Contacts of the helix formed by residues 78 - 84 (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 THR 78 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7X ARG* 4.6 1.3 - - - -
77X VAL* 1.3 76.8 - - - +
79X GLU* 1.3 61.8 + - - +
80X LYS* 3.2 10.1 - - - -
81X GLN* 3.2 11.7 + - - +
82X PHE* 2.8 27.3 + - - +
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Residues in contact with GLU 79 (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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7X ARG* 5.1 3.0 - - - +
78X THR* 1.3 74.3 - - - +
80X LYS* 1.3 57.1 + - - +
82X PHE* 3.2 8.7 + - - +
83X ALA* 2.9 30.1 + - - +
19Z ASN* 5.7 9.4 - - + -
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Residues in contact with LYS 80 (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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78X THR* 3.2 6.7 - - - -
79X GLU* 1.3 78.8 - - - +
81X GLN* 1.3 61.6 + - - +
83X ALA* 3.6 5.6 + - - +
84X ARG* 3.2 21.8 + - - +
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Residues in contact with GLN 81 (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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75W LEU* 5.3 3.0 - - + +
76W THR* 3.2 31.0 + - - +
77W VAL* 5.4 0.7 - - - -
77X VAL* 4.5 9.6 - - + -
78X THR* 3.2 22.2 + - - +
80X LYS* 1.3 77.1 - - - +
82X PHE* 1.3 64.5 + - - +
84X ARG* 3.3 9.0 + - - +
85X MET* 3.2 18.4 + - - +
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Residues in contact with PHE 82 (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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7X ARG* 4.8 13.2 - - + -
77X VAL* 5.0 4.2 - - + +
78X THR 2.8 16.8 + - - +
79X GLU* 3.2 9.1 + - - +
81X GLN* 1.3 76.6 - - - +
83X ALA* 1.3 61.2 + - - +
85X MET* 3.3 21.9 + - - +
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Residues in contact with ALA 83 (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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79X GLU 2.9 16.9 + - - +
80X LYS* 4.1 5.6 - - - +
82X PHE* 1.3 76.6 - - - +
84X ARG* 1.3 58.3 + - - +
85X MET 3.2 3.7 + - - +
97X ALA* 3.7 25.9 - - + +
32Z MET* 5.2 15.9 - - + +
34Z HIS* 6.3 2.2 - - + +
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Residues in contact with ARG 84 (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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74W ILE 4.3 2.8 - - - +
75W LEU* 5.2 2.5 - - - -
76W THR* 5.0 14.4 + - - -
80X LYS 3.2 17.6 + - - +
81X GLN* 3.6 10.8 - - - +
82X PHE 3.2 1.2 - - - -
83X ALA* 1.3 75.5 - - - +
85X MET* 1.3 63.2 + - - +
86X ILE* 3.3 7.4 + - - +
97X ALA 6.2 1.1 - - - -
98X ASN* 5.2 5.5 - - - +
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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