Contacts of the helix formed by residues 82 - 90 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASN 5.5 1.3 - - - -
74A TRP 3.7 16.2 - - - -
75A ILE* 4.3 2.0 - - - -
76A SER 4.8 0.2 - - - -
77A ASN* 3.1 33.6 + - - +
78A LEU 2.8 20.3 + - - -
79A PRO 4.3 0.4 + - - -
81A ASN* 1.3 77.4 - - - +
83A LEU* 1.3 68.6 + - - +
84A ALA 3.3 1.1 - - - -
85A PHE* 2.9 29.4 + - - +
86A ILE* 3.1 11.7 + - - +
357A ILE 5.9 1.3 - - - -
367A TYR* 4.5 0.7 - - - -
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Residues in contact with LEU 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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63A LEU* 4.1 8.5 - - + -
74A TRP* 3.8 39.7 + - + +
82A SER* 1.3 70.6 - - - +
84A ALA* 1.3 54.4 + - - +
86A ILE* 3.1 10.9 + - + +
87A LEU* 2.7 60.5 + - + +
150A VAL* 4.0 20.2 - - + -
179A LEU* 5.0 0.9 - - + -
367A TYR* 3.6 49.3 + - + +
370A ILE* 4.6 14.1 - - + -
371A VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 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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45A ILE* 4.3 2.4 - - + +
63A LEU* 3.7 23.8 - - + +
74A TRP* 3.1 8.9 + - + +
75A ILE* 3.0 34.1 - - + -
82A SER 3.0 2.8 + - - -
83A LEU* 1.3 76.1 - - - +
85A PHE* 1.3 61.5 + - - +
87A LEU* 3.4 3.9 + - - +
88A ALA* 3.0 23.9 + - - +
94A VAL* 3.7 18.5 - - + +
96A LEU* 4.1 1.3 - - + -
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Residues in contact with PHE 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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19A MET 4.3 0.2 - - - -
20A ILE* 4.1 13.9 - - + -
23A TRP* 3.5 35.9 - + - -
25A TYR* 3.7 39.4 - + - +
45A ILE* 3.9 14.1 - - + -
74A TRP 4.2 0.2 + - - -
75A ILE* 3.3 44.9 - - + -
77A ASN 4.4 3.1 - - - -
78A LEU 4.0 0.2 - - - -
79A PRO* 3.5 34.3 - - + +
82A SER* 2.9 21.0 + - - +
84A ALA* 1.3 70.7 - - - +
86A ILE* 1.3 67.1 + - - +
88A ALA* 3.1 4.4 + - - +
89A ASP* 3.0 28.9 + - - +
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Residues in contact with ILE 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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79A PRO 3.8 15.7 + - - +
80A ASN* 4.3 11.2 - - - +
81A ASN* 4.3 2.2 - - - +
82A SER 3.1 27.5 + - - +
83A LEU* 3.5 9.6 - - + +
85A PHE* 1.3 75.6 - - - +
87A LEU* 1.3 67.8 + - - +
89A ASP* 3.2 9.6 + - - +
90A ALA* 2.9 23.6 + - + +
363A PRO* 5.6 2.9 - - + -
367A TYR* 3.8 24.2 - - + -
368A ASN* 4.1 12.8 - - - +
371A VAL* 3.5 28.9 - - + -
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Residues in contact with LEU 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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61A VAL* 3.5 30.7 - - + -
63A LEU* 4.0 14.8 - - + -
83A LEU* 2.7 48.3 + - + +
84A ALA 3.6 4.9 - - - +
86A ILE* 1.3 74.9 - - + +
88A ALA* 1.3 61.3 + - - +
90A ALA* 3.3 5.4 + - - -
92A TYR* 3.1 48.2 + - + +
94A VAL* 3.7 13.2 - - + -
150A VAL* 5.4 0.9 - - + -
370A ILE* 5.4 1.3 - - + -
371A VAL* 4.4 16.8 - - + -
374A ILE* 4.2 20.0 - - + -
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Residues in contact with ALA 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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25A TYR* 4.4 3.1 - - + -
45A ILE* 3.8 28.0 - - + -
47A TYR 3.8 12.6 - - - +
48A GLY* 3.2 17.6 + - - +
51A ASN 3.6 0.3 - - - +
58A ARG* 3.5 7.8 + - - -
84A ALA 3.0 13.4 + - - +
85A PHE 3.1 8.0 + - - +
87A LEU* 1.3 76.5 - - - +
89A ASP* 1.3 58.5 + - - +
91A GLY* 3.0 16.1 + - - -
92A TYR 3.7 11.4 - - - +
94A VAL* 3.8 6.0 - - + +
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Residues in contact with ASP 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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25A TYR* 2.6 25.9 + - - -
48A GLY* 3.1 1.6 - - - -
49A LYS* 3.0 36.1 + - - +
51A ASN* 2.9 51.1 + - + +
52A SER* 2.8 19.4 + - - -
79A PRO* 4.4 3.6 - - - +
85A PHE 3.0 14.9 + - - +
86A ILE* 3.2 10.0 + - - +
88A ALA* 1.3 75.4 - - - +
90A ALA* 1.3 52.6 + - - +
91A GLY 3.1 0.7 - - - -
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Residues in contact with ALA 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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51A ASN* 5.4 0.9 - - - +
52A SER* 3.4 3.1 - - - -
86A ILE* 2.9 17.0 + - + +
87A LEU* 3.5 9.2 - - - +
88A ALA 3.1 0.4 - - - -
89A ASP* 1.3 75.0 - - - +
91A GLY* 1.3 57.7 + - - +
92A TYR* 3.4 22.1 - - + -
371A VAL* 3.7 22.0 - - + -
379A LYS* 2.9 18.4 + - - +
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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