Contacts of the helix formed by residues 495 - 503 (chain C) in PDB entry 4L28
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 495 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C TRP* 2.5 33.6 + - + +
411C HIS* 3.9 7.9 + - - -
412C LEU 3.3 10.6 + - - -
413C ARG* 4.6 4.7 - - - +
414C VAL* 4.9 1.4 - - - +
493C THR 3.8 1.4 + - - -
494C ASP* 1.3 77.0 - - - +
496C LEU* 1.3 63.5 + - - +
497C GLY* 3.3 2.0 + - - -
498C ARG* 3.1 35.7 + - + +
499C LEU* 3.2 10.6 + - - +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C TRP* 3.5 49.7 - - + +
412C LEU* 2.7 27.8 + - + +
413C ARG 4.1 3.4 - - - +
414C VAL* 4.1 12.1 - - + -
417C LEU* 3.9 33.7 - - + -
495C THR* 1.3 72.7 + - - +
497C GLY* 1.3 57.6 + - - +
499C LEU* 3.1 14.8 + - + +
500C SER 2.9 21.3 + - - -
539C LEU* 4.0 11.8 - - + +
542C PHE* 3.8 31.9 - - + -
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Residues in contact with GLY 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TRP* 4.1 0.4 - - - -
410C TRP* 3.3 60.7 + - - -
495C THR* 3.2 1.6 - - - -
496C LEU* 1.3 74.9 - - - +
498C ARG* 1.3 64.9 + - - +
500C SER* 2.9 4.4 + - - -
501C HIS* 2.9 21.6 + - - -
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Residues in contact with ARG 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C LYS* 3.5 28.3 - - - +
490C ILE* 5.1 0.6 - - + +
494C ASP* 4.5 20.7 + - + +
495C THR* 3.1 33.2 + - + +
497C GLY* 1.3 76.4 - - - +
499C LEU* 1.3 63.8 + - - +
501C HIS* 3.2 19.8 + - - +
502C ILE* 2.9 61.0 + - + +
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Residues in contact with LEU 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C VAL* 5.6 3.6 - - + -
417C LEU* 4.2 6.3 - - + -
490C ILE* 3.7 16.1 - - + +
494C ASP* 6.5 0.4 - - + -
495C THR 3.2 5.3 + - - +
496C LEU* 3.1 27.8 + - + +
497C GLY 3.1 0.4 - - - -
498C ARG* 1.3 80.8 - - - +
500C SER* 1.3 56.9 + - - +
502C ILE* 3.0 11.3 + - + +
503C LEU* 2.9 46.9 + - + +
509C ALA* 3.6 30.5 - - + -
534C VAL* 3.7 30.7 - - + -
539C LEU* 4.0 21.3 - - + -
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Residues in contact with SER 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE 5.2 0.3 - - - +
409C TRP* 3.8 17.2 - - - -
410C TRP* 3.9 20.1 - - - -
496C LEU 2.9 13.2 + - - -
497C GLY 2.9 9.4 + - - -
499C LEU* 1.3 78.4 - - - +
501C HIS* 1.3 59.3 + - - +
503C LEU* 3.4 12.8 + - - +
504C GLU* 3.5 19.2 + - - +
539C LEU* 4.4 11.1 - - - +
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Residues in contact with HIS 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.6 31.5 + - - +
388C ASP* 4.9 9.4 - - + -
402C LEU* 4.9 10.3 - - + +
406C LYS* 4.7 8.1 + - - -
410C TRP* 4.0 22.1 - + - -
497C GLY 2.9 19.6 + - - -
498C ARG* 3.6 20.0 - - - +
499C LEU 3.2 0.2 - - - -
500C SER* 1.3 73.5 - - - +
502C ILE* 1.3 67.0 + - - +
504C GLU* 3.2 25.0 + - - +
505C MET* 4.1 6.4 + - - +
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Residues in contact with ILE 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C LYS* 3.6 37.9 - - + +
489C GLN 4.6 0.4 - - - +
490C ILE* 3.5 31.6 - - + -
498C ARG* 2.9 56.7 + - + +
499C LEU* 3.0 9.6 + - - +
501C HIS* 1.3 76.7 - - - +
503C LEU* 1.3 58.5 + - + +
504C GLU 3.1 0.2 - - - -
505C MET* 3.1 6.7 + - - +
506C ASP* 3.0 27.8 + - + +
509C ALA* 4.6 14.8 - - + -
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ILE 3.9 6.9 - - - +
189A VAL* 3.9 1.2 - - - +
190A ARG 3.5 17.7 + - - -
499C LEU* 2.9 42.1 + - + +
500C SER* 3.9 6.5 - - - +
501C HIS 3.1 0.6 - - - -
502C ILE* 1.3 75.0 - - + +
504C GLU* 1.3 59.8 + - - +
505C MET 3.1 5.1 + - - -
506C ASP 3.2 25.8 - - - +
507C HIS 3.8 17.0 - - - +
508C PHE 4.8 0.4 - - - -
509C ALA* 4.5 7.0 - - + +
534C VAL 4.4 9.2 - - - +
535C THR 3.9 4.7 - - - +
536C ALA* 3.6 38.8 - - + +
539C LEU* 4.2 12.8 - - + -
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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