Contacts of the helix formed by residues 499 - 510 (chain C) in PDB entry 4P0S
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 499 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472C ARG* 5.9 1.1 + - - -
475C PHE* 4.1 8.7 - - - -
497C TYR 3.3 1.8 + - - +
498C SER* 1.3 82.9 - - - +
500C PRO* 1.3 74.3 - - - +
501C ALA* 3.8 4.9 + - + +
502C SER* 2.7 49.5 + - - +
503C LEU 3.2 5.0 + - - -
556D GLN 4.7 2.4 + - - -
557D MET 5.8 0.2 - - - -
559D THR* 3.2 24.0 + - - +
560D LEU* 4.0 28.0 - - + +
562D PRO* 5.2 6.0 - - - +
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Residues in contact with PRO 500 (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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472C ARG* 5.9 1.6 - - - +
475C PHE* 3.9 38.8 - - + -
478C GLN* 4.1 6.7 - - - +
499C THR* 1.3 90.7 - - - +
501C ALA* 1.3 61.1 + - - +
502C SER 3.2 0.7 + - - -
503C LEU* 3.3 4.6 + - + +
504C LEU* 3.2 26.8 + - + +
544C TYR* 5.9 6.1 - - + -
556D GLN* 3.9 29.8 - - - +
557D MET* 3.9 31.9 - - + +
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Residues in contact with ALA 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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499C THR* 3.0 1.7 + - + -
500C PRO* 1.3 81.2 - - - +
502C SER* 1.3 61.2 + - - +
504C LEU* 3.3 14.8 + - + +
505C ALA* 3.1 23.4 + - - +
557D MET 3.9 10.7 + - - +
558D THR* 3.5 25.4 - - - +
559D THR 4.2 8.1 - - - +
560D LEU* 4.2 14.0 - - + +
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Residues in contact with SER 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C ARG 4.8 0.7 + - - -
497C TYR* 3.7 27.0 - - - -
498C SER* 4.0 6.7 + - - -
499C THR* 2.7 42.4 + - - +
501C ALA* 1.3 72.5 - - - +
503C LEU* 1.3 64.1 + - - +
504C LEU 3.3 0.2 + - - -
505C ALA* 3.4 12.6 + - - +
506C ALA* 3.6 8.0 + - - +
560D LEU* 4.8 7.6 - - - -
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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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475C PHE* 4.4 14.8 - - + -
479C LEU* 5.6 1.8 - - + -
497C TYR* 3.8 32.8 - - + +
499C THR 3.2 6.4 + - - +
500C PRO 3.3 6.9 + - - +
502C SER* 1.3 79.3 - - - +
504C LEU* 1.3 63.6 + - + +
506C ALA* 3.5 1.7 + - - +
507C TYR* 3.2 53.9 + - + -
519C LEU* 5.3 1.8 - - + -
520C LEU* 3.7 26.7 - - + -
540C LEU* 5.5 2.2 - - + -
544C TYR* 3.6 35.0 - - + -
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Residues in contact with LEU 504 (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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500C PRO* 3.2 19.0 + - + +
501C ALA* 3.5 15.5 - - + +
502C SER 3.2 0.6 - - - -
503C LEU* 1.3 77.5 - - + +
505C ALA* 1.3 65.2 + - - +
507C TYR* 4.1 5.9 - - + +
508C ASP* 2.9 28.7 + - - +
544C TYR* 4.0 38.8 - - + +
507D PRO* 5.7 5.6 - - + -
508D GLN* 4.1 13.5 - - - +
511D VAL* 4.4 29.2 - - + -
557D MET* 4.9 13.2 - - + +
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Residues in contact with ALA 505 (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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501C ALA 3.1 15.3 + - - +
502C SER* 3.4 7.2 + - - +
503C LEU 3.4 0.4 - - - -
504C LEU* 1.3 75.9 - - - +
506C ALA* 1.3 53.5 + - - +
508C ASP* 3.6 5.1 - - - +
509C ALA* 2.7 38.5 + - + +
560D LEU* 6.3 1.8 - - + -
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Residues in contact with ALA 506 (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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497C TYR* 3.8 26.2 - - + +
502C SER 3.6 3.6 + - - +
503C LEU 3.5 5.5 + - - +
504C LEU 3.3 0.2 - - - -
505C ALA* 1.3 77.2 - - - +
507C TYR* 1.3 65.6 + - - +
509C ALA* 3.2 13.2 + - - +
510C CYS* 2.9 20.3 + - - -
519C LEU* 3.6 21.3 - - + -
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Residues in contact with TYR 507 (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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503C LEU* 3.2 46.7 + - + +
504C LEU* 4.1 5.8 - - + +
506C ALA* 1.3 78.5 - - - +
508C ASP* 1.3 57.3 + - - +
510C CYS* 3.1 18.5 - - - +
516C GLN* 2.9 63.1 + - + +
519C LEU* 3.9 18.4 - - + -
520C LEU* 3.0 28.4 - - + +
537C SER 3.8 4.0 + - - -
540C LEU* 3.7 15.4 - - - +
541C SER* 3.6 23.9 + - - -
544C TYR* 4.2 11.0 - - + -
545C CYS* 3.9 20.4 - - - -
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Residues in contact with ASP 508 (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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504C LEU* 2.9 21.9 + - + +
505C ALA* 3.9 4.8 - - - +
507C TYR* 1.3 73.7 - - - +
509C ALA* 1.3 60.7 + - - +
510C CYS 3.0 13.9 + - - +
516C GLN* 4.6 3.6 - - - +
547C TYR* 4.9 8.0 + - - -
508D GLN* 6.1 2.5 - - - +
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Residues in contact with ALA 509 (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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505C ALA* 2.7 24.6 + - + +
506C ALA* 3.2 8.7 + - - +
508C ASP* 1.3 68.4 - - - +
510C CYS* 1.3 67.7 + - - +
511C ALA* 5.1 0.9 - - - +
515C GLU* 4.6 0.3 - - - +
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Residues in contact with CYS 510 (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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506C ALA 2.9 27.6 + - - -
507C TYR* 3.1 20.2 - - - +
508C ASP 3.0 10.0 - - - +
509C ALA* 1.3 87.2 - - - +
511C ALA* 1.3 61.5 + - - +
512C THR 4.2 2.0 - - - +
515C GLU* 3.0 44.0 - - + +
516C GLN* 4.0 14.1 + - + +
519C LEU* 4.1 12.1 - - - -
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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