Contacts of the helix formed by residues 98 - 101 (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 ARG 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D TYR* 3.5 27.8 - - + +
78D PRO* 4.0 3.1 - - - +
79D SER* 2.7 37.5 + - - +
80D ARG* 5.3 1.4 - - - +
97D CYS* 1.3 72.9 - - - +
99D ALA* 1.3 56.2 + - - +
100D SER 3.1 4.6 + - - -
101D TRP* 3.2 53.4 + - + +
166D TYR* 4.0 16.6 + - + -
168D TYR* 3.5 7.3 + - - -
241D ASP* 2.7 41.2 + - - +
245D THR* 3.4 29.6 - - - +
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Residues in contact with ALA 99 (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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77D TYR* 4.2 9.2 + - - +
97D CYS* 3.1 14.3 + - - +
98D ARG* 1.3 75.8 - - - +
100D SER* 1.3 56.6 + - - +
105D TYR* 4.0 9.2 + - + -
168D TYR* 3.3 35.4 + - + -
238D TYR* 5.6 0.7 - - + -
291D SER* 2.9 15.0 + - - -
503D B12 4.2 31.7 + - + +
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Residues in contact with SER 100 (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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96D PHE* 3.6 17.7 - - - +
97D CYS* 2.9 13.8 + - - -
99D ALA* 1.3 80.0 - - - +
101D TRP* 1.3 60.8 + - - +
102D GLY 3.9 1.0 + - - -
238D TYR* 3.8 20.4 - - - -
268D ALA* 5.6 2.3 - - - +
290D VAL* 3.7 18.9 - - - +
291D SER* 3.4 14.3 + - - +
292D GLY* 2.8 28.8 + - - -
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Residues in contact with TRP 101 (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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78D PRO* 3.5 28.7 - - + -
79D SER 3.8 9.6 - - - -
80D ARG* 3.7 21.3 - - - -
81D MET* 3.6 41.4 - - + +
95D ILE* 4.7 4.7 - - + -
96D PHE* 3.0 24.9 + - + -
97D CYS 3.2 10.7 + - - -
98D ARG* 3.2 41.7 + - + +
99D ALA 3.6 0.2 - - - -
100D SER* 1.3 79.8 - - - +
102D GLY* 1.3 64.4 + - - +
103D LYS 4.4 3.3 - - - +
168D TYR* 4.0 11.1 + - - -
261D MET* 3.2 18.9 - - - +
263D PRO* 3.6 29.6 - - + -
268D ALA* 4.0 16.0 - - + +
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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