Contacts of the helix formed by residues 82 - 90 (chain B) in PDB entry 1HLG
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 SER 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASN 5.5 0.7 - - - -
74B TRP 3.6 17.7 - - - -
75B ILE* 4.3 4.0 - - - -
76B SER 4.8 0.2 - - - -
77B ASN* 3.1 30.5 + - - +
78B LEU 2.8 20.6 + - - -
79B PRO 4.3 0.2 + - - -
81B ASN* 1.3 77.7 - - - +
83B LEU* 1.3 68.8 + - - +
84B ALA 3.3 0.9 - - - -
85B PHE* 2.9 25.4 + - - -
86B ILE* 3.1 14.0 + - - +
357B ILE 5.8 1.3 - - - -
367B TYR* 4.5 0.9 - - - -
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Residues in contact with LEU 83 (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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63B LEU* 3.8 27.8 - - + -
74B TRP* 4.1 23.6 + - + +
82B SER* 1.3 71.0 - - - +
84B ALA* 1.3 53.2 + - - +
86B ILE* 3.1 9.6 + - + +
87B LEU* 2.7 56.1 + - + +
150B VAL* 4.0 18.8 - - + -
179B LEU* 5.6 0.7 - - + -
367B TYR* 3.6 55.4 + - + +
370B ILE* 4.6 13.2 - - + -
371B VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 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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45B ILE* 4.2 4.1 - - + +
63B LEU* 3.9 14.9 - - + +
74B TRP* 3.0 31.8 + - + +
75B ILE* 3.2 18.2 - - + -
82B SER 3.0 2.2 + - - -
83B LEU* 1.3 75.8 - - - +
85B PHE* 1.3 63.3 + - - +
87B LEU* 3.4 1.9 + - - -
88B ALA* 3.0 22.5 + - - +
94B VAL* 3.6 19.8 - - + +
96B LEU* 4.0 2.9 - - + -
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Residues in contact with PHE 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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19B MET 4.4 0.4 - - - -
20B ILE* 4.2 14.4 - - - -
23B TRP* 3.6 33.0 - + - -
25B TYR* 3.7 42.8 - + - +
45B ILE* 4.2 8.7 - - + -
75B ILE* 3.3 48.5 - - + -
77B ASN 4.4 3.4 - - - -
78B LEU 4.0 0.2 - - - -
79B PRO* 3.5 32.1 - - + +
82B SER* 2.9 19.3 + - - +
84B ALA* 1.3 72.9 - - - +
86B ILE* 1.3 67.9 + - - +
88B ALA* 3.0 5.2 + - - +
89B ASP* 3.0 27.3 + - - +
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Residues in contact with ILE 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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79B PRO 3.8 13.9 + - - +
80B ASN* 4.3 11.4 - - - +
81B ASN* 4.5 1.3 - - - -
82B SER 3.1 27.5 + - - +
83B LEU* 3.6 9.4 - - + +
85B PHE* 1.3 74.9 - - - +
87B LEU* 1.3 62.1 + - - +
89B ASP* 3.3 10.4 + - - +
90B ALA* 2.9 28.9 + - - +
363B PRO* 5.4 3.1 - - + -
367B TYR* 3.9 24.7 - - + -
368B ASN* 4.4 10.5 - - - +
371B VAL* 3.5 29.2 - - + -
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Residues in contact with LEU 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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61B VAL* 3.5 28.9 - - + -
63B LEU* 4.1 15.7 - - + -
83B LEU* 2.7 46.8 + - + +
84B ALA 3.7 4.9 - - - +
86B ILE* 1.3 76.6 - - + +
88B ALA* 1.3 59.8 + - - +
90B ALA* 3.4 4.4 + - - -
92B TYR* 3.1 51.7 + - + +
94B VAL* 3.8 11.4 - - + -
150B VAL* 5.4 1.3 - - + -
370B ILE* 5.3 1.6 - - + -
371B VAL* 4.6 16.2 - - + +
374B ILE* 4.4 19.5 - - + -
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Residues in contact with ALA 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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25B TYR* 4.1 5.2 - - + -
45B ILE* 4.1 16.8 - - + +
47B TYR 3.9 21.1 - - - +
48B GLY* 3.3 9.5 + - - +
51B ASN 3.7 0.7 - - - +
58B ARG* 3.2 16.5 + - - -
84B ALA 3.0 13.3 + - - +
85B PHE 3.0 9.2 + - - +
87B LEU* 1.3 77.9 - - - +
89B ASP* 1.3 58.1 + - - +
91B GLY 3.0 15.6 + - - -
92B TYR 3.8 10.8 - - - +
94B VAL* 3.8 4.9 - - + +
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Residues in contact with ASP 89 (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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25B TYR* 2.5 25.0 + - - -
48B GLY* 3.1 20.3 - - - -
49B LYS* 3.2 16.8 + - - +
51B ASN* 2.6 62.3 + - + +
52B SER* 3.2 8.1 + - - -
79B PRO 4.4 4.0 - - - +
85B PHE 3.0 12.3 + - - +
86B ILE* 3.7 10.2 - - - +
88B ALA* 1.3 75.2 - - - +
90B ALA* 1.3 54.8 + - - +
91B GLY 3.2 0.9 - - - -
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Residues in contact with ALA 90 (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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51B ASN* 5.2 1.1 - - - +
52B SER* 3.7 3.6 - - - -
86B ILE* 2.9 17.2 + - + +
87B LEU* 3.7 5.2 - - - +
88B ALA 3.1 0.6 - - - -
89B ASP* 1.3 74.9 - - - +
91B GLY* 1.3 56.7 + - - +
92B TYR* 3.4 24.7 - - + -
371B VAL* 3.9 23.1 - - + -
379B LYS* 2.9 18.5 + - - -
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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