Contacts of the helix formed by residues 79 - 96 (chain D) in PDB entry 5AN5
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 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0D ALA 3.1 5.7 + - - -
76D THR* 3.1 13.6 + - - +
77D ASN 4.1 6.5 - - - +
78D PHE* 1.3 79.7 - - - +
80D ILE* 1.3 64.9 + - - +
81D LEU 3.4 2.2 + - - -
82D LYS* 3.4 15.0 + - + +
83D ARG* 3.0 31.8 + - + +
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Residues in contact with ILE 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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80C ILE* 3.6 26.7 - - + -
81C LEU* 4.0 4.9 - - + -
84C LEU* 3.9 22.8 - - + +
-1D MET* 3.7 25.4 - - + -
0D ALA* 3.0 31.3 + - + +
78D PHE* 3.9 12.1 - - + +
79D ASP* 1.3 77.3 - - - +
81D LEU* 1.3 59.3 + - - +
83D ARG* 3.2 1.2 + - - +
84D LEU* 2.8 48.9 + - + +
80J ILE* 3.9 21.5 - - + -
84J LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ALA* 4.9 3.1 + - + -
79D ASP 3.4 0.6 - - - -
80D ILE* 1.3 77.2 - - + +
82D LYS* 1.3 63.4 + - - +
84D LEU* 3.4 5.8 + - + +
85D SER* 3.0 24.7 + - - -
79J ASP* 6.1 2.9 - - + -
80J ILE* 4.0 30.3 - - + +
83J ARG* 4.1 23.0 + - - +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASP* 3.4 16.2 + - + +
80D ILE 3.3 0.4 - - - -
81D LEU* 1.3 78.2 - - - +
83D ARG* 1.3 67.8 + - + +
85D SER* 3.3 6.8 + - - -
86D ASN* 2.9 52.4 + - - +
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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
----------------------------------------------------------
81C LEU* 4.5 4.9 + - - +
84C LEU* 3.4 33.3 - - + +
85C SER* 3.9 14.8 - - - +
88C GLU* 2.8 45.0 + - - +
78D PHE* 2.9 44.0 + - - +
79D ASP* 3.0 22.8 + - + +
80D ILE 3.7 3.1 - - - +
82D LYS* 1.3 85.6 - - + +
84D LEU* 1.3 59.6 + - - +
86D ASN* 3.5 5.5 + - - +
87D LEU* 3.0 30.2 + - - +
92H PHE 4.7 2.8 + - - -
94H SER* 3.5 33.2 - - - +
96H LEU* 6.1 2.5 - - + -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.8 9.2 - - + -
80D ILE* 2.8 38.6 + - + +
81D LEU* 3.7 5.2 - - - +
83D ARG* 1.3 74.1 - - - +
85D SER* 1.3 59.7 + - - +
87D LEU* 3.2 5.3 + - - +
88D GLU* 2.9 34.4 + - - +
80J ILE* 4.0 27.6 - - + +
83J ARG* 4.0 30.7 - - + +
84J LEU* 3.8 36.6 - - + +
87J LEU* 3.8 17.7 - - + +
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Residues in contact with SER 85 (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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81D LEU 3.0 18.3 + - - -
82D LYS* 3.6 7.9 - - - -
84D LEU* 1.3 75.1 - - - +
86D ASN* 1.3 61.5 + - - +
88D GLU* 3.3 4.4 + - - +
89D LYS* 2.9 53.8 + - - +
83J ARG* 3.7 15.4 - - - +
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Residues in contact with ASN 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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92C PHE* 4.3 9.8 - - + -
82D LYS* 2.9 42.0 + - - +
83D ARG* 4.0 5.3 - - - +
85D SER* 1.3 79.1 + - - +
87D LEU* 1.3 63.4 + - - +
89D LYS* 4.0 13.5 - - - +
90D HIS* 3.1 24.1 + - - +
96H LEU* 5.8 8.2 - - + +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.7 25.6 - - + -
87C LEU* 3.9 29.8 - - + +
88C GLU* 4.0 14.1 - - + +
91C VAL* 3.9 27.4 - - + -
92C PHE* 3.8 24.2 - - + -
83D ARG 3.0 20.5 + - - +
84D LEU 3.2 3.8 + - - +
86D ASN* 1.3 75.2 - - - +
88D GLU* 1.3 59.8 + - - +
90D HIS* 3.2 3.3 + - - +
91D VAL* 2.8 35.2 + - + +
87J LEU* 3.9 21.1 - - + -
