Contacts of the helix formed by residues 502 - 508 (chain D) in PDB entry 1R0X
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 ILE 502 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501D THR* 1.3 73.5 - - - +
503D LYS* 1.3 64.1 + - - +
505D ASN* 3.0 5.8 + - - +
506D ILE* 2.9 46.1 + - + +
526D LEU* 5.7 0.7 - - + -
530D ILE* 4.3 21.1 - - + -
533D PHE* 3.8 35.9 - - + -
536D GLN 3.9 4.7 - - - +
537D ASP* 3.7 12.1 - - - +
539D THR* 3.0 24.0 + - + +
541D LEU* 3.9 27.8 - - + +
548D LEU* 6.0 0.4 - - + -
556D ILE* 4.3 18.6 - - + -
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Residues in contact with LYS 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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597A ASN* 5.7 4.2 - - - +
501D THR* 3.9 3.8 - - - +
502D ILE* 1.3 78.4 - - - +
504D GLU* 1.3 65.3 + - + +
506D ILE* 3.1 2.8 + - - +
507D ILE* 3.0 37.9 + - + +
512D TYR* 3.3 37.5 + - + -
514D GLU* 4.9 1.4 + - - -
517D TYR* 3.4 21.8 - - - +
537D ASP* 3.1 34.3 + - - +
538D ASN* 4.6 15.7 - - - +
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Residues in contact with GLU 504 (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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499D PRO 5.8 0.2 - - - +
500D GLY* 3.3 13.6 - - - -
501D THR* 2.9 46.6 + - - +
503D LYS* 1.3 76.9 - - + +
505D ASN* 1.3 54.4 + - - +
507D ILE* 5.0 2.9 - - - -
508D PHE* 2.7 34.7 + - - +
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Residues in contact with ASN 505 (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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497D ILE* 3.5 7.7 - - - -
498D MET* 2.8 51.9 + - - +
499D PRO 4.8 0.4 + - - -
500D GLY* 3.9 9.3 + - - -
501D THR 2.8 23.2 + - - +
502D ILE* 3.0 9.8 + - - +
504D GLU* 1.3 78.3 - - - +
506D ILE* 1.3 59.8 + - - +
508D PHE* 3.5 7.5 - - - +
541D LEU* 3.9 9.9 - - + +
556D ILE* 4.1 13.0 - - + -
560D ARG* 2.7 50.8 + - - +
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Residues in contact with ILE 506 (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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502D ILE* 2.9 35.5 + - + +
503D LYS 3.1 5.8 + - - +
505D ASN* 1.3 78.3 - - - +
507D ILE* 1.3 62.0 + - - +
517D TYR* 3.8 36.1 - - + +
520D VAL* 5.1 1.8 - - + -
521D VAL* 4.1 8.7 - - + -
526D LEU* 3.9 22.9 - - + -
530D ILE* 6.1 0.9 - - + -
537D ASP* 5.3 0.2 - - - +
556D ILE* 4.2 13.0 - - + +
559D ALA* 4.1 30.1 - - + +
560D ARG* 3.3 28.1 - - - +
563D TYR* 4.1 12.9 - - + +
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Residues in contact with ILE 507 (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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503D LYS* 3.0 32.1 + - + +
504D GLU* 4.5 2.9 - - - +
506D ILE* 1.3 75.2 - - - +
508D PHE* 1.3 72.5 + - - +
509D GLY 4.4 2.0 - - - +
510D VAL* 2.9 49.0 + - - +
512D TYR* 3.0 45.8 - - + +
517D TYR* 3.6 14.6 - - + -
563D TYR* 3.7 28.1 - - + -
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Residues in contact with PHE 508 (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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496D TRP* 2.8 43.5 - + - -
498D MET* 4.6 16.2 - - + -
504D GLU 2.7 22.1 + - - -
505D ASN* 3.5 16.2 - - - +
506D ILE 4.1 0.2 - - - +
507D ILE* 1.3 75.8 - - - +
509D GLY* 1.3 60.3 + - - +
510D VAL* 3.2 7.3 + - + +
560D ARG* 3.7 26.9 - - + -
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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