Contacts of the helix formed by residues 498 - 503 (chain D) in PDB entry 5ON2
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 TRP 498 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D TYR* 3.5 53.0 + + - -
135D TRP* 3.8 15.0 - + + -
136D GLU* 3.0 39.6 + - + +
494D MET 3.1 20.6 + - - -
495D GLU 3.6 3.3 + - - -
497D SER* 1.3 78.5 - - - +
499D TYR* 1.3 63.5 + - - +
500D TYR* 3.3 11.9 - - - -
501D ALA* 3.3 11.8 + - - +
502D ARG* 3.4 30.8 + - + -
512D MET* 3.6 32.3 - - + -
513D LEU* 4.9 4.3 - - + -
544D PHE* 3.8 29.8 - + + -
548D MET* 4.2 10.8 - - + -
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Residues in contact with TYR 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 4.2 11.7 - - + -
39D SER 3.8 0.9 + - - -
40D MET* 3.4 15.9 - - - -
41D LEU* 3.7 36.6 - - + -
125D LEU* 4.3 4.7 - - + +
127D THR* 5.3 1.6 - - + -
132D TYR* 3.2 28.8 + - + +
495D GLU 3.6 4.0 + - - +
496D SER* 3.2 33.4 - - - -
498D TRP* 1.3 76.2 - - - +
500D TYR* 1.3 71.6 + + + +
502D ARG* 3.2 12.2 + - - +
503D TYR* 3.3 57.0 + + - -
527D TYR* 2.8 38.6 + + - -
537D HIS* 4.6 0.4 - + - -
541D PHE* 5.8 0.7 - + - -
901D LSS 3.8 9.5 - - + +
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Residues in contact with TYR 500 (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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36D TYR* 2.6 33.1 + - - +
38D LEU* 3.4 29.6 - - + -
497D SER 3.4 25.6 - - - -
498D TRP* 3.9 8.7 - - - -
499D TYR* 1.3 88.0 - + + +
501D ALA* 1.3 74.6 + - + +
503D TYR* 3.7 7.3 + - - +
504D THR* 4.4 1.0 - - - +
522D LEU* 3.6 28.5 - - + -
524D VAL* 4.2 7.6 - - + -
541D PHE* 3.5 26.9 - + + -
545D HIS* 2.7 42.8 + + - +
548D MET* 3.3 16.7 - - + +
554D VAL* 5.5 0.2 - - - +
559D PRO* 4.0 12.6 - - + -
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Residues in contact with ALA 501 (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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498D TRP 3.3 8.0 + - - +
499D TYR 3.2 0.6 - - - -
500D TYR* 1.3 99.7 - - + +
502D ARG* 1.3 62.0 + - - +
503D TYR 3.3 0.2 - - - -
504D THR* 2.6 29.0 + - - -
513D LEU* 3.3 34.6 - - + +
522D LEU* 4.2 15.5 - - + -
548D MET* 4.5 6.3 - - + -
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Residues in contact with ARG 502 (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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125D LEU* 3.8 14.6 - - + +
131D GLU* 4.0 10.1 + - - +
132D TYR* 3.8 28.1 - - + +
135D TRP* 3.3 22.6 - - - +
498D TRP* 3.4 24.0 + - + +
499D TYR 3.2 9.7 + - - +
501D ALA* 1.3 77.2 - - - +
503D TYR* 1.3 59.5 + - - +
504D THR 3.2 0.2 - - - -
505D CYS 3.2 20.8 + - - +
506D PRO* 3.0 51.8 + - - +
507D GLN 4.5 0.4 - - - -
508D TYR* 3.1 29.9 + - - +
509D LYS* 5.4 2.6 - - - +
511D GLY 3.4 7.1 + - - -
512D MET 2.9 34.1 + - - -
513D LEU* 3.8 4.4 - - - +
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Residues in contact with TYR 503 (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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36D TYR* 3.4 22.4 - - + +
38D LEU* 3.7 6.3 - - + -
39D SER 5.5 0.3 + - - -
41D LEU* 3.8 7.7 - - + +
74D LEU* 4.8 3.7 - - + +
76D PRO* 3.3 35.4 - - + -
77D ILE* 3.2 14.7 - - - -
78D GLY* 2.8 29.5 + - - -
123D ARG* 2.8 60.4 + - + +
125D LEU* 3.6 21.8 - - + -
499D TYR* 3.3 47.9 + + - -
500D TYR* 4.1 1.1 - - - -
501D ALA 3.3 0.6 - - - -
502D ARG* 1.3 77.1 - - - +
504D THR* 1.3 50.1 + - - +
505D CYS 3.3 0.6 + - - -
506D PRO* 3.6 6.9 - - - +
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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