Contacts of the helix formed by residues 77 - 84 (chain D) in PDB entry 5HP1
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 PHE 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D THR* 3.8 15.9 - - + -
75D VAL* 3.0 39.9 + - + -
76D ASP* 1.3 70.0 + - - +
78D ARG* 1.3 53.2 + - - +
79D GLU 3.3 2.0 - - - -
80D LEU* 3.3 33.4 + - + -
81D ASN* 2.7 45.3 + - - +
128D THR* 4.4 15.5 - - - -
146D TYR* 4.4 10.1 - + - -
150D PRO* 3.7 30.3 - - + -
151D GLN 3.3 27.6 - - - -
152D GLY* 3.5 26.7 + - - +
153D TRP* 3.6 5.2 - - + -
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Residues in contact with ARG 78 (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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24D TRP* 5.2 1.8 - - - -
76D ASP* 2.7 42.0 + - - +
77D PHE* 1.3 76.9 - - - +
79D GLU* 1.3 62.5 + - - +
81D ASN* 3.4 9.2 + - - +
82D LYS* 3.1 29.4 + - - +
402D TRP* 4.6 5.7 - - - -
411D ILE* 3.1 40.3 - - + +
412D PRO 3.1 24.0 + - - -
413D GLU* 4.3 9.0 - - - +
414D TRP* 3.4 31.5 - - - -
1H GLC 3.2 51.5 + - - +
2H FRU 4.5 2.4 + - - -
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Residues in contact with GLU 79 (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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19D PRO* 3.8 21.5 - - + -
20D LYS 5.1 0.2 - - - +
21D VAL* 4.0 20.6 - - + +
58D THR* 5.6 1.1 - - + +
76D ASP 4.5 3.2 + - - +
77D PHE 3.3 0.2 - - - -
78D ARG* 1.3 78.7 - - - +
80D LEU* 1.3 63.4 + - - +
82D LYS* 3.2 18.2 + - - +
83D ARG* 2.8 68.0 + - - +
1H GLC 2.4 40.4 + - - +
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Residues in contact with LEU 80 (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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12D LEU* 4.4 7.4 - - + -
19D PRO* 3.9 24.4 - - + +
58D THR* 4.7 0.8 + - - +
77D PHE* 3.3 41.5 + - + +
79D GLU* 1.3 77.9 - - - +
81D ASN* 1.3 59.6 + - - +
83D ARG* 3.0 5.4 + - + +
84D THR* 2.6 44.2 + - - +
124D PHE* 3.9 9.9 - - + -
127D TYR* 3.9 33.0 - - + +
128D THR* 4.2 13.0 - - + -
153D TRP* 3.6 20.4 - - + +
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Residues in contact with ASN 81 (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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77D PHE 2.7 28.6 + - - +
78D ARG* 3.7 8.7 - - - +
80D LEU* 1.3 72.5 - - - +
82D LYS* 1.3 62.2 + - + +
83D ARG 3.4 0.7 + - - -
84D THR* 3.5 3.3 + - - -
152D GLY 3.2 20.7 + - - -
153D TRP* 3.1 13.9 - - - -
154D LYS* 2.6 73.6 + - + +
184D MET* 4.7 8.0 - - + +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D LYS* 3.9 22.5 + - - +
16D MET* 4.4 6.4 - - - +
78D ARG 3.1 22.9 + - - +
79D GLU* 3.9 13.2 + - - +
81D ASN* 1.3 76.9 - - + +
83D ARG* 1.3 61.5 + - + +
84D THR 3.5 0.2 - - - -
154D LYS* 5.3 0.7 - - - +
413D GLU* 2.3 46.6 + - - +
1H GLC 3.1 23.9 + - - -
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Residues in contact with ARG 83 (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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12D LEU* 3.4 16.0 - - + +
13D LYS* 3.1 25.4 + - - +
16D MET* 4.2 25.4 - - + +
17D ASP* 2.7 52.3 + - - +
18D GLY* 3.6 18.6 + - - -
19D PRO* 4.2 2.9 - - - -
20D LYS 5.8 0.8 - - - +
79D GLU* 2.8 49.3 + - - +
80D LEU* 3.0 8.9 + - + +
82D LYS* 1.3 78.6 - - + +
84D THR* 1.3 59.9 + - - +
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Residues in contact with THR 84 (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 VAL* 4.2 10.1 - - + -
11D LYS 4.8 0.2 - - - +
12D LEU* 4.6 4.0 - - - +
13D LYS* 3.3 9.6 - - - -
80D LEU* 2.6 30.0 + - - +
81D ASN 3.5 6.1 + - - -
83D ARG* 1.3 78.6 - - - +
85D GLN* 1.3 77.6 + - - +
86D ASP 3.3 1.0 + - - -
87D PHE* 4.0 11.0 - - + -
124D PHE* 3.8 6.0 - - + -
153D TRP* 3.1 43.7 + - + +
154D LYS* 3.2 20.5 + - - -
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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