Contacts of the helix formed by residues 354 - 359 (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 LEU 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ALA* 6.1 1.6 - - + -
152A HIS* 4.2 13.7 - - + -
240A LEU* 3.5 47.8 - - + +
241A PHE* 3.7 20.6 - - + -
244A CYS* 3.8 23.1 + - + +
245A GLY 4.4 4.5 - - - +
251A PHE* 3.8 17.0 - - + -
352A ASN* 3.4 5.6 + - - +
353A HIS* 1.3 84.0 - - + +
355A ASP* 1.3 65.0 + - - +
356A PHE 3.2 2.9 - - - -
357A ILE* 3.3 7.7 + - + +
358A TRP* 3.0 38.5 + - + +
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Residues in contact with ASP 355 (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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247A ASP 5.1 0.2 - - - +
250A ASN* 3.0 37.3 + - - +
251A PHE* 3.2 20.0 - - - -
350A PHE 3.5 1.6 - - - +
351A TYR* 3.1 26.6 - - + -
352A ASN* 2.7 46.4 + - - +
354A LEU* 1.3 78.3 - - - +
356A PHE* 1.3 58.7 + - - +
357A ILE 2.9 2.8 + - - -
359A ALA* 2.8 35.3 + - + +
362A ALA* 4.1 2.1 - - - +
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Residues in contact with PHE 356 (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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74A TRP* 5.2 0.2 - - - -
152A HIS* 4.0 18.2 - - + -
179A LEU* 4.0 24.5 - - + +
180A ALA* 3.8 20.2 - - + -
319A TRP* 3.6 25.4 - - + -
320A ASN 3.3 26.9 - - - -
321A GLY* 3.4 16.4 - - - -
324A ASP* 4.3 1.3 - - - -
348A ILE* 4.4 4.0 - - + -
351A TYR* 3.9 22.0 - + - -
352A ASN 3.5 12.8 - - - -
353A HIS 3.5 15.0 - - - +
354A LEU 3.2 0.4 - - - -
355A ASP* 1.3 75.1 - - - +
357A ILE* 1.3 53.8 + - - +
362A ALA* 4.5 1.1 - - - +
366A VAL* 4.0 19.2 - - + +
367A TYR* 2.7 34.2 + - - -
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Residues in contact with ILE 357 (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 GLY 5.3 0.7 - - - +
73A ASN* 3.2 56.9 - - + +
74A TRP* 4.4 18.2 - - + +
77A ASN* 4.0 6.2 + - - -
81A ASN 5.0 3.8 - - - +
82A SER* 5.9 1.4 - - - -
152A HIS* 2.8 54.1 - - + +
179A LEU* 5.7 0.2 - - + -
354A LEU* 3.3 7.5 + - + +
355A ASP 3.0 0.2 - - - -
356A PHE* 1.3 83.2 - - - +
358A TRP* 1.3 74.2 + - + +
359A ALA 3.8 0.7 - - - -
362A ALA* 5.3 0.6 - - - +
367A TYR* 3.3 14.4 + - - +
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Residues in contact with TRP 358 (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 ASN* 3.5 21.7 + - - -
76A SER* 2.8 28.5 + - - -
77A ASN* 3.8 17.0 + - - +
240A LEU* 3.4 26.9 - - + -
241A PHE* 3.6 22.9 - + - -
251A PHE* 3.8 47.4 - + + +
252A ASN 4.5 1.9 + - - -
259A TYR* 3.4 51.4 + + + -
263A ASN* 3.7 10.8 - - - -
354A LEU* 3.0 23.3 + - + +
357A ILE* 1.3 101.1 - - + +
359A ALA* 1.3 63.7 + - - +
360A MET* 3.5 2.8 + - - +
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Residues in contact with ALA 359 (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 ASN* 5.6 0.9 + - - -
81A ASN* 5.2 4.5 - - - +
250A ASN* 3.3 14.8 - - + -
251A PHE* 4.4 1.1 - - - -
351A TYR* 3.6 27.4 - - + +
355A ASP* 2.8 40.3 + - + +
357A ILE 3.8 0.4 - - - +
358A TRP* 1.3 72.3 - - - +
360A MET* 1.3 64.7 + - - +
361A ASP* 3.2 5.4 - - - +
362A ALA* 3.1 17.2 + - - +
363A PRO* 4.4 1.0 - - - +
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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