Contacts of the helix formed by residues 51 - 66 (chain X) 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 ASN 51 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6X MET* 5.2 7.1 - - - +
49X LEU* 3.4 5.6 - - - +
50X LEU* 1.3 81.7 - - + +
52X HIS* 1.3 65.6 + - - +
53X THR* 3.3 7.9 - - - +
54X ALA* 3.6 6.9 + - + +
55X ASN* 3.2 22.1 + - - +
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Residues in contact with HIS 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X MET* 6.2 0.7 - - - -
51X ASN* 1.3 75.7 - - - +
53X THR* 1.3 60.6 + - - +
55X ASN* 3.2 8.1 + - - +
56X THR* 2.9 29.3 + - - -
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Residues in contact with THR 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X ASN* 3.3 5.6 - - - +
52X HIS* 1.3 79.2 - - - +
54X ALA* 1.3 57.7 + - - +
56X THR* 3.1 7.2 + - - -
57X ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LEU* 4.8 4.4 - - + +
50X LEU* 4.5 13.7 - - + +
51X ASN* 3.6 18.5 + - + +
52X HIS 3.4 0.4 - - - -
53X THR* 1.3 78.7 - - - +
55X ASN* 1.3 57.2 + - - +
57X ALA* 3.9 6.5 - - - +
58X MET* 2.9 29.5 + - - +
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Residues in contact with ASN 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X MET* 5.3 7.4 - - + -
49X LEU* 4.4 14.1 - - + +
51X ASN 3.2 15.9 + - - +
52X HIS* 3.4 12.8 - - - +
53X THR 3.1 0.6 - - - -
54X ALA* 1.3 75.6 - - - +
56X THR* 1.3 60.6 + - - +
58X MET* 3.3 6.0 + - - +
59X VAL* 2.9 27.5 + - - +
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Residues in contact with THR 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X HIS 2.9 15.8 + - - -
53X THR* 3.1 6.7 + - - -
55X ASN* 1.3 73.9 - - - +
57X ALA* 1.3 65.4 + - - +
59X VAL* 3.0 9.3 + - - +
60X GLY* 2.9 20.1 + - - -
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Residues in contact with ALA 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X THR 2.9 15.8 + - - +
54X ALA* 4.0 7.9 - - - +
56X THR* 1.3 76.2 - - - +
58X MET* 1.3 56.7 + - - +
60X GLY* 3.3 2.7 + - - +
61X ARG* 2.9 29.4 + - - +
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Residues in contact with MET 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ALA 2.9 19.8 + - - +
55X ASN* 3.6 7.6 - - - +
56X THR 3.2 0.2 - - - -
57X ALA* 1.3 74.0 - - - +
59X VAL* 1.3 60.3 + - - +
61X ARG* 3.8 5.8 - - - +
62X LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W ASN* 6.5 1.3 - - + -
55X ASN 2.9 13.1 + - - +
56X THR* 3.0 12.7 + - - +
58X MET* 1.3 77.4 - - - +
60X GLY* 1.3 56.7 + - - +
62X LEU* 3.3 7.0 + - - +
63X LYS* 2.9 29.3 + - - +
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Residues in contact with GLY 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X THR 2.9 13.3 + - - -
57X ALA* 3.3 2.7 + - - -
59X VAL* 1.3 78.0 - - - +
61X ARG* 1.3 55.7 + - - +
63X LYS* 3.3 7.6 + - - +
64X ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X ALA 2.9 17.6 + - - +
58X MET* 3.8 7.2 - - - +
60X GLY* 1.3 74.6 - - - +
62X LEU* 1.3 58.2 + - - +
64X ALA* 3.1 8.3 + - - +
65X ASN* 2.9 31.2 + - - +
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Residues in contact with LEU 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X MET 2.9 19.1 + - - +
59X VAL* 3.7 6.3 - - - +
61X ARG* 1.3 76.3 - - - +
63X LYS* 1.3 63.0 + - - +
65X ASN* 3.8 4.7 - - - +
66X ASN* 3.1 25.6 + - - +
72X ILE* 6.1 5.2 - - + -
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Residues in contact with LYS 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88W LEU* 5.6 9.2 - - + -
94W THR* 5.4 11.9 - - - -
59X VAL 2.9 17.8 + - - +
60X GLY* 3.3 7.4 + - - +
62X LEU* 1.3 78.1 - - - +
64X ALA* 1.3 62.2 + - - +
66X ASN* 3.7 14.3 + - - +
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Residues in contact with ALA 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X GLY 2.9 16.6 + - - +
61X ARG* 3.1 8.2 + - - +
63X LYS* 1.3 80.1 - - - +
65X ASN* 1.3 58.3 + - + +
66X ASN 3.6 3.6 + - - +
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Residues in contact with ASN 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X PHE* 4.7 13.0 - - - +
31X PHE* 5.2 14.4 - - + -
61X ARG 2.9 15.8 + - - +
62X LEU* 3.4 4.9 + - - +
63X LYS 3.4 0.2 - - - -
64X ALA* 1.3 74.5 - - + +
66X ASN* 1.3 65.2 + - - +
67X PRO* 3.4 2.9 - - - +
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Residues in contact with ASN 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88W LEU* 5.9 7.0 - - + +
90W GLY* 4.8 15.2 - - - +
28X PHE* 6.0 0.7 - - - -
62X LEU 3.1 16.8 + - - +
63X LYS* 3.9 11.8 - - - +
64X ALA 3.4 5.3 - - - +
65X ASN* 1.3 78.0 - - - +
67X PRO* 1.3 68.3 - - - +
70X GLY 5.2 5.6 - - - +
72X ILE* 6.0 6.3 - - + -
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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