Contacts of the helix formed by residues 65 - 71 (chain L) in PDB entry 2WQT
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 HIS 65 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.4 0.6 - - - +
64L THR* 1.3 85.5 - - - +
66L PRO* 1.4 70.5 - - + +
67L LYS* 4.4 5.4 - - + +
68L VAL* 3.1 25.4 + - + +
69L GLN* 3.0 22.6 + - - +
199L GLU* 3.2 47.4 + - + +
232L ALA* 2.8 38.3 + - + +
234L GLY* 4.1 15.7 - - - -
235L PRO* 4.7 3.1 - - + -
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Residues in contact with PRO 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L THR 3.5 8.3 - - - +
65L HIS* 1.4 82.7 - - + +
67L LYS* 1.3 60.8 + - - +
69L GLN* 3.6 20.3 - - + +
70L GLN* 3.2 29.5 + - + +
199L GLU 4.5 6.3 - - - +
201L LEU* 5.5 8.3 - - + +
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Residues in contact with LYS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L HIS* 3.1 5.3 - - + -
66L PRO* 1.3 75.5 - - - +
68L VAL* 1.3 68.3 + - + +
70L GLN* 3.2 6.8 + - - +
71L GLN* 3.1 29.9 + - - +
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Residues in contact with VAL 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L LEU* 3.9 31.4 - - + -
65L HIS* 3.1 25.2 + - + +
67L LYS* 1.3 77.2 - - + +
69L GLN* 1.3 61.4 + - - +
71L GLN* 3.6 22.6 + - - +
72L LEU* 3.4 30.0 + - + +
1262L PO4 5.6 2.2 - - - +
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Residues in contact with GLN 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.1 30.3 - - + +
64L THR* 4.5 0.5 - - - -
65L HIS 3.0 16.8 + - - +
66L PRO* 3.6 23.2 + - - +
67L LYS 3.2 0.2 - - - -
68L VAL* 1.3 76.5 - - - +
70L GLN* 1.3 62.0 + - - +
72L LEU* 3.2 3.3 + - - -
73L GLY 3.2 4.5 + - - -
74L VAL* 2.9 39.5 + - - +
75L ASP* 3.4 25.3 + - - +
76L GLN 3.5 23.4 - - - +
77L PRO* 3.7 6.1 - - - +
201L LEU* 4.1 14.8 - - - +
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Residues in contact with GLN 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L PRO 3.2 13.0 + - - +
67L LYS* 3.2 8.5 + - - +
69L GLN* 1.3 74.6 + - - +
71L GLN* 1.3 55.6 + - - +
72L LEU 2.8 15.2 + - - -
73L GLY* 2.9 16.7 + - - +
74L VAL 3.6 18.6 + - - +
75L ASP* 4.9 6.8 - - - +
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Residues in contact with GLN 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L LYS* 3.1 17.8 + - - +
68L VAL* 3.9 23.4 - - - +
70L GLN* 1.3 75.7 - - - +
72L LEU* 1.3 77.6 + - + +
150L GLN* 4.4 7.3 + - - +
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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