Contacts of the helix formed by residues 72 - 90 (chain e) in PDB entry 6QXT
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 THR 72 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69e ASP* 5.2 5.4 - - - -
70e ILE 3.6 5.0 + - - -
71e ASN* 1.3 74.3 - - - +
73e SER* 1.3 61.6 + - - +
74e GLN* 3.3 4.0 - - - -
75e VAL* 3.8 17.3 - - - +
76e LEU* 2.8 31.1 + - - +
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Residues in contact with SER 73 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431 T 4.5 20.2 - - - -
72e THR* 1.3 74.2 - - - +
74e GLN* 1.3 58.1 + - - +
76e LEU* 3.9 3.6 - - - +
77e LYS* 2.9 29.7 + - - +
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Residues in contact with GLN 74 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72e THR* 3.3 4.3 - - - -
73e SER* 1.3 75.2 - - - +
75e VAL* 1.3 61.2 + - - +
77e LYS* 3.3 6.4 + - - +
78e LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 75 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70e ILE 4.0 13.0 - - - +
71e ASN* 5.1 0.7 - - - -
72e THR* 3.4 24.7 + - - +
73e SER 3.4 0.2 - - - -
74e GLN* 1.3 79.0 - - - +
76e LEU* 1.3 57.9 + - - +
78e LEU* 3.4 5.3 + - - +
79e LEU* 2.9 30.4 + - - +
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Residues in contact with LEU 76 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71e ASN* 5.9 3.3 - - + +
72e THR 2.8 23.0 + - - +
73e SER* 4.1 3.6 - - - +
75e VAL* 1.3 73.8 - - - +
77e LYS* 1.3 58.3 + - - +
79e LEU* 3.9 5.8 - - - +
80e HIS* 2.9 32.4 + - - +
135e VAL 5.1 11.3 - - - +
136e ARG* 6.0 4.7 - - + +
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Residues in contact with LYS 77 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73e SER 2.9 19.7 + - - +
74e GLN* 3.6 7.6 - - - +
75e VAL 3.2 0.2 - - - -
76e LEU* 1.3 77.7 - - - +
78e LEU* 1.3 57.6 + - - +
80e HIS* 4.0 3.3 - - - +
81e THR* 2.9 31.4 + - - -
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Residues in contact with LEU 78 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74e GLN 2.9 17.4 + - - +
75e VAL* 4.0 4.5 - - - +
77e LYS* 1.3 76.3 - - - +
79e LEU* 1.3 58.4 + - - +
81e THR* 3.8 5.5 - - - -
82e ASP* 2.9 28.9 + - - +
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Residues in contact with LEU 79 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75e VAL 2.9 19.4 + - - +
76e LEU* 3.9 6.5 - - - +
78e LEU* 1.3 74.6 - - - +
80e HIS* 1.3 60.0 + - - +
82e ASP* 3.1 7.3 + - - +
83e ILE* 2.9 29.0 + - - +
135e VAL 5.7 4.5 - - - +
136e ARG* 6.2 3.4 - - - -
137e ILE 6.4 0.2 - - - +
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Residues in contact with HIS 80 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76e LEU 2.9 18.8 + - - +
77e LYS* 4.0 4.3 - - - +
79e LEU* 1.3 76.0 - - - +
81e THR* 1.3 58.3 + - - +
83e ILE* 3.4 5.8 + - - +
84e VAL* 2.9 30.0 + - - +
127e LEU* 5.9 5.4 - - + +
130e ILE* 5.0 17.5 - - + +
131e LYS* 6.0 1.3 - - + +
135e VAL* 6.4 2.5 - - + -
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Residues in contact with THR 81 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77e LYS 2.9 20.1 + - - -
78e LEU* 3.9 6.7 - - - -
80e HIS* 1.3 76.5 - - - +
82e ASP* 1.3 58.0 + - - +
