Contacts of the helix formed by residues 51 - 66 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6T MET* 4.9 8.3 - - - +
49T LEU* 3.4 5.0 - - - +
50T LEU* 1.3 81.9 - - + +
52T HIS* 1.3 65.6 + - - +
53T THR* 3.3 7.9 - - - +
54T ALA* 3.6 7.5 + - + +
55T ASN* 3.2 21.7 + - - +
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Residues in contact with HIS 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T ASN* 1.3 75.4 - - - +
53T THR* 1.3 60.6 + - - +
55T ASN* 3.2 8.4 + - - +
56T THR* 2.9 29.5 + - - -
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Residues in contact with THR 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P LYS* 5.5 11.4 - - - -
30P THR 5.0 13.0 - - - -
51T ASN* 3.3 5.2 - - - +
52T HIS* 1.3 79.0 - - - +
54T ALA* 1.3 58.3 + - - +
56T THR* 3.1 6.8 + - - -
57T ALA* 2.9 29.7 + - - +
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Residues in contact with ALA 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T LEU* 4.9 5.1 - - + +
50T LEU* 4.5 13.5 - - + +
51T ASN* 3.6 19.0 + - + +
52T HIS 3.4 0.2 - - - -
53T THR* 1.3 78.4 - - - +
55T ASN* 1.3 57.2 + - - +
57T ALA* 4.0 6.1 - - - +
58T MET* 2.9 30.3 + - - +
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Residues in contact with ASN 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T MET* 5.1 8.3 - - + -
49T LEU* 4.4 14.3 - - + +
51T ASN 3.2 15.3 + - - +
52T HIS* 3.4 13.0 - - - +
53T THR 3.1 0.6 - - - -
54T ALA* 1.3 74.7 - - - +
56T THR* 1.3 59.3 + - - +
58T MET* 3.3 6.8 + - - +
59T VAL* 2.9 27.7 + - - +
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Residues in contact with THR 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T HIS 2.9 15.8 + - - -
53T THR* 3.7 6.3 - - - -
55T ASN* 1.3 74.3 - - - +
57T ALA* 1.3 65.3 + - - +
59T VAL* 3.0 8.7 + - - +
60T GLY* 2.9 19.9 + - - -
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Residues in contact with ALA 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53T THR 2.9 16.5 + - - +
54T ALA* 4.0 7.0 - - - +
56T THR* 1.3 74.5 - - - +
58T MET* 1.3 57.9 + - - +
60T GLY* 3.3 2.1 + - - +
61T ARG* 2.9 29.5 + - - +
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Residues in contact with MET 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T ALA 2.9 21.2 + - - +
55T ASN* 3.6 7.4 - - - +
57T ALA* 1.3 74.2 - - - +
59T VAL* 1.3 60.1 + - - +
61T ARG* 3.8 6.2 - - - +
62T LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q ILE* 5.8 8.5 - - + -
55T ASN 2.9 14.7 + - - +
56T THR* 3.0 11.2 + - - +
58T MET* 1.3 77.7 - - - +
60T GLY* 1.3 56.9 + - - +
62T LEU* 3.3 6.2 + - - +
63T LYS* 2.9 29.5 + - - +
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Residues in contact with GLY 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T THR 2.9 13.3 + - - -
57T ALA* 3.8 2.9 - - - -
59T VAL* 1.3 77.2 - - - +
61T ARG* 1.3 55.9 + - - +
63T LYS* 3.3 7.7 + - - +
64T ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57T ALA 2.9 16.8 + - - +
58T MET* 3.8 7.2 - - - +
60T GLY* 1.3 74.8 - - - +
62T LEU* 1.3 57.6 + - - +
64T ALA* 3.1 7.4 + - - +
65T ASN* 2.9 31.9 + - - +
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Residues in contact with LEU 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q LEU* 5.1 6.2 - - + +
58T MET 2.9 19.1 + - - +
59T VAL* 3.7 5.6 - - - +
61T ARG* 1.3 76.5 - - - +
63T LYS* 1.3 62.4 + - - +
65T ASN* 3.8 4.3 - - - +
66T ASN* 3.1 26.0 + - - +
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Residues in contact with LYS 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q LEU* 4.4 21.0 - - + +
59T VAL 2.9 17.1 + - - +
60T GLY* 3.3 7.8 + - - +
62T LEU* 1.3 76.7 - - - +
64T ALA* 1.3 61.3 + - - +
66T ASN* 3.8 12.4 + - - +
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Residues in contact with ALA 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T GLY 2.9 17.0 + - - +
61T ARG* 3.1 8.0 + - - +
63T LYS* 1.3 80.0 - - - +
65T ASN* 1.3 59.1 + - - +
66T ASN 3.4 3.5 + - - +
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Residues in contact with ASN 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T PHE* 4.7 12.7 - - - +
31T PHE* 5.2 14.4 - - + -
61T ARG 2.9 15.4 + - - +
62T LEU* 3.4 5.6 + - - +
63T LYS 3.4 0.2 - - - -
64T ALA* 1.3 74.9 - - + +
66T ASN* 1.3 64.9 + - - +
67T PRO* 3.3 3.6 - - - +
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Residues in contact with ASN 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q LEU* 4.8 9.2 - - + +
89Q TYR 4.9 0.4 - - - -
90Q GLY* 3.9 28.3 - - - +
28T PHE* 6.0 0.7 - - - -
62T LEU 3.1 15.5 + - - +
63T LYS* 3.9 11.6 - - - +
64T ALA 3.4 5.8 - - - +
65T ASN* 1.3 77.3 - - - +
67T PRO* 1.3 63.3 - - - +
68T LYS 3.9 0.2 + - - -
70T GLY 5.1 3.4 - - - +
72T ILE* 5.9 3.8 - - + -
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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