Contacts of the helix formed by residues 22 - 30 (chain B) in PDB entry 1HXD
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B HIS 3.8 1.4 + - - -
21B SER* 1.3 69.8 - - - +
23B GLU* 1.3 57.3 + - - +
25B LEU* 4.2 9.4 - - - -
26B GLY* 2.6 33.6 + - - -
33B ARG* 4.0 24.4 - - - +
36B ILE* 4.8 4.4 - - - +
56B LYS 3.1 15.0 + - - -
57B GLY* 4.1 1.2 - - - -
58B TYR* 4.6 10.5 - - - -
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Residues in contact with GLU 23 (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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21B SER* 3.0 14.5 + - - +
22B GLY* 1.3 73.0 - - - +
24B GLN* 1.3 70.8 + - + +
27B GLU* 2.8 33.7 + - - +
33B ARG* 3.5 31.9 + - - +
56B LYS* 5.6 4.9 - - - +
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Residues in contact with GLN 24 (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 PHE 4.3 4.8 + - - -
20B HIS* 4.0 26.1 - - - +
21B SER* 2.6 38.2 + - - +
23B GLU* 1.3 74.8 - - + +
25B LEU* 1.3 68.4 + - - +
27B GLU* 2.9 25.8 - - - +
28B THR* 2.6 47.4 + - - +
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Residues in contact with LEU 25 (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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10B LEU* 5.3 6.7 - - + -
13B LEU* 5.1 17.5 - - + -
14B LEU* 4.4 9.4 - - + -
20B HIS* 3.3 39.3 - - + -
21B SER 2.8 21.6 + - - +
22B GLY* 4.0 2.0 - - - +
24B GLN* 1.3 84.2 - - - +
26B GLY* 1.3 63.2 + - - +
28B THR* 3.7 5.3 + - + -
29B LEU* 2.9 33.0 + - + +
36B ILE* 3.7 18.6 - - + -
40B ILE* 5.1 2.2 - - + -
58B TYR* 3.9 29.2 - - + -
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Residues in contact with GLY 26 (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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22B GLY 2.6 20.2 + - - -
23B GLU 3.8 0.4 - - - -
25B LEU* 1.3 74.2 - - - +
27B GLU* 1.3 54.1 - - - +
30B GLY* 2.8 14.4 + - - -
31B MET 2.7 42.4 + - - -
32B SER 4.6 3.4 - - - -
33B ARG 4.8 0.4 - - - -
36B ILE* 3.0 21.7 - - - +
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Residues in contact with GLU 27 (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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23B GLU* 2.8 17.2 + - + +
24B GLN* 2.9 41.5 + - - +
26B GLY* 1.3 78.0 - - - +
28B THR* 1.3 71.8 + - - +
29B LEU 2.8 1.9 + - - -
30B GLY* 3.3 8.4 + - - -
31B MET 4.7 0.4 - - - -
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Residues in contact with THR 28 (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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9B LYS* 5.6 2.9 + - - -
13B LEU* 4.5 14.2 - - + +
24B GLN* 2.6 44.4 + - - +
25B LEU* 4.2 4.9 - - + -
27B GLU* 1.3 83.5 - - - +
29B LEU* 1.3 67.7 + - - +
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Residues in contact with LEU 29 (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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6B VAL* 5.5 4.3 - - + +
9B LYS* 4.3 29.2 - - + +
10B LEU* 4.8 11.7 - - + -
13B LEU* 3.5 27.4 - - + -
25B LEU* 2.9 27.6 - - + +
26B GLY 3.1 0.6 + - - -
27B GLU 3.0 0.8 - - - -
28B THR* 1.3 84.5 - - - +
30B GLY* 1.3 60.8 + - - +
31B MET* 3.7 17.6 - - + +
36B ILE* 3.2 27.8 - - + -
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Residues in contact with GLY 30 (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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26B GLY 2.8 7.3 + - - -
27B GLU 3.3 6.7 + - - -
29B LEU* 1.3 75.9 - - - +
31B MET* 1.3 67.0 + - - +
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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