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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
----------------------------------------------------------
84D LEU* 2.9 17.5 + - - +
85D SER* 3.7 4.7 - - - +
87D LEU* 1.3 72.0 - - - +
89D LYS* 1.3 68.5 + - + +
92D PHE* 2.9 47.6 + - + +
83J ARG* 2.8 57.4 + - - +
86J ASN* 5.4 0.8 + - - +
87J LEU* 4.0 19.2 - - + +
1098J GOL 3.4 18.4 + - - -
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Residues in contact with LYS 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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85D SER* 2.9 39.4 + - - +
86D ASN* 4.0 13.0 - - - +
88D GLU* 1.3 76.7 - - + +
90D HIS* 1.3 59.1 + - - +
92D PHE* 5.4 0.2 - - - -
93D GLY* 3.0 26.5 + - - -
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Residues in contact with HIS 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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91C VAL* 3.5 30.2 + - + +
92C PHE* 3.5 28.6 - + + -
86D ASN 3.1 16.0 + - - +
87D LEU 3.7 2.5 - - - +
88D GLU 3.1 0.4 - - - -
89D LYS* 1.3 78.8 - - - +
91D VAL* 1.3 67.6 + - - +
93D GLY* 3.3 8.2 + - - -
94D SER* 3.9 9.4 + - - -
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 3.9 24.9 - - + -
87D LEU* 2.8 24.4 + - + +
88D GLU 4.3 0.7 - - - +
90D HIS* 1.3 74.8 - - - +
92D PHE* 1.3 79.7 + - + +
94D SER* 3.4 15.5 + - - -
95D LYS* 3.6 30.2 - - - +
87J LEU* 4.1 12.1 - - + -
90J HIS* 4.5 3.6 - - + -
91J VAL* 3.9 31.6 - - + -
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Residues in contact with PHE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU* 2.9 39.9 + - + +
89D LYS* 5.4 0.4 - - - -
91D VAL* 1.3 78.8 - - + +
93D GLY* 1.3 57.5 + - - +
94D SER 3.2 1.3 - - - -
95D LYS* 3.7 13.5 - - + -
96D LEU* 3.0 56.4 + - + +
86J ASN* 3.7 20.4 - - - -
87J LEU* 4.2 19.3 - - + -
90J HIS* 3.5 52.5 - + + -
1098J GOL 6.1 0.2 - - - -
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Residues in contact with GLY 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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89D LYS 3.0 21.4 + - - -
90D HIS 3.3 3.1 + - - -
91D VAL 3.3 1.0 - - - -
92D PHE* 1.3 76.5 - - - +
94D SER* 1.3 57.3 + - - +
96D LEU 3.6 13.1 - - - +
98D ASP* 6.4 2.0 - - - -
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Residues in contact with SER 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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90D HIS 3.9 6.4 + - - -
91D VAL 3.4 11.8 + - - -
93D GLY* 1.3 76.2 - - - +
95D LYS* 1.3 68.0 + - - +
96D LEU 3.5 1.3 - - - -
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Residues in contact with LYS 95 (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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91D VAL* 3.6 33.7 - - - +
92D PHE* 3.2 23.5 + - + +
94D SER* 1.3 83.9 - - - +
96D LEU* 1.3 71.7 + - + +
90J HIS* 3.8 30.7 + - - +
91J VAL* 6.0 0.2 - - - +
95J LYS* 4.0 23.7 - - - +
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Residues in contact with LEU 96 (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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92D PHE* 3.0 36.4 + - + +
93D GLY* 3.6 17.8 - - - +
94D SER 3.5 1.0 - - - -
95D LYS* 1.3 91.5 - - + +
97D TYR* 1.3 72.3 + - - +
98D ASP* 3.7 4.5 + - + +
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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