Contacts of the helix formed by residues 47 - 54 (chain A) in PDB entry 1HDZ
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 GLY 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A CYS* 1.4 68.9 - - - +
48A THR* 1.3 58.7 + - - +
49A ASP 3.2 0.2 - - - -
50A ASP* 3.2 11.6 + - - +
51A HIS* 2.9 36.7 + - - -
362A LEU* 4.9 4.1 - - - +
369A ARG* 4.5 0.2 - - - +
377A NAD 3.0 44.8 + - - -
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Residues in contact with THR 48 (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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46A CYS 3.2 0.6 + - - -
47A GLY* 1.3 73.5 - - - +
49A ASP* 1.4 62.3 + - - +
51A HIS* 2.9 21.7 + - + +
52A VAL* 3.4 9.9 + - - +
57A LEU* 3.6 23.7 - - + +
67A HIS* 3.8 18.8 - - + +
93A PHE* 6.1 3.1 - - + -
116A LEU* 5.3 5.6 - - + -
140A PHE* 4.3 10.8 - - + -
141A LEU* 4.6 8.5 - - + -
294A VAL* 5.0 8.1 - - + -
376A ZN 3.5 4.0 - - - -
377A NAD 3.0 41.4 + - - +
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Residues in contact with ASP 49 (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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44A GLY 4.2 3.3 - - - +
46A CYS* 3.0 27.1 + - - +
48A THR* 1.4 75.5 - - - +
50A ASP* 1.3 62.9 + - - +
52A VAL* 3.3 13.9 + - - +
53A VAL* 3.4 14.2 + - - +
65A LEU* 3.8 7.5 - - + +
66A GLY* 3.2 24.5 + - - -
67A HIS* 2.9 32.1 + - - -
140A PHE* 3.4 11.2 - - - -
146A PHE* 3.7 14.3 - - + -
359A PHE* 4.0 19.1 - - + -
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Residues in contact with ASP 50 (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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46A CYS 3.4 1.8 + - - -
47A GLY* 3.2 14.0 + - - +
49A ASP* 1.3 80.4 - - - +
51A HIS* 1.3 57.4 + - - +
53A VAL* 3.2 6.3 + - - +
54A SER* 2.8 36.0 + - - -
359A PHE* 3.0 26.5 - - + -
362A LEU* 3.8 18.1 - - + +
363A HIS* 2.7 40.5 + - - -
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Residues in contact with HIS 51 (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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47A GLY* 2.9 21.5 + - - -
48A THR* 2.9 11.3 + - + +
50A ASP* 1.3 79.1 + - - +
52A VAL* 1.3 56.0 + - - +
54A SER* 3.0 8.5 + - - -
55A GLY 3.0 8.3 + - - -
56A ASN* 2.9 49.7 + - + -
57A LEU* 3.4 17.2 + - + -
269A ILE 4.0 9.0 - - - -
270A GLY* 5.3 1.3 - - - -
294A VAL* 3.8 25.9 + - + -
377A NAD 2.6 47.9 + - - -
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Residues in contact with VAL 52 (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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14A LEU* 4.2 14.2 - - + +
17A VAL* 3.8 14.5 - - + +
48A THR 3.8 3.1 - - - +
49A ASP 3.3 6.5 + - - +
50A ASP 3.3 0.4 - - - -
51A HIS* 1.3 72.3 - - - +
53A VAL* 1.3 67.5 + - - +
55A GLY* 3.5 7.6 + - - -
57A LEU* 3.6 30.0 - - + +
59A THR* 3.4 26.2 - - + +
61A LEU* 4.8 2.5 - - + -
63A VAL* 4.5 0.7 - - + -
65A LEU* 3.9 16.2 - - + -
140A PHE* 3.4 37.0 - - + -
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Residues in contact with VAL 53 (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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14A LEU* 4.2 12.3 - - + -
17A VAL* 3.3 2.8 - - - +
18A LYS* 2.8 35.8 + - - +
19A LYS 4.2 18.8 - - - +
21A PHE* 3.7 34.3 - - + -
49A ASP 3.5 14.6 - - - +
50A ASP* 3.2 15.5 + - - +
52A VAL* 1.3 79.4 - - - +
54A SER* 1.3 61.1 + - - +
65A LEU* 4.2 3.8 - - + -
359A PHE* 4.2 6.1 - - + -
363A HIS* 5.5 8.5 - - + -
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Residues in contact with SER 54 (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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18A LYS* 3.0 29.2 + - - +
50A ASP* 2.8 28.1 + - - -
51A HIS* 3.0 17.2 + - - -
52A VAL 3.2 0.2 - - - -
53A VAL* 1.3 78.8 - - - +
55A GLY* 1.3 56.5 + - - +
56A ASN* 3.3 21.3 + - - +
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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