Contacts of the helix formed by residues 51 - 66 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ASP* 4.8 16.6 - - + -
6Q MET* 5.2 7.8 - - - +
49Q LEU* 3.4 5.2 - - - +
50Q LEU* 1.3 82.2 - - + +
52Q HIS* 1.3 66.5 + - - +
53Q THR* 3.2 9.2 - - - +
54Q ALA* 3.6 5.0 + - + +
55Q ASN* 3.1 21.2 + - - +
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Residues in contact with HIS 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER* 4.4 3.9 - - - +
105B THR* 4.9 19.1 - - - -
106B ASP* 5.6 3.3 - - - +
51Q ASN* 1.3 74.6 - - - +
53Q THR* 1.3 59.8 + - - +
55Q ASN* 3.4 8.8 - - - +
56Q THR* 2.9 29.6 + - - -
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Residues in contact with THR 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER 5.4 0.4 - - - -
102B SER* 3.5 37.6 + - - -
103B LEU* 4.4 5.2 - - - -
106B ASP* 4.9 7.6 - - - +
51Q ASN* 3.2 5.2 - - - +
52Q HIS* 1.3 78.3 - - - +
54Q ALA* 1.3 63.2 + - - +
56Q THR* 3.1 4.2 + - - -
57Q ALA* 3.0 25.0 + - - +
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Residues in contact with ALA 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q LEU* 4.7 6.0 - - + +
50Q LEU* 4.4 20.9 - - + +
51Q ASN* 3.6 9.8 + - + +
52Q HIS 3.5 0.2 - - - -
53Q THR* 1.3 78.6 - - - +
55Q ASN* 1.3 57.0 + - - +
57Q ALA* 4.1 6.5 - - - +
58Q MET* 2.9 30.5 + - - +
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Residues in contact with ASN 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q MET* 5.3 7.9 - - + -
49Q LEU* 4.4 13.2 - - + +
51Q ASN 3.1 15.1 + - - +
52Q HIS* 3.4 13.7 - - - +
53Q THR 3.1 0.6 - - - -
54Q ALA* 1.3 75.6 - - - +
56Q THR* 1.3 59.8 + - - +
58Q MET* 3.3 5.3 + - - +
59Q VAL* 2.9 28.6 + - - +
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Residues in contact with THR 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASP* 4.6 17.2 - - - +
99B SER* 6.0 0.4 - - - -
102B SER* 4.4 14.1 - - - -
52Q HIS 2.9 17.3 + - - -
53Q THR 3.7 3.4 - - - -
55Q ASN* 1.3 73.0 - - - +
57Q ALA* 1.3 67.4 + - - +
59Q VAL* 3.0 9.4 + - - +
60Q GLY* 3.0 19.9 + - - -
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Residues in contact with ALA 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 6.5 1.8 - - - -
53Q THR 3.0 16.1 + - - +
54Q ALA* 4.1 7.2 - - - +
56Q THR* 1.3 76.2 - - - +
58Q MET* 1.3 57.2 + - - +
60Q GLY* 3.3 2.2 + - - +
61Q ARG* 2.9 28.8 + - - +
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Residues in contact with MET 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q ALA 2.9 21.2 + - - +
55Q ASN* 3.6 6.5 - - - +
57Q ALA* 1.3 72.8 - - - +
59Q VAL* 1.3 61.3 + - - +
61Q ARG* 3.8 6.3 - - - +
62Q LEU* 2.9 30.5 + - - +
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Residues in contact with VAL 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q ASN 2.9 13.2 + - - +
56Q THR* 3.0 12.3 + - - +
58Q MET* 1.3 77.2 - - - +
60Q GLY* 1.3 62.4 + - - +
62Q LEU* 3.3 6.3 + - - +
63Q LYS* 2.9 24.8 + - - +
88T LEU* 5.5 1.2 - - - +
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Residues in contact with GLY 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q THR 3.0 12.5 + - - -
57Q ALA* 3.3 3.3 + - - -
59Q VAL* 1.3 77.2 - - - +
61Q ARG* 1.3 56.1 + - - +
63Q LYS* 3.3 7.5 + - - +
64Q ALA* 2.9 28.1 + - - +
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Residues in contact with ARG 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q ALA 2.9 17.5 + - - +
58Q MET* 3.8 7.2 - - - +
60Q GLY* 1.3 75.3 - - - +
62Q LEU* 1.3 58.7 + - - +
64Q ALA* 3.1 8.9 + - - +
65Q ASN* 2.9 31.3 + - - +
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Residues in contact with LEU 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Q MET 2.9 18.5 + - - +
59Q VAL* 3.7 6.7 - - - +
60Q GLY 3.3 0.2 - - - -
61Q ARG* 1.3 75.7 - - - +
63Q LYS* 1.3 61.3 + - - +
65Q ASN* 3.4 4.9 + - - +
66Q ASN* 3.1 25.5 + - - +
88T LEU* 4.6 8.2 - - + +
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Residues in contact with LYS 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q VAL 2.9 16.5 + - - +
60Q GLY* 3.3 8.0 + - - +
62Q LEU* 1.3 77.1 - - - +
64Q ALA* 1.3 61.4 + - - +
66Q ASN* 3.8 11.4 + - - +
88T LEU* 4.1 20.6 - - + +
89T TYR 5.7 0.9 - - - +
90T GLY* 5.1 4.0 - - - -
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Residues in contact with ALA 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q GLY 2.9 16.8 + - - +
61Q ARG* 3.1 8.5 + - - +
63Q LYS* 1.3 80.1 - - - +
65Q ASN* 1.3 58.6 + - - +
66Q ASN 3.6 3.3 + - - +
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Residues in contact with ASN 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q PHE* 4.7 12.9 - - - +
31Q PHE* 5.2 14.4 - - + -
61Q ARG 2.9 16.4 + - - +
62Q LEU* 3.4 5.1 + - - +
64Q ALA* 1.3 75.2 - - + +
66Q ASN* 1.3 64.4 + - - +
67Q PRO* 3.3 3.5 - - - +
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Residues in contact with ASN 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q PHE* 6.0 0.7 - - - -
62Q LEU 3.1 15.6 + - - +
63Q LYS* 4.0 8.8 - - - +
64Q ALA 3.4 5.5 - - - +
65Q ASN* 1.3 77.5 - - - +
67Q PRO* 1.3 63.7 - - - +
68Q LYS 3.9 0.2 + - - -
70Q GLY* 5.2 3.4 - - - +
72Q ILE* 5.9 3.4 - - + -
88T LEU* 4.5 11.2 - - + +
89T TYR 4.3 1.6 - - - -
90T GLY* 3.5 32.9 - - - +
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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