Contacts of the helix formed by residues 72 - 79 (chain D) in PDB entry 4DOH
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 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ASN* 3.3 10.3 - - - -
70D TYR* 4.3 3.4 - - - -
71D GLN* 1.3 75.4 - - - +
73D GLU* 1.3 67.1 + - - -
74D TYR 3.2 3.1 - - - -
75D GLU* 3.0 19.6 + - - -
76D SER* 2.9 20.9 + - - -
108D PRO 4.0 1.6 - - - -
109D TYR* 3.7 23.9 - - - -
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Residues in contact with GLU 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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206B GLN* 5.3 6.4 + - - -
217B ALA* 6.1 0.5 - - - -
218B PHE* 5.4 4.5 - - - -
114C ASN* 2.9 4.6 + - - -
117C LEU* 3.9 7.0 - - + +
121C LYS* 2.8 37.9 + - - +
72D GLY* 1.3 70.4 - - - -
74D TYR* 1.3 64.4 + - - +
76D SER* 3.0 13.0 + - - -
77D LEU* 2.9 47.1 + - + +
107D VAL* 3.7 17.0 - - + +
108D PRO* 3.3 37.6 + - + +
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Residues in contact with TYR 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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91C LEU* 3.0 48.6 + - + -
95C PHE* 3.5 12.1 - - + +
96C LYS* 3.1 34.6 + - + +
109C ILE* 6.4 0.2 - - + -
113C ALA* 3.5 20.6 - - + -
114C ASN* 2.8 27.4 + - - +
117C LEU* 3.2 15.4 - - + +
73D GLU* 1.3 75.9 - - - +
75D GLU* 1.3 81.7 + - + +
77D LEU 3.0 2.4 + - - -
78D TYR* 2.9 62.6 + + + +
79D THR* 5.2 3.4 - - + -
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER* 3.0 34.9 + - - -
114C ASN* 2.8 26.0 + - - -
71D GLN* 3.8 17.3 - - + -
72D GLY 3.0 15.3 + - - +
74D TYR* 1.3 87.5 - - + +
76D SER* 1.3 62.6 + - - +
79D THR* 2.9 46.5 + - - +
80D SER* 3.6 0.3 - - - -
82D ILE* 4.2 9.0 - - + +
84D ILE* 3.5 22.8 - - + +
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Residues in contact with SER 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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71D GLN* 3.1 15.8 + - - +
72D GLY 2.9 13.6 + - - -
73D GLU* 3.1 17.0 - - - -
75D GLU* 1.3 77.4 - - - +
77D LEU* 1.3 66.5 + - - +
80D SER* 3.5 20.0 - - - +
110D ASN* 3.0 28.9 + - - -
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Residues in contact with LEU 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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204B LYS* 4.3 20.9 - - - +
218B PHE* 4.7 19.3 - - + -
117C LEU* 4.4 13.2 - - + -
73D GLU* 2.9 45.8 + - + +
76D SER* 1.3 82.1 - - - +
78D TYR* 1.3 81.2 + - + +
80D SER* 5.1 1.2 - - - -
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Residues in contact with TYR 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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91C LEU* 3.5 41.0 - - + +
92C ASP* 3.5 25.2 + - - -
96C LYS* 4.2 21.9 + - + +
117C LEU* 4.6 17.1 - - + +
120C LYS* 5.0 6.8 - - - +
74D TYR* 2.9 44.3 + + + +
77D LEU* 1.3 98.4 - - + +
79D THR* 1.3 73.9 + - + +
80D SER 3.9 1.6 - - - -
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Residues in contact with THR 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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96C LYS* 3.7 34.1 - - + -
74D TYR* 5.2 4.4 - - + -
75D GLU* 2.9 27.3 + - - +
78D TYR* 1.3 92.0 - - + +
80D SER* 1.3 51.4 + - - +
81D HIS 2.7 17.4 + - - -
82D ILE* 2.9 38.6 + - - +
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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