Contacts of the helix formed by residues 72 - 90 (chain g) 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 g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69g ASP* 5.2 4.7 - - - -
70g ILE 3.6 4.7 + - - -
71g ASN* 1.3 74.3 - - - +
73g SER* 1.3 62.7 + - - +
74g GLN* 3.3 7.0 - - - -
75g VAL* 3.8 12.9 - - - +
76g LEU* 2.8 30.8 + - - +
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Residues in contact with SER 73 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 A 6.1 4.9 - - - -
232 A 5.2 13.2 - - - -
72g THR* 1.3 73.3 - - - +
74g GLN* 1.3 59.3 + - - +
76g LEU* 3.9 3.7 - - - +
77g LYS* 2.9 29.3 + - - +
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Residues in contact with GLN 74 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72g THR* 3.3 4.2 - - - -
73g SER* 1.3 75.6 - - - +
75g VAL* 1.3 61.1 + - - +
77g LYS* 3.6 5.8 - - - +
78g LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 75 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70g ILE 4.0 12.3 - - - +
71g ASN* 5.1 0.4 - - - -
72g THR* 3.4 24.3 + - - +
73g SER 3.4 0.2 - - - -
74g GLN* 1.3 78.8 - - - +
76g LEU* 1.3 56.5 + - - +
78g LEU* 3.4 5.3 + - - +
79g LEU* 2.9 30.2 + - - +
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Residues in contact with LEU 76 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71g ASN* 5.9 3.6 - - + +
72g THR 2.8 22.6 + - - +
73g SER* 4.1 4.0 - - - +
75g VAL* 1.3 71.3 - - - +
77g LYS* 1.3 59.1 + - - +
79g LEU* 3.9 5.7 - - - +
80g HIS* 2.9 31.9 + - - +
135g VAL 5.1 10.7 - - - +
136g ARG* 6.0 4.5 - - + +
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Residues in contact with LYS 77 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73g SER 2.9 19.9 + - - +
74g GLN* 3.6 7.9 - - - +
75g VAL 3.2 0.2 - - - -
76g LEU* 1.3 79.3 - - - +
78g LEU* 1.3 56.9 + - - +
80g HIS* 4.0 3.5 - - - +
81g THR* 2.9 31.4 + - - -
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Residues in contact with LEU 78 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74g GLN 2.9 16.8 + - - +
75g VAL* 4.0 4.0 - - - +
77g LYS* 1.3 76.7 - - - +
79g LEU* 1.3 57.8 + - - +
81g THR* 3.8 5.8 - - - -
82g ASP* 2.9 28.8 + - - +
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Residues in contact with LEU 79 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75g VAL 2.9 18.6 + - - +
76g LEU* 3.9 6.7 - - - +
78g LEU* 1.3 75.4 - - - +
80g HIS* 1.3 59.1 + - - +
82g ASP* 3.1 7.2 + - - +
83g ILE* 2.9 28.9 + - - +
135g VAL 5.7 4.3 - - - +
136g ARG* 6.2 3.6 - - - -
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Residues in contact with HIS 80 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76g LEU 2.9 19.4 + - - +
77g LYS* 4.0 4.0 - - - +
79g LEU* 1.3 75.6 - - - +
81g THR* 1.3 57.9 + - - +
83g ILE* 3.4 6.7 + - - +
84g VAL* 2.9 29.5 + - - +
127g LEU* 5.9 5.4 - - + +
130g ILE* 5.0 17.7 - - + +
131g LYS* 6.0 2.0 - - + +
135g VAL* 6.4 2.5 - - + -
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Residues in contact with THR 81 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77g LYS 2.9 18.5 + - - -
78g LEU* 3.9 7.0 - - - -
80g HIS* 1.3 76.1 - - - +
82g ASP* 1.3 58.4 + - - +
84g VAL* 3.4 6.9 + - - +
85g SER* 2.9 28.4 + - - -
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Residues in contact with ASP 82 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78g LEU 2.9 19.2 + - - +
79g LEU* 3.5 7.6 - - - +
81g THR* 1.3 75.3 - - - +
83g ILE* 1.3 60.6 + - - +
85g SER* 3.2 7.1 + - - -
86g GLN* 2.9 27.4 + - - +
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Residues in contact with ILE 83 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111f GLU* 5.4 14.3 - - + +
112f CYS* 6.5 0.7 - - - -
79g LEU 2.9 16.2 + - - +
80g HIS* 3.9 6.1 - - - +
82g ASP* 1.3 76.2 - - - +
84g VAL* 1.3 57.0 + - - +
86g GLN* 3.3 8.3 + - - +
87g LEU* 2.9 29.8 + - - +
130g ILE* 5.9 6.3 - - + -
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Residues in contact with VAL 84 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80g HIS 2.9 19.4 + - - +
81g THR* 3.7 7.9 - - - +
83g ILE* 1.3 75.9 - - - +
85g SER* 1.3 58.7 + - - +
87g LEU* 3.5 6.4 + - - +
88g ASN* 2.9 29.2 + - - +
126g LEU* 5.9 8.3 - - + -
127g LEU* 5.9 9.0 - - + +
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Residues in contact with SER 85 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81g THR 2.9 17.4 + - - -
82g ASP* 3.2 8.0 + - - -
84g VAL* 1.3 74.6 - - - +
86g GLN* 1.3 59.8 + - - +
88g ASN* 3.1 7.2 + - - +
89g ASP* 2.9 28.9 + - - +
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Residues in contact with GLN 86 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111f GLU* 5.4 12.8 - - + +
114f GLU* 6.5 1.3 - - + -
82g ASP 2.9 16.3 + - - +
83g ILE* 3.3 8.5 + - - +
85g SER* 1.3 76.4 - - - +
87g LEU* 1.3 60.5 + - - +
89g ASP* 3.3 19.2 + - - +
90g LYS* 3.8 7.3 + - - +
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Residues in contact with LEU 87 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111f GLU* 5.7 7.5 - - + +
83g ILE 2.9 17.2 + - - +
84g VAL* 3.9 6.3 - - - +
86g GLN* 1.3 76.3 - - - +
88g ASN* 1.3 57.0 + - - +
90g LYS* 3.1 25.3 + - - +
93g VAL* 5.3 3.9 - - + +
94g ARG* 3.6 17.0 + - + +
126g LEU* 6.2 4.5 - - + -
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Residues in contact with ASN 88 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X GLY* 5.6 10.8 - - - +
48X LEU* 5.6 6.2 - - - +
84g VAL 2.9 18.1 + - - +
85g SER* 3.1 8.9 + - - +
87g LEU* 1.3 73.2 - - - +
89g ASP* 1.3 64.3 + - - +
90g LYS 3.2 5.0 + - - -
91g PRO* 4.7 2.4 - - - +
94g ARG* 5.2 4.7 - - - -
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Residues in contact with ASP 89 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85g SER 2.9 12.3 + - - +
86g GLN* 3.6 13.9 - - - +
87g LEU 3.3 0.8 - - - -
88g ASN* 1.3 78.0 - - - +
90g LYS* 1.3 57.8 + - - +
91g PRO 4.0 1.8 - - - -
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Residues in contact with LYS 90 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86g GLN 3.8 5.5 + - - +
87g LEU* 3.1 18.5 + - - +
88g ASN 3.2 2.1 - - - +
89g ASP* 1.3 77.9 - - - +
91g PRO* 1.3 65.6 - - - +
92g GLU* 3.4 2.0 - - + +
93g VAL* 4.2 19.7 - - + +
94g ARG* 3.4 11.1 + - - +
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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