Contacts of the helix formed by residues 59 - 64 (chain D) in PDB entry 5D0A
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 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D THR* 3.9 21.4 - - + +
55D GLU* 2.7 28.8 + - - -
56D LYS 3.5 4.9 + - - +
57D ARG 3.5 0.6 - - - -
58D VAL* 1.3 89.3 + - - +
60D PRO* 1.3 66.8 - - + +
61D LYS* 4.3 8.5 - - + +
62D LEU* 2.9 43.9 + - + +
63D LEU* 3.6 6.8 + - - +
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Residues in contact with PRO 60 (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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27D ALA* 3.5 31.4 - - + +
28D ASP 3.7 14.6 - - - +
29D THR* 4.2 0.2 - - - -
30D PHE* 3.7 23.3 - - + -
58D VAL 3.4 9.4 - - - +
59D THR* 1.3 87.5 - - + +
61D LYS* 1.3 55.9 + - - +
63D LEU* 3.1 11.3 + - + +
64D LEU* 2.9 25.8 + - - +
67D ALA* 4.2 2.4 - - - +
70D ILE* 3.7 17.7 - - + -
138D LEU* 4.4 4.7 - - + -
173D ILE* 4.1 19.6 - - + +
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Residues in contact with LYS 61 (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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27D ALA* 3.3 25.7 + - + +
28D ASP* 3.5 20.8 + - - +
59D THR* 3.0 9.2 + - + +
60D PRO* 1.3 74.4 - - - +
62D LEU* 1.3 63.7 + - - +
63D LEU 3.3 0.2 - - - -
64D LEU 3.3 22.3 - - - +
65D PRO* 3.6 7.6 - - - +
66D LYS* 4.5 6.2 + - - +
67D ALA* 3.4 30.2 + - + +
68D LYS* 5.5 7.2 - - - +
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Residues in contact with LEU 62 (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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357B GLU* 6.1 1.1 - - - +
55D GLU* 4.0 37.9 - - + +
56D LYS* 4.5 9.2 - - + +
59D THR* 2.9 26.4 + - + +
61D LYS* 1.3 79.2 - - - +
63D LEU* 1.3 66.9 + - + +
65D PRO* 4.9 3.8 - - - +
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Residues in contact with LEU 63 (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 LYS* 3.6 41.5 - - + +
59D THR 3.9 6.1 - - - +
60D PRO* 3.1 5.5 + - + +
62D LEU* 1.3 83.1 - - - +
64D LEU* 1.3 60.2 + - - +
65D PRO* 3.7 6.5 - - - +
130D LYS* 3.6 25.5 - - + +
132D MET* 4.3 1.6 - - + -
137D GLU* 3.8 39.3 - - + +
138D LEU* 3.7 32.1 - - + -
173D ILE* 3.9 14.8 - - + -
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Residues in contact with LEU 64 (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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60D PRO 2.9 6.9 + - - -
61D LYS* 3.3 8.6 - - - +
63D LEU* 1.3 78.5 - - - +
65D PRO* 1.3 73.1 - - + +
66D LYS 3.2 0.7 + - - -
67D ALA* 3.0 21.9 + - + +
128D ARG* 3.6 40.2 - - + +
129D THR* 4.0 22.9 - - - +
130D LYS* 4.2 10.3 - - + -
173D ILE* 3.6 42.2 - - + +
174D THR* 3.8 15.9 - - - -
175D ASN* 4.0 2.0 - - - +
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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