Contacts of the helix formed by residues 85 - 94 (chain D) in PDB entry 4HXD
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 SER 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.7 1.8 - - - -
83D GLY 3.5 5.2 + - - -
84D ILE* 1.3 80.2 - - - +
86D LYS* 1.3 76.8 + - - +
87D ASP* 3.5 8.1 + - - +
88D GLU* 3.1 29.1 + - - +
89D TYR* 3.0 17.5 + - - +
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Residues in contact with LYS 86 (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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69D ALA* 4.9 7.6 - - + +
70D GLU* 6.1 1.3 - - - +
73D TYR* 3.5 34.0 - - + -
74D ASP* 3.2 34.2 + - - +
85D SER* 1.3 79.3 - - - +
87D ASP* 1.3 91.7 + - - +
89D TYR* 3.1 4.7 + - - +
90D ILE* 3.1 27.4 + - + +
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Residues in contact with ASP 87 (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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85D SER* 3.3 6.7 + - - +
86D LYS* 1.3 109.2 + - - +
88D GLU* 1.3 62.4 + - - +
89D TYR 3.3 0.2 + - - -
90D ILE* 3.2 29.7 - - + +
91D LYS* 3.4 15.7 + - - +
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Residues in contact with GLU 88 (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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84D ILE* 4.1 18.4 - - + +
85D SER* 3.1 20.9 + - - +
87D ASP* 1.3 76.9 - - - +
89D TYR* 1.3 65.5 + - - +
91D LYS* 3.4 32.3 + - - +
92D VAL* 3.4 19.6 + - - +
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Residues in contact with TYR 89 (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 LEU* 3.6 10.2 - - + +
69D ALA* 4.4 5.4 - - + -
73D TYR* 3.5 30.3 - + + +
84D ILE* 3.9 8.3 - - + +
85D SER 3.0 13.1 + - - +
86D LYS 3.3 9.0 - - - +
87D ASP 3.1 0.4 - - - -
88D GLU* 1.3 73.7 - - - +
90D ILE* 1.3 86.9 + - + +
91D LYS 3.0 1.6 - - - -
92D VAL* 2.8 14.0 + - + +
93D ALA* 2.8 45.2 + - + +
103D LEU* 3.6 16.8 - - + -
104D GLU* 2.6 41.4 + - - +
107D MET* 3.4 27.1 - - + +
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Residues in contact with ILE 90 (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 LEU* 5.4 1.1 - - + +
66D GLN* 3.9 36.3 - - - +
69D ALA* 4.4 15.3 - - + -
70D GLU* 6.0 2.5 - - - +
86D LYS* 3.1 12.1 + - + +
87D ASP* 3.2 30.1 - - + +
89D TYR* 1.3 95.1 - - + +
91D LYS* 1.3 64.4 + - + +
93D ALA* 4.3 1.6 - - - +
94D MET* 2.9 48.2 + - + +
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Residues in contact with LYS 91 (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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87D ASP* 3.4 17.2 + - - +
88D GLU* 3.4 39.9 + - + +
89D TYR 2.9 0.2 + - - -
90D ILE* 1.3 82.9 - - + +
92D VAL* 1.3 57.8 + - + +
95D LYS* 3.5 25.2 + - - +
201D SO4 3.6 31.4 + - - +
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Residues in contact with VAL 92 (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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84D ILE* 6.0 1.3 - - + -
88D GLU 3.4 13.5 - - - +
89D TYR* 2.8 25.0 + - + +
91D LYS* 1.3 75.5 - - + +
93D ALA* 1.3 59.7 + - + +
94D MET 3.4 0.9 - - - -
95D LYS* 2.9 34.5 - - + +
98D GLU* 3.3 29.9 - - - +
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Residues in contact with ALA 93 (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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42D TYR* 4.8 5.0 + - - +
62D LYS* 3.0 24.3 + - - -
65D LEU* 4.7 7.2 - - + -
89D TYR* 2.8 58.8 + - + +
90D ILE* 4.4 0.9 - - - -
92D VAL* 1.3 75.2 - - + +
94D MET* 1.3 56.6 + - + +
95D LYS 3.1 3.3 + - - +
98D GLU* 3.7 14.2 - - - +
99D TRP 5.6 2.9 - - - +
104D GLU* 4.8 2.9 - - - +
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Residues in contact with MET 94 (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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62D LYS* 3.4 56.5 + - + +
63D GLU* 4.5 3.1 - - - +
65D LEU* 4.5 9.2 - - - -
66D GLN* 3.6 36.6 - - + +
90D ILE* 2.9 34.9 + - + +
93D ALA* 1.3 73.2 - - + +
95D LYS* 1.3 64.1 + - - +
96D ASP* 3.5 2.4 + - - -
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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