84e VAL* 3.4 6.8 + - - +
85e SER* 2.9 28.2 + - - -
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Residues in contact with ASP 82 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78e LEU 2.9 19.4 + - - +
79e LEU* 3.1 8.5 + - - +
81e THR* 1.3 73.9 - - - +
83e ILE* 1.3 59.7 + - - +
85e SER* 3.2 8.0 + - - -
86e GLN* 2.9 27.4 + - - +
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Residues in contact with ILE 83 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79e LEU 2.9 15.8 + - - +
80e HIS* 3.9 6.1 - - - +
82e ASP* 1.3 75.9 - - - +
84e VAL* 1.3 58.8 + - - +
86e GLN* 3.3 7.7 + - - +
87e LEU* 2.9 29.5 + - - +
130e ILE* 5.9 6.7 - - + -
111h GLU* 5.3 14.7 - - + +
112h CYS* 6.5 0.4 - - - -
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Residues in contact with VAL 84 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80e HIS 2.9 18.3 + - - +
81e THR* 3.7 8.7 - - - +
82e ASP 3.2 0.2 - - - -
83e ILE* 1.3 76.0 - - - +
85e SER* 1.3 57.5 + - - +
87e LEU* 3.5 5.8 + - - +
88e ASN* 2.9 29.1 + - - +
126e LEU* 5.9 9.0 - - + -
127e LEU* 5.9 8.1 - - + +
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Residues in contact with SER 85 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81e THR 2.9 18.0 + - - -
82e ASP* 3.2 8.0 + - - -
84e VAL* 1.3 74.8 - - - +
86e GLN* 1.3 59.1 + - - +
88e ASN* 3.1 7.8 + - - +
89e ASP* 2.9 28.1 + - - +
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Residues in contact with GLN 86 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82e ASP 2.9 15.4 + - - +
83e ILE* 3.3 9.4 + - - +
85e SER* 1.3 76.9 - - - +
87e LEU* 1.3 59.4 + - - +
89e ASP* 3.3 18.9 + - - +
90e LYS* 3.8 7.3 + - - +
111h GLU* 5.3 13.2 - - + +
114h GLU* 6.5 1.6 - - + -
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Residues in contact with LEU 87 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83e ILE 2.9 16.1 + - - +
84e VAL* 3.9 6.1 - - - +
86e GLN* 1.3 76.1 - - - +
88e ASN* 1.3 57.8 + - - +
90e LYS* 3.1 25.3 + - - +
93e VAL* 5.3 3.1 - - + +
94e ARG* 3.6 17.0 + - + +
126e LEU* 6.2 4.3 - - + -
111h GLU* 5.7 7.7 - - + +
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Residues in contact with ASN 88 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84e VAL 2.9 19.5 + - - +
85e SER* 3.1 8.9 + - - +
87e LEU* 1.3 74.1 - - - +
89e ASP* 1.3 63.5 + - - +
90e LYS 3.2 5.3 + - - -
91e PRO* 4.7 2.3 - - - +
94e ARG* 5.2 4.3 - - - -
36w GLY* 5.2 15.0 - - - +
48w LEU* 6.0 1.7 - - - +
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Residues in contact with ASP 89 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85e SER 2.9 12.4 + - - +
86e GLN* 3.6 13.9 - - - +
87e LEU 3.3 0.8 - - - -
88e ASN* 1.3 76.7 - - - +
90e LYS* 1.3 58.0 + - - +
91e PRO 4.0 2.2 - - - -
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Residues in contact with LYS 90 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86e GLN 3.8 6.0 + - - +
87e LEU* 3.1 18.6 + - - +
88e ASN 3.2 2.4 - - - +
89e ASP* 1.3 79.9 - - + +
91e PRO* 1.3 64.2 - - - +
92e GLU* 3.4 1.8 - - + +
93e VAL* 4.2 18.6 - - + +
94e ARG* 3.4 11.4 + - - +
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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