
69B LEU 4.1 0.2 - - - -
70B ASN* 1.3 85.6 - - - +
72B ARG* 1.3 65.9 - - - +
73B PHE* 3.2 31.6 - - - +
74B TYR* 3.8 19.0 + - + +
75B ALA* 3.3 20.1 + - - +
235B ASN* 5.7 3.2 + - - +
237B LEU* 4.1 10.2 - - - +
263B ASP* 3.7 16.4 + - - +
265B ASN* 3.2 22.4 + - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 4.4 2.8 - - - +
70B ASN 3.8 0.4 + - - -
71B ASN* 1.3 75.6 + - - +
73B PHE* 1.3 66.4 + - - +
75B ALA* 4.6 3.4 - - - -
76B GLN* 2.9 53.0 + - + +
263B ASP* 3.2 22.3 + - + +
264B ASN* 3.5 25.8 + - - +
265B ASN* 3.6 24.5 + - - +
266B ILE* 4.5 6.0 - - - +
279B ASP* 3.4 31.0 + - - -
281B ASN* 5.6 0.6 - - - +
282B PRO* 3.5 20.7 - - + +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 3.2 20.8 - - - +
72B ARG* 1.3 80.0 - - - +
74B TYR* 1.3 85.5 + + + +
77B ILE* 3.1 52.8 + - + +
141B ASP* 3.5 37.5 - - + -
154B SER* 5.9 1.6 - - - -
263B ASP* 5.0 7.0 - - + +
280B GLN* 3.5 44.9 - - + -
282B PRO* 3.4 14.5 - - + +
285B ILE* 4.0 17.0 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 4.7 4.7 - - + -
67B PRO* 3.6 41.0 - - + +
68B ASP* 3.2 27.1 - - - +
69B LEU* 4.6 1.3 - - - -
71B ASN* 3.8 19.7 + - + +
73B PHE* 1.3 105.3 - + + +
75B ALA* 1.3 65.6 + - - +
77B ILE* 3.7 5.4 - - + +
78B ILE* 3.0 29.2 + - - +
123B SER* 5.0 5.0 - - - -
140B TYR* 4.0 26.7 - + - -
141B ASP* 3.9 15.5 + - - -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.4 25.5 - - + +
70A ASN* 4.2 13.2 - - - +
69B LEU* 3.3 29.2 + - - +
70B ASN 4.7 1.1 - - - +
71B ASN 3.3 18.6 + - - +
72B ARG* 4.1 3.8 - - - +
74B TYR* 1.3 77.0 - - - +
76B GLN* 1.3 58.6 + - + +
78B ILE 3.4 0.7 + - - -
79B ASP* 2.9 27.2 + - - +
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 2.6 37.0 + - - +
72B ARG* 2.9 51.4 + - + +
75B ALA* 1.3 76.0 - - + +
77B ILE* 1.3 60.3 + - - +
79B ASP* 3.5 12.6 + - - +
80B GLY 2.9 24.1 + - - -
282B PRO* 3.5 21.5 - - + +
283B LYS* 3.4 40.5 + - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 5.5 0.9 - - + -
73B PHE* 3.1 59.7 + - + +
74B TYR* 3.3 7.4 + - + +
76B GLN* 1.3 75.8 - - - +
78B ILE* 1.3 61.3 + - + +
80B GLY 3.2 1.7 + - - -
81B ILE* 2.9 45.3 + - + +
140B TYR* 3.7 40.6 - - + -
282B PRO* 3.5 23.3 - - + +
285B ILE* 4.2 9.9 - - + -
286B GLY* 3.4 10.1 - - - -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.6 7.0 - - + -
96A PHE* 3.5 35.0 - - + -
64B ILE* 3.6 25.8 - - + -
66B ILE* 3.5 34.3 - - + -
69B LEU* 3.4 22.2 - - + -
74B TYR 3.0 17.2 + - - +
75B ALA 3.7 4.3 - - - +
77B ILE* 1.3 75.0 - - + +
79B ASP* 1.3 59.1 + - - +
81B ILE* 3.2 9.7 + - + +
82B GLN* 2.8 29.7 + - + +
94B ILE* 4.6 5.6 - - + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.3 15.2 - - + +
70A ASN* 3.1 26.1 + - - +
75B ALA 2.9 17.9 + - - +
76B GLN* 3.5 14.0 + - - +
77B ILE 3.2 0.2 - - - -
78B ILE* 1.3 74.7 - - - +
80B GLY* 1.3 63.6 + - - +
82B GLN* 3.0 24.0 + - - +
83B GLU* 3.0 24.4 + - - +
283B LYS* 2.8 27.5 + - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN 2.9 11.7 + - - -
