Contacts of the helix formed by residues 71 - 77 (chain D) in PDB entry 1XHU
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 ILE 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D PRO 3.9 13.0 - - - +
69D ALA* 3.4 11.2 + - - +
70D ILE* 1.3 78.1 - - - +
72D GLY* 1.3 80.2 + - - +
75D ALA* 2.9 18.8 - - - +
76D ARG* 3.7 21.5 - - - +
97D GLU* 5.0 7.0 - - - +
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Residues in contact with GLY 72 (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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71D ILE* 1.3 89.3 - - - +
73D HIS* 1.3 70.0 + - - -
74D GLU* 3.0 5.4 + - - -
75D ALA 3.1 1.0 + - - -
76D ARG* 3.0 25.5 + - - +
96D THR 4.7 0.2 - - - -
97D GLU* 3.0 21.0 + - - -
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Residues in contact with HIS 73 (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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72D GLY* 1.3 72.0 - - - +
74D GLU* 1.3 80.6 + - + +
76D ARG* 3.8 0.2 - - - +
77D TYR* 2.8 38.8 + + + -
93D LYS* 3.2 61.7 - - + +
96D THR* 3.6 24.5 - - - -
97D GLU* 2.5 26.2 + - + +
13L G 4.3 14.3 + - - -
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Residues in contact with GLU 74 (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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72D GLY* 4.8 2.0 - - - -
73D HIS* 1.3 98.1 + - + +
75D ALA* 1.3 63.6 + - - +
77D TYR* 3.6 12.8 + - - +
78D LYS* 3.7 14.6 + - - +
13L G 6.0 1.6 - - - +
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Residues in contact with ALA 75 (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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70D ILE* 3.4 23.8 - - + +
71D ILE 2.9 25.8 + - - +
72D GLY 3.1 2.0 + - - -
74D GLU* 1.3 76.6 - - - +
76D ARG* 1.3 63.7 + - - +
78D LYS* 3.0 24.7 - - - +
79D LEU* 4.0 2.1 + - - +
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Residues in contact with ARG 76 (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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64D PHE* 4.1 24.6 - - + +
68D PRO 5.2 1.8 + - - -
70D ILE* 2.9 29.8 + - - +
71D ILE* 3.7 26.9 - - - +
72D GLY 3.0 16.3 + - - +
75D ALA* 1.3 72.2 - - - +
77D TYR* 1.3 53.0 + - - +
78D LYS 2.5 16.9 + - - -
79D LEU* 2.5 41.3 + - + +
80D PHE* 4.1 0.7 + - - -
96D THR* 2.6 55.0 + - + -
97D GLU* 3.3 8.9 + - - +
99D TRP* 2.7 49.9 + - - +
100D SER* 5.1 1.0 - - - +
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Residues in contact with TYR 77 (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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64D PHE* 5.8 1.1 - + - -
73D HIS* 2.8 40.8 + - + +
74D GLU* 3.9 8.3 - - - +
76D ARG* 1.3 70.8 - - - +
78D LYS* 1.3 61.4 + - - +
79D LEU 3.2 0.8 + - - -
80D PHE* 3.5 18.0 + + - +
86D LEU* 2.9 35.7 - - + +
90D SER* 3.2 32.3 - - - -
92D GLY 2.9 32.7 + - - -
93D LYS* 3.0 2.5 + - - -
96D THR* 3.6 20.6 - - + -
13L G 3.0 55.9 - + + +
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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