Contacts of the helix formed by residues 76 - 89 (chain D) in PDB entry 5IYB
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 ASN 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D PHE* 3.5 1.6 - - - +
75D LYS* 1.3 80.7 - - - +
77D ARG* 1.3 65.4 + - - +
78D GLU* 2.9 26.7 + - - +
79D THR* 3.2 27.1 + - - +
80D ILE* 3.0 29.5 + - - +
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Residues in contact with ARG 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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39D MET* 3.7 43.2 - - + +
76D ASN* 1.3 73.3 + - - +
78D GLU* 1.3 59.4 + - - +
80D ILE* 3.1 14.0 + - + +
81D ALA* 2.8 31.8 + - + +
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Residues in contact with GLU 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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76D ASN* 2.9 14.6 + - - +
77D ARG* 1.3 75.4 - - - +
79D THR* 1.3 61.1 + - - +
81D ALA* 3.8 6.4 - - + +
82D SER* 2.8 42.2 + - - +
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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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74D PHE* 4.0 23.1 - - + -
76D ASN* 3.2 33.2 + - - +
78D GLU* 1.3 78.7 - - - +
80D ILE* 1.3 58.3 + - - +
82D SER* 3.3 4.8 + - - -
83D VAL* 2.9 35.4 + - + +
137D LYS* 4.0 38.3 - - + +
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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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33D LEU* 3.9 11.0 - - + +
35D SER* 3.6 32.5 - - - +
36D GLU* 3.4 36.3 - - + +
39D MET* 5.6 6.1 - - + -
74D PHE* 3.5 30.9 - - + +
76D ASN 3.0 28.1 + - - +
77D ARG* 3.3 13.0 - - + +
79D THR* 1.3 75.1 - - - +
81D ALA* 1.3 59.8 + - - +
83D VAL* 3.4 1.2 + - - +
84D ARG* 2.9 28.9 + - - +
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Residues in contact with ALA 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 ARG* 2.8 22.1 + - + +
78D GLU* 3.8 7.6 - - - +
80D ILE* 1.3 76.4 - - - +
82D SER* 1.3 56.1 + - - +
84D ARG* 3.9 5.3 - - - +
85D SER* 3.1 30.8 + - - -
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Residues in contact with SER 82 (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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78D GLU* 2.8 30.7 + - - +
79D THR* 3.7 5.4 - - - -
81D ALA* 1.3 73.8 - - - +
83D VAL* 1.3 60.4 + - - +
85D SER* 4.0 3.8 - - - -
86D LEU* 3.0 30.2 + - - +
137D LYS* 6.2 4.9 - - - -
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Residues in contact with VAL 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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74D PHE* 3.7 35.9 - - + -
79D THR* 2.9 27.6 + - + +
80D ILE 3.8 3.4 - - - +
82D SER* 1.3 74.5 - - - +
84D ARG* 1.3 66.5 + - - +
86D LEU* 3.3 10.2 + - + +
87D LEU* 3.0 43.3 + - + +
101D ALA* 5.9 4.3 - - + -
133D ASP* 5.3 6.7 - - - +
134D ILE* 5.0 13.9 - - + -
137D LYS* 4.6 13.9 - - + -
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Residues in contact with ARG 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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31D THR* 3.3 32.0 + - - +
32D LEU* 3.8 8.3 - - - +
33D LEU* 3.4 27.6 - - + +
36D GLU* 3.5 28.0 + - - +
80D ILE* 2.9 19.1 + - + +
81D ALA* 3.9 6.1 - - - +
83D VAL* 1.3 78.6 - - - +
85D SER* 1.3 53.5 + - - +
87D LEU* 3.3 5.9 + - - +
88D LEU* 2.7 49.2 + - + +
97D LEU* 3.3 32.2 - - - +
98D ALA* 5.3 2.2 - - - +
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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 ALA 3.1 17.1 + - - -
82D SER* 4.0 4.5 - - - -
84D ARG* 1.3 78.1 - - - +
86D LEU* 1.3 68.5 + - - +
88D LEU* 3.4 12.8 + - - +
89D GLN* 3.4 23.3 + - - +
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Residues in contact with LEU 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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82D SER 3.0 19.9 + - - +
83D VAL* 3.4 11.2 - - + +
85D SER* 1.3 76.5 - - - +
87D LEU* 1.3 68.8 + - + +
89D GLN* 3.2 40.7 - - - +
90D LYS* 3.3 14.8 - - + +
130D ILE* 5.4 11.2 - - + +
133D ASP* 3.4 34.3 - - + +
134D ILE* 6.2 2.0 - - + -
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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
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83D VAL* 3.0 36.6 + - + +
84D ARG* 3.8 3.6 - - - +
86D LEU* 1.3 80.5 - - + +
88D LEU* 1.3 66.8 + - - +
89D GLN 3.2 2.5 - - - -
90D LYS* 2.9 25.7 + - + +
92D LEU* 4.7 16.8 - - + +
97D LEU* 3.8 45.3 - - + +
100D LEU* 5.0 6.3 - - + -
101D ALA* 4.8 9.0 - - + -
130D ILE* 3.6 34.5 - - + -
134D ILE* 5.0 11.9 - - + -
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Residues in contact with LEU 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 ARG* 2.7 32.2 + - + +
85D SER* 3.4 13.4 + - - +
87D LEU* 1.3 72.8 - - - +
89D GLN* 1.3 60.4 + - - +
90D LYS 3.2 7.3 + - - +
94D LYS* 6.1 7.2 - - + -
97D LEU* 3.8 13.5 - - + +
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Residues in contact with GLN 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* 3.4 10.4 + - - +
86D LEU* 3.2 33.7 + - - +
88D LEU* 1.3 77.8 - - - +
90D LYS* 1.3 69.4 + - + +
91D LYS* 4.0 2.6 + - - +
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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