Contacts of the helix formed by residues 82 - 93 (chain L) in PDB entry 6QX2
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 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122J ARG* 3.7 18.6 - - - +
81L HIS* 1.3 79.5 - - - +
83L ASP* 1.3 66.2 + - - -
84L SER* 3.3 3.6 - - - -
85L SER* 3.4 16.8 + - - -
86L ILE* 3.4 15.1 + - - +
8O C 2.9 15.4 + - - -
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Residues in contact with ASP 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J MET* 5.2 13.1 - - + +
122J ARG* 3.5 31.8 + - - +
71L VAL* 3.9 13.3 - - + +
75L MET* 3.6 27.6 - - + +
81L HIS 3.7 1.4 + - - -
82L GLY* 1.3 67.2 - - - -
84L SER* 1.3 65.8 + - - +
86L ILE* 3.3 2.9 + - - +
87L TYR* 2.9 30.7 + - - +
121L MET* 3.8 21.2 - - + +
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Residues in contact with SER 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L GLY* 3.3 1.7 - - - -
83L ASP* 1.3 85.7 + - - +
85L SER* 1.3 61.3 + - - +
87L TYR* 4.6 4.7 - - - +
88L GLU* 2.9 54.5 + - - +
121L MET* 5.1 1.8 - - - -
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Residues in contact with SER 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L VAL* 4.3 1.9 - - - +
81L HIS* 5.1 0.7 - - - -
82L GLY* 3.4 14.4 + - - -
83L ASP 3.3 1.0 - - - -
84L SER* 1.3 79.5 + - - +
86L ILE* 1.3 62.0 + - - +
88L GLU* 4.5 2.2 - - - +
89L ALA* 3.4 21.7 + - - +
6O T 4.2 14.7 - - - +
7O A 3.4 59.6 + - - -
8O C 4.2 5.9 + - - -
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Residues in contact with ILE 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL* 4.1 8.1 - - + -
49L ILE* 3.5 23.0 - - + +
70L ILE* 6.4 0.4 - - + -
71L VAL* 3.9 26.5 - - + +
74L VAL* 4.2 8.5 - - + -
75L MET* 3.7 38.4 - - + +
79L HIS* 3.6 37.5 - - + +
81L HIS 4.2 2.0 - - - +
82L GLY 3.4 14.8 + - - +
83L ASP 3.3 6.6 + - - +
84L SER 3.2 0.2 - - - -
85L SER* 1.3 74.1 - - - +
87L TYR* 1.3 66.6 + - - +
89L ALA* 3.2 5.5 + - - +
90L MET* 3.1 20.2 + - + +
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Residues in contact with TYR 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L SER* 3.6 13.0 - - - -
71L VAL* 4.1 12.3 - - + +
83L ASP 2.9 21.4 + - - +
84L SER* 4.2 3.6 - - - +
86L ILE* 1.3 72.3 - - - +
88L GLU* 1.3 64.2 + - + +
90L MET* 3.1 22.3 + - + +
91L VAL* 2.8 51.6 + - + +
110L PHE* 4.6 1.1 - + - -
118L ALA* 4.0 7.3 - - + +
119L ALA 2.8 29.2 + - - -
120L ALA* 3.8 2.5 + - - -
121L MET* 3.6 40.4 - - + -
124L THR* 2.6 35.2 + - - +
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Residues in contact with GLU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L SER* 2.9 38.7 + - - +
85L SER* 4.5 2.6 - - - +
87L TYR* 1.3 84.4 - - + +
89L ALA* 1.3 61.7 + - - +
91L VAL* 3.4 10.4 + - + +
92L ARG* 3.1 28.1 + - - +
6O T 4.1 22.8 - - + +
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Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL* 4.0 25.1 - - + -
46L HIS* 3.9 11.9 - - - +
49L ILE* 4.1 7.2 - - + -
85L SER 3.4 17.9 + - - +
86L ILE 3.2 6.1 + - - +
88L GLU* 1.3 77.7 - - - +
90L MET* 1.3 61.8 + - - +
92L ARG* 3.8 3.6 + - - +
93L MET* 3.4 28.2 + - - +
6O T 3.9 17.2 + - - +
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Residues in contact with MET 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ILE* 3.9 22.4 - - + +
53L LEU* 5.5 1.8 - - + -
67L SER* 3.6 27.8 - - - +
70L ILE* 4.1 27.8 - - - -
71L VAL* 5.0 5.6 - - + -
86L ILE* 3.1 13.5 + - + +
87L TYR* 3.1 28.0 + - + +
89L ALA* 1.3 74.8 - - - +
91L VAL* 1.3 64.9 + - - +
93L MET* 3.2 22.8 + - - +
94L ALA* 3.4 10.9 + - - +
104L VAL* 4.1 16.0 - - + +
110L PHE* 4.3 10.8 - - + -
126L ALA* 3.9 20.6 - - + -
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Residues in contact with VAL 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L TYR* 2.8 44.6 + - + +
88L GLU* 3.5 13.7 - - + +
89L ALA 3.4 0.2 - - - -
90L MET* 1.3 75.1 - - - +
92L ARG* 1.3 53.3 + - + +
94L ALA* 2.8 28.2 + - - +
95L GLN* 3.3 33.8 + - - +
110L PHE* 3.7 18.7 - - + +
118L ALA* 3.6 35.2 - - + +
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Residues in contact with ARG 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L HIS* 5.6 1.0 + - - +
88L GLU 3.1 14.7 + - - +
89L ALA* 3.9 6.3 - - - +
90L MET 3.3 0.2 - - - -
91L VAL* 1.3 78.7 - - + +
93L MET* 1.3 58.4 + - - +
94L ALA 3.1 4.7 + - - -
95L GLN* 3.1 32.7 + - - +
98L SER* 3.7 28.7 + - - +
99L TYR* 3.1 34.9 + - + -
172L ALA* 6.0 2.2 - - - +
173L SER* 5.0 10.3 + - - +
266L PHE* 6.0 3.0 - - - -
267L GLN* 4.8 12.7 - - - +
5O G 2.9 44.9 + - - +
6O T 3.9 29.9 + - - +
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Residues in contact with MET 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L HIS* 3.9 25.6 - - + +
49L ILE* 3.6 40.2 - - + -
50L LEU* 4.1 19.1 - - + -
89L ALA 3.4 18.6 + - - +
90L MET* 3.2 14.5 + - - +
92L ARG* 1.3 75.5 - - - +
94L ALA* 1.3 56.7 + - - +
95L GLN 3.5 0.2 - - - -
99L TYR* 3.5 31.4 - - + +
102L PRO* 3.4 8.3 - - - +
103L LEU* 3.0 40.6 + - + -
104L VAL* 3.2 17.2 + - + +
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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