Contacts of the helix formed by residues 80 - 90 (chain S) in PDB entry 6Y5D
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 80 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76S LYS* 4.3 15.0 - - + +
78S ARG* 4.3 16.6 - - + +
79S ILE* 1.3 81.4 - - - +
81S PRO* 1.3 66.3 - - + +
82S ARG* 3.8 19.7 - - + +
83S HIS* 2.7 53.0 + - + +
84S LEU 3.2 7.1 + - - -
56T SER* 3.6 12.8 - - - +
59T ALA* 3.9 5.2 - - - -
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Residues in contact with PRO 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80S ILE* 1.3 90.7 - - + +
82S ARG* 1.3 62.9 + - - +
84S LEU* 3.3 8.9 + - + +
85S GLN* 3.1 20.8 + - - +
103S ILE* 4.1 2.9 - - - +
104S ALA 3.2 26.2 - - - +
105S GLN* 3.4 14.4 - - + +
106S GLY* 3.7 3.2 - - - -
56T SER* 3.7 11.4 - - - +
58T LYS* 3.4 35.7 - - + -
59T ALA* 4.0 1.5 - - - +
62T ILE* 3.5 18.2 - - + -
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Residues in contact with ARG 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M GLN 3.0 16.1 + - - -
57M LYS* 3.4 22.8 + - - +
59M THR* 4.0 19.5 - - + -
74S ASN* 5.3 2.5 - - - +
80S ILE* 2.9 19.4 + - + +
81S PRO* 1.3 82.1 - - - +
83S HIS* 1.3 63.3 + - + +
85S GLN* 3.2 3.1 + - - +
86S LEU* 3.0 58.7 + - + +
105S GLN 3.5 1.9 + - - -
106S GLY 3.0 31.7 + - - -
107S GLY* 3.3 1.4 - - - -
108S VAL 2.7 41.2 + - - +
110S PRO* 4.4 8.7 - - - +
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Residues in contact with HIS 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S ALA* 3.7 19.8 - - - +
70S ALA* 3.7 14.1 - - + +
71S ALA* 3.5 19.6 - - - +
74S ASN* 3.0 31.1 + - - -
76S LYS* 3.6 27.8 + - + -
78S ARG 2.9 27.2 + - - -
79S ILE* 4.2 4.9 - - + -
80S ILE* 2.7 39.7 + - + +
82S ARG* 1.3 74.4 - - + +
84S LEU* 1.3 57.5 + - - +
86S LEU* 3.5 5.3 + - + -
87S ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S ILE* 3.8 13.7 - - + -
64S LEU* 4.6 4.0 - - + -
67S ALA* 3.9 8.3 - - + -
79S ILE* 3.7 24.0 - - + -
80S ILE 3.2 3.2 + - - +
81S PRO* 3.6 7.0 - - + +
82S ARG 3.2 0.4 - - - -
83S HIS* 1.3 74.9 - - - +
85S GLN* 1.3 65.2 + - - +
87S ALA* 3.3 2.3 + - - +
88S ILE* 3.1 34.8 + - + +
103S ILE* 4.6 9.2 - - + -
59T ALA* 3.5 37.5 - - + +
62T ILE* 3.6 27.1 - - + -
63T MET* 3.7 25.8 - - + -
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Residues in contact with GLN 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S PRO 3.1 3.0 + - - +
82S ARG* 3.2 7.8 + - - +
84S LEU* 1.3 80.1 - - - +
86S LEU* 1.3 62.8 + - + +
88S ILE* 4.0 1.2 - - - +
89S ARG* 3.1 62.5 + - + +
101S VAL 5.4 0.2 + - - -
103S ILE* 3.3 37.3 + - + +
106S GLY* 3.2 36.3 - - - +
107S GLY 3.6 18.4 + - - +
108S VAL* 4.8 8.7 - - - +
109S LEU* 5.5 1.1 - - + +
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Residues in contact with LEU 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S ALA* 4.1 13.7 - - + +
73S ASP* 6.5 0.4 - - + -
74S ASN* 4.4 17.7 - - - +
82S ARG* 3.0 63.1 + - + +
83S HIS* 3.9 8.3 - - + +
85S GLN* 1.3 74.9 - - + +
87S ALA* 1.3 66.3 + - - +
90S ASN* 2.8 36.2 + - - +
108S VAL 5.3 0.2 - - - -
109S LEU* 3.8 21.8 - - + -
110S PRO* 4.7 5.8 - - + -
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Residues in contact with ALA 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S ILE* 3.8 7.2 - - + +
66S LEU* 3.5 34.8 - - + +
67S ALA* 3.2 33.9 - - + +
70S ALA* 4.5 1.5 - - - +
83S HIS 2.9 16.7 + - - +
84S LEU* 3.5 5.6 - - - +
86S LEU* 1.3 79.3 - - - +
88S ILE* 1.3 63.9 + - + +
90S ASN* 3.7 6.3 + - - +
91S ASP* 3.8 4.5 + - - +
94S LEU* 5.2 0.2 - - - -
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Residues in contact with ILE 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N TYR* 6.2 1.6 - - + -
63S ILE* 4.2 32.1 - - + -
84S LEU* 3.1 19.8 + - + +
85S GLN* 4.0 2.7 - - - +
87S ALA* 1.3 80.4 - - - +
89S ARG* 1.3 83.2 + - - +
91S ASP* 3.1 26.0 + - - +
94S LEU* 4.0 17.0 - - + +
95S ASN* 3.3 17.4 + - - +
98S LEU* 3.9 25.1 - - + -
103S ILE* 3.7 23.3 - - + -
63T MET* 6.2 0.7 - - - -
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Residues in contact with ARG 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85S GLN* 3.1 48.8 + - + +
88S ILE* 1.3 97.9 - - - +
90S ASN* 1.3 59.8 + - - +
91S ASP 3.3 2.1 + - - -
95S ASN* 3.0 37.1 + - - +
98S LEU* 3.3 24.3 + - - +
99S GLY 4.0 12.5 + - - -
100S LYS 4.9 0.4 - - - -
101S VAL* 2.8 28.5 + - - +
103S ILE* 5.0 3.4 - - - +
109S LEU* 3.7 34.1 - - + +
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Residues in contact with ASN 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L LYS* 5.2 8.5 + - - -
86S LEU* 2.8 32.9 + - - +
87S ALA* 4.2 2.5 - - - +
88S ILE 3.2 0.8 - - - -
89S ARG* 1.3 78.8 - - - +
91S ASP* 1.3 57.7 + - - +
92S GLU* 4.2 7.9 - - - +
109S LEU* 3.2 33.2 - - - +
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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