Contacts of the helix formed by residues 519 - 525 (chain C) in PDB entry 1JZ3
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 SER 519 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C ARG 3.2 11.0 - - - -
506C VAL 2.7 17.9 + - - -
507C ASP* 3.5 22.4 + - - -
508C GLU 3.9 4.7 - - - -
509C ASP* 2.8 25.7 + - - +
517C LYS 3.8 1.0 + - - -
518C TRP* 1.3 72.7 - - - +
520C ILE* 1.3 57.8 + - - +
521C LYS* 3.4 2.9 + - - +
522C LYS* 3.1 16.0 + - - +
523C TRP* 2.7 26.7 + - - +
558D GLN* 3.8 5.5 + - - -
559D TYR* 4.4 1.6 + - - -
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Residues in contact with ILE 520 (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 ALA* 3.6 31.4 - - + +
505C ARG 2.9 13.0 + - - +
506C VAL* 4.0 12.1 - - + +
518C TRP 4.1 0.9 - - - -
519C SER* 1.3 71.0 + - - +
521C LYS* 1.3 66.8 + - + +
523C TRP* 3.3 10.0 + - - +
524C LEU* 3.4 20.3 + - - +
533C LEU* 3.8 23.7 - - + +
535C LEU* 4.2 7.6 - - + -
552C TYR* 4.1 17.3 - - + -
555C ALA* 4.8 2.7 - - + -
556C PHE* 4.0 24.2 - - + -
562C LEU* 3.8 34.4 - - + +
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Residues in contact with LYS 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C VAL* 3.4 24.5 - - + +
507C ASP* 2.7 31.1 + - - +
519C SER* 3.3 4.4 + - - +
520C ILE* 1.3 77.7 - - + +
522C LYS* 1.3 62.5 + - - +
524C LEU* 3.7 11.9 + - - +
525C SER* 3.8 9.2 + - - -
554C GLN* 4.8 10.9 + - - -
555C ALA* 4.2 3.8 - - + +
558C GLN* 5.3 2.8 + - - -
559C TYR* 3.5 54.3 - - + +
562C LEU* 4.1 13.0 - - + -
507D ASP* 4.8 8.3 + - - +
521D LYS* 4.4 12.3 - - - +
525D SER* 4.7 1.0 + - - -
559D TYR* 3.1 21.2 - - - +
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C ASP* 2.8 34.1 + - - +
518C TRP* 3.6 29.2 - - + -
519C SER* 3.1 17.4 + - - +
521C LYS* 1.3 81.4 - - - +
523C TRP* 1.3 66.1 + - - +
525C SER* 3.2 13.2 + - - -
526C LEU* 3.4 28.6 + - + +
558D GLN* 2.9 31.1 + - + +
559D TYR* 3.3 25.5 + - + -
560D PRO* 4.1 11.8 - - + +
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Residues in contact with TRP 523 (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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490C GLY 3.1 27.4 - - - -
491C ALA* 3.8 17.0 - - + -
492C ASP* 3.0 26.7 + - - +
499C ILE* 3.7 26.5 - - + +
501C PRO* 3.6 28.0 - - + -
504C ALA* 4.1 1.8 - - + -
516C PRO* 3.6 16.6 - - + -
517C LYS* 4.0 5.6 - - + -
518C TRP* 3.4 49.8 - + + -
519C SER 2.7 17.1 + - - +
520C ILE 3.6 6.5 - - - +
521C LYS 3.3 0.2 - - - -
522C LYS* 1.3 74.9 - - - +
524C LEU* 1.3 64.0 + - - +
525C SER 3.2 0.7 + - - -
526C LEU* 3.2 27.6 + - + +
529C GLU* 3.9 7.7 - - + +
533C LEU* 3.8 8.5 - - + -
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Residues in contact with LEU 524 (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 ILE* 4.6 2.2 - - + -
520C ILE 3.4 11.8 + - - +
521C LYS 3.9 5.2 - - - +
522C LYS 3.2 0.2 - - - -
523C TRP* 1.3 81.3 - - - +
525C SER* 1.3 58.7 + - - +
526C LEU 3.7 0.2 + - - -
529C GLU* 3.6 12.2 - - - +
531C ARG 3.7 20.4 - - - +
533C LEU* 3.6 26.7 - - + -
559C TYR* 4.1 10.8 - - + -
561C ARG* 2.9 55.0 + - + +
562C LEU* 3.6 28.0 - - + +
525D SER* 3.6 23.3 - - - +
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Residues in contact with SER 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LYS 3.8 8.5 + - - -
522C LYS 3.5 9.1 + - - -
523C TRP 3.2 0.6 - - - -
524C LEU* 1.3 77.2 - - - +
526C LEU* 1.3 70.0 + - - +
527C PRO* 3.4 0.3 - - - +
521D LYS 4.7 0.9 + - - -
524D LEU* 3.5 23.9 - - - +
525D SER* 4.2 9.1 - - - -
559D TYR* 3.8 18.9 - - - -
560D PRO* 5.7 1.2 - - - +
561D ARG* 3.1 40.7 + - - +
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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