Contacts of the helix formed by residues 65 - 69 (chain D) in PDB entry 5D4D
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 ARG 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766C GLU* 4.0 30.3 + - - +
767C PRO 3.1 22.6 + - - -
768C THR* 5.1 0.4 - - - +
769C PRO* 3.6 25.6 - - - +
772C ARG* 3.8 19.6 - - - +
56D TYR* 3.3 12.5 + - - +
63D TYR 3.6 0.4 - - - -
64D LYS* 1.3 87.3 - - - +
66D GLN* 1.3 64.3 + - + +
67D ARG* 3.0 17.9 + - + +
68D PHE* 3.3 18.4 + - + -
80D VAL* 3.6 9.5 - - - +
373F LYS 4.7 1.8 + - - -
374F GLY* 5.5 0.4 - - - -
378F GLY* 3.1 35.5 + - - +
379F ARG* 6.0 0.4 - - - -
380F GLU* 4.8 9.1 + - - +
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Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.5 56.5 + - + +
65D ARG* 1.3 72.7 - - + +
67D ARG* 1.3 65.7 + - - +
68D PHE 3.0 4.1 + - - -
69D GLU* 3.0 23.0 + - - +
378F GLY* 6.3 1.6 - - - -
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG* 3.0 15.5 - - + +
66D GLN* 1.3 78.4 - - - +
68D PHE* 1.3 98.0 + - + +
69D GLU 3.7 0.9 + - - +
377F ASP* 3.1 44.6 + - + +
378F GLY* 5.3 0.2 - - - -
379F ARG* 3.3 44.3 - - - +
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS 5.1 2.0 - - - -
63D TYR* 3.5 54.1 - + + -
64D LYS 4.5 3.8 - - - -
65D ARG* 3.3 19.8 + - + +
66D GLN 3.0 1.0 - - - -
67D ARG* 1.3 128.2 - - + +
69D GLU* 1.3 64.7 + - - +
71D LYS* 2.8 32.5 + - + +
80D VAL* 3.9 14.1 - - + +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.1 36.9 + - + -
66D GLN* 3.0 26.5 + - + +
67D ARG 3.5 2.1 + - - +
68D PHE* 1.3 77.1 - - - +
70D GLY* 1.3 62.9 + - - +
71D LYS 3.7 0.2 + - - -
79D GLU* 5.8 0.2 - - - +
80D VAL* 3.2 17.1 - - - +
81D THR* 3.8 15.7 + - - -
82D LYS* 4.3 7.8 - - - +
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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