77B ILE 3.2 2.4 + - - -
79B ASP* 1.3 79.0 - - - +
81B ILE* 1.3 62.1 + - - +
83B GLU* 3.5 4.0 + - - +
84B VAL* 3.4 26.2 + - - +
283B LYS* 3.6 28.9 - - - +
287B GLN* 3.6 16.1 - - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.7 36.6 - - + -
77B ILE* 2.9 38.2 + - + +
78B ILE* 3.7 7.4 - - + +
80B GLY* 1.3 76.1 - - - +
82B GLN* 1.3 63.3 + - - +
84B VAL* 3.2 3.6 + - - +
85B ILE* 3.0 37.2 + - + +
121B ILE* 3.8 44.6 - - + -
140B TYR* 5.0 0.4 - - + -
286B GLY* 3.3 20.2 - - - +
289B ALA* 4.7 1.3 - - + -
290B ALA* 4.2 2.7 - - + -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.6 0.9 - - + +
96A PHE* 3.5 46.9 - - + +
98A THR* 6.0 1.7 - - - +
64B ILE* 6.3 0.4 - - + -
78B ILE* 2.8 24.6 + - + +
79B ASP* 3.0 34.1 + - - +
81B ILE* 1.3 71.8 - - - +
83B GLU* 1.3 85.0 + - - +
85B ILE* 3.9 10.3 - - + -
86B GLN* 2.9 55.1 + - - +
92B ALA* 5.7 2.2 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP* 3.0 16.6 + - - +
80B GLY* 3.6 4.5 - - - +
81B ILE 3.2 0.2 - - - -
82B GLN* 1.3 95.7 + - - +
84B VAL* 1.3 63.0 + - + +
86B GLN* 4.8 0.5 - - - +
87B LYS* 3.6 19.4 + - - +
283B LYS* 3.7 21.4 + - - +
287B GLN* 2.8 31.8 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY 3.4 13.7 + - - +
81B ILE 3.2 2.3 + - - +
83B GLU* 1.3 81.0 - - + +
85B ILE* 1.3 61.8 + - - +
87B LYS* 3.5 16.6 - - - +
88B GLU* 3.7 11.4 - - + +
287B GLN* 3.9 21.1 - - + +
290B ALA* 3.6 22.7 - - + -
291B HIS* 3.7 41.3 - - + +
294B LEU* 4.1 15.0 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 4.0 35.2 - - + -
64B ILE* 4.8 0.2 - - + -
81B ILE* 3.0 34.0 + - + +
82B GLN* 3.9 7.9 - - - -
84B VAL* 1.3 73.9 - - + +
86B GLN* 1.3 71.3 + - + +
87B LYS 3.1 1.8 - - - -
88B GLU* 3.1 9.2 + - - +
90B TYR* 3.0 45.4 + - + +
91B THR 4.5 0.2 - - - -
92B ALA* 4.3 25.1 - - + +
121B ILE* 5.4 1.3 - - + -
290B ALA* 3.8 21.5 - - + +
293B LEU* 5.9 2.0 - - + -
294B LEU* 5.2 8.5 - - + -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE 4.3 2.8 + - - -
95A SER* 3.8 9.3 + - - +
96A PHE* 2.9 61.7 - - - +
98A THR* 5.5 4.0 - - - +
82B GLN* 2.9 34.6 + - + +
83B GLU 4.8 0.7 - - - +
85B ILE* 1.3 79.5 - - + +
87B LYS* 1.3 62.7 + - - +
89B GLY* 3.0 13.7 + - - -
90B TYR 3.5 18.6 - - - +
91B THR* 5.3 2.6 - - - +
92B ALA* 5.5 2.8 - - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU 3.6 14.2 + - - +
84B VAL* 3.5 13.7 + - - +
85B ILE 3.1 0.2 - - - -
86B GLN* 1.3 80.0 - - - +
88B GLU* 1.3 71.4 + - - +
89B GLY 3.4 0.9 + - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.3 20.4 + - - -
84B VAL* 3.7 13.7 - - + +
85B ILE* 3.1 8.5 + - - +
86B GLN 3.0 0.8 - - - -
87B LYS* 1.3 100.6 - - - +
89B GLY* 1.3 57.8 + - - -
90B TYR* 3.4 18.7 - - + -
294B LEU* 4.3 18.6 - - + -
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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
------------------------------------------------------------
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