Contacts of the helix formed by residues 60 - 69 (chain D) in PDB entry 1H5R
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 ASP 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ALA 5.3 1.0 - - - +
24D VAL* 4.5 2.1 - - - -
25D SER* 3.7 40.5 + - - -
28D LEU* 5.8 0.5 - - - +
56D SER* 3.6 12.1 + - - +
57D THR* 2.7 26.0 + - - +
59D GLN* 1.3 95.6 - - - +
61D THR* 1.3 67.4 + - - +
62D PRO* 3.2 3.1 - - - -
63D ARG* 2.9 24.1 + - + +
64D PHE* 3.1 17.3 + - + -
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE 4.9 0.9 - - - +
56D SER* 3.0 31.7 + - - +
57D THR 2.8 20.7 + - - -
60D ASP* 1.3 76.4 - - - +
62D PRO* 1.3 72.5 - - + +
64D PHE* 3.2 5.9 + - + +
65D GLN* 3.0 22.2 + - - +
80D TYR* 3.7 31.4 - - + -
81D LYS* 3.8 11.8 + - - +
82D VAL* 3.7 17.1 - - + +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PRO 3.4 18.4 - - - +
59D GLN 3.5 7.6 - - - +
60D ASP 3.3 4.0 - - - -
61D THR* 1.3 98.0 - - + +
63D ARG* 1.3 73.3 + - - +
65D GLN* 3.7 12.9 - - + +
66D GLN* 2.9 28.1 + - - +
82D VAL* 5.6 1.1 - - + -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA 5.5 6.7 - - - +
59C GLN* 2.3 34.1 + - - -
63C ARG* 3.3 29.0 - - - +
28D LEU* 3.9 23.1 - - + +
59D GLN* 4.5 11.4 + - + +
60D ASP* 2.9 16.8 + - + +
62D PRO* 1.3 95.5 + - - +
64D PHE* 1.3 66.8 + - - +
66D GLN* 3.0 38.2 + - - +
67D LEU* 3.0 23.6 + - - +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 3.9 6.3 - - + -
25D SER* 3.5 24.2 - - - -
27D GLN* 3.8 18.6 - - + -
28D LEU* 3.5 33.0 - - + -
37D ILE* 3.7 30.1 - - + -
54D ILE* 4.4 7.2 - - + -
56D SER* 3.3 34.8 - - - -
60D ASP* 3.1 27.3 + - + -
61D THR* 3.5 5.2 - - - +
63D ARG* 1.3 77.1 - - - +
65D GLN* 1.3 57.2 + - - +
67D LEU* 3.2 5.7 + - + +
68D LEU* 2.8 39.2 + - + +
80D TYR* 3.6 17.2 + - + -
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR* 3.0 16.5 + - - +
62D PRO* 3.8 12.1 - - + +
63D ARG 3.2 0.2 - - - -
64D PHE* 1.3 76.5 - - - +
66D GLN* 1.3 57.8 + - - +
69D GLY* 2.8 35.4 + - - -
80D TYR* 3.6 44.6 - - + +
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Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C MET 6.0 1.8 - - - +
59C GLN* 2.9 32.9 + - - +
62D PRO 2.9 12.3 + - - +
63D ARG* 3.0 34.9 + - - +
65D GLN* 1.3 77.6 - - - +
67D LEU* 1.3 64.1 + - - +
69D GLY* 4.5 1.6 + - - -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO 4.9 1.6 - - - +
22C MET* 3.8 41.7 - - + +
23C ALA* 4.0 10.5 - - + +
28D LEU* 3.7 28.7 - - + -
35D PRO* 4.3 2.9 - - + -
37D ILE* 5.1 1.6 - - + -
38D TYR* 4.3 29.2 - - + +
63D ARG 3.0 13.7 + - - +
64D PHE* 3.2 8.0 + - + +
66D GLN* 1.3 81.4 - - - +
68D LEU* 1.3 75.5 + - + +
73D GLN* 4.8 3.8 + - - -
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE* 4.5 20.9 - - + -
38D TYR* 4.1 17.3 - - + +
41D LEU* 5.8 6.7 - - + -
54D ILE* 3.5 30.1 - - + -
64D PHE* 2.8 19.7 + - + +
67D LEU* 1.3 84.1 - - + +
69D GLY* 1.3 67.5 + - - +
71D GLY 3.3 8.1 + - - -
73D GLN* 3.1 24.1 + - - +
74D TRP* 3.6 37.5 - - + -
78D LEU* 3.7 11.5 - - + +
80D TYR* 3.4 11.4 - - - +
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLN* 2.8 24.8 + - - -
66D GLN 4.5 0.8 + - - -
67D LEU 3.7 0.8 - - - -
68D LEU* 1.3 79.7 - - - +
70D ASP* 1.3 60.6 + - - -
71D GLY 3.3 0.2 + - - -
73D GLN* 5.2 0.7 - - - -
78D LEU* 3.8 2.1 - - - +
80D TYR* 2.8 27.6 + - - -
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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