Contacts of the helix formed by residues 502 - 506 (chain B) in PDB entry 5IYB
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 HIS 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801A GLY* 3.5 41.1 + - - -
837A PHE* 4.5 0.7 - - - -
841A MET* 3.9 0.9 - - - +
384B ASP* 3.3 25.8 + - - -
386B ASP* 3.4 39.7 + - + +
387B HIS* 4.0 5.8 - + - +
388B TYR* 5.1 0.2 - - + -
497B LYS* 6.4 0.2 - - + -
500B GLN* 3.4 7.2 + - - +
501B LEU* 1.3 77.1 - - - +
503B ASN* 1.3 77.1 + - - +
504B THR* 2.9 26.2 + - + +
505B LEU* 3.1 32.9 + - + +
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Residues in contact with ASN 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A ILE* 3.7 5.9 - - - +
799A PRO* 3.2 38.0 + - - +
801A GLY* 3.7 20.9 - - - -
802A PHE* 3.9 8.2 - - + -
806A THR* 3.0 37.1 + - - +
807A LEU* 4.2 3.7 - - + +
837A PHE* 4.2 1.7 - - - -
838A PHE* 4.5 1.0 - - - -
841A MET* 3.2 28.6 - - + +
501B LEU 4.4 0.5 - - - +
502B HIS* 1.3 79.0 + - - +
504B THR* 1.3 59.4 + - - +
505B LEU 3.1 2.2 + - - -
506B TRP* 3.2 19.6 + - - +
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Residues in contact with THR 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A PHE* 3.5 29.2 - - + -
387B HIS* 3.3 39.3 - - + +
388B TYR* 3.5 34.4 + - - -
502B HIS* 2.9 17.9 + - + -
503B ASN* 1.3 68.6 - - - +
505B LEU* 1.3 64.1 + - - +
506B TRP 3.0 7.0 + - - +
508B MET* 3.9 13.3 - - - +
667B THR* 3.9 10.8 - - - +
670B GLU* 4.2 3.3 - - - +
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A PHE* 4.3 4.3 - - + -
844A ARG* 5.8 1.6 - - - +
388B TYR* 3.3 37.0 - - + +
500B GLN 5.0 2.2 - - - +
501B LEU* 3.4 24.2 - - + -
502B HIS* 3.1 41.0 + - + +
503B ASN 3.1 2.2 - - - -
504B THR* 1.3 77.5 - - - +
506B TRP* 1.3 65.4 + - - +
507B GLY 2.8 4.3 + - - -
508B MET* 2.9 16.6 + - - -
509B VAL* 3.4 50.3 + - + +
510B CYS 4.4 4.3 - - - +
524B LYS* 5.0 5.8 - - + +
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Residues in contact with TRP 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A PHE* 5.5 0.7 - - + -
807A LEU* 3.7 26.5 - - + -
808A PRO* 4.6 11.0 - - + -
809A HIS* 2.9 37.2 + + - -
833A PRO* 3.5 33.7 - - + -
834A THR* 4.4 0.7 - - - -
837A PHE* 3.4 55.2 - + + -
503B ASN 3.2 14.4 + - - +
504B THR 3.0 3.9 - - - +
505B LEU* 1.3 75.6 - - - +
507B GLY* 1.3 58.3 + - - +
508B MET* 3.5 3.8 + - - +
623B ARG* 3.1 16.4 - - - +
670B GLU* 3.4 23.1 - - - +
677B MET* 4.2 8.7 - - + -
697B GLU* 3.0 15.2 + - - -
700B PRO* 5.5 1.8 - - + -
703B ILE* 3.7 28.0 - - + +
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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