Contacts of the helix formed by residues 557 - 568 (chain C) in PDB entry 3HZJ
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 ASN 557 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A ALA 5.8 0.4 - - - -
555C HIS* 3.5 37.6 + - + +
556C ASP* 1.3 74.6 - - - +
558C GLN* 1.3 59.1 + - - +
559C ALA* 3.2 14.9 + - - +
560C MSE 2.9 38.8 + - + +
561C LEU* 2.9 28.1 + - - +
637C GLU* 4.5 2.1 - - - +
641C CYS* 6.3 1.2 - - - -
907C UNX 4.4 6.3 - - - -
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Residues in contact with GLN 558 (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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541A GLU* 4.7 17.7 + - + +
542A ALA* 4.4 24.8 + - + +
545A ALA* 4.6 6.1 + - + +
632A LEU 2.9 26.2 + - - -
633A HIS* 3.2 39.0 - - - +
556C ASP 3.5 4.6 + - - +
557C ASN* 1.3 70.1 - - - +
559C ALA* 1.3 56.4 + - - +
561C LEU* 3.1 12.6 + - - +
562C ASP* 2.7 67.8 + - - +
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Residues in contact with ALA 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C ASN* 3.2 10.8 + - - +
558C GLN* 1.3 78.8 - - - +
560C MSE 1.3 59.3 + - + +
562C ASP* 3.6 8.4 + - - +
563C ARG* 2.9 28.2 + - - +
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Residues in contact with MSE 560 (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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557C ASN* 2.9 27.6 + - + +
558C GLN 3.2 0.2 - - - -
559C ALA* 1.3 76.4 - - + +
561C LEU* 1.3 56.3 + - - +
563C ARG* 4.2 20.2 - - + +
564C TYR* 2.8 33.8 + - - +
613C TYR* 4.7 18.8 - - + +
637C GLU* 3.7 0.4 - - - -
640C PHE* 4.1 23.3 - - + -
641C CYS* 3.4 30.5 - - + -
644C VAL* 6.0 2.7 - - - -
907C UNX 4.3 7.2 - - - -
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Residues in contact with LEU 561 (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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633A HIS 3.6 26.5 - - - +
634A MSE 3.6 17.7 - - - +
635A PRO* 4.3 10.1 - - + -
557C ASN 2.9 16.5 + - - +
558C GLN* 3.4 17.5 - - - +
560C MSE 1.3 76.7 - - - +
562C ASP* 1.3 57.3 + - - +
564C TYR* 3.4 2.6 + - - +
565C ARG* 3.1 69.5 + - + +
637C GLU* 3.2 37.8 + - + +
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Residues in contact with ASP 562 (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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632A LEU 4.7 1.6 - - - +
558C GLN* 2.7 52.9 + - - +
559C ALA* 3.8 8.1 - - - +
561C LEU* 1.3 72.9 - - - +
563C ARG* 1.3 63.4 + - - +
565C ARG* 3.4 13.6 + - - +
566C ILE* 3.3 30.6 + - + +
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Residues in contact with ARG 563 (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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559C ALA 2.9 20.0 + - - +
560C MSE 3.8 21.8 - - + +
562C ASP* 1.3 72.5 - - - +
564C TYR* 1.3 67.5 + - - +
566C ILE* 3.2 14.9 + - - +
567C LEU* 2.9 52.3 + - + +
612C VAL 5.4 0.8 + - - -
613C TYR* 3.5 38.7 + - - +
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Residues in contact with TYR 564 (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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560C MSE 2.8 22.6 + - - +
561C LEU* 3.6 3.4 - - + +
563C ARG* 1.3 74.5 - - - +
565C ARG* 1.3 70.9 + - + +
567C LEU* 3.3 9.2 + - - +
568C ILE* 3.1 48.6 + - + +
605C LYS* 3.4 17.5 - - - +
606C ILE* 3.7 2.2 + - - +
609C ALA* 3.7 17.0 - - + -
636C GLU* 2.5 41.7 + - + +
637C GLU* 3.5 34.5 - - + -
640C PHE* 3.5 41.1 - + + -
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Residues in contact with ARG 565 (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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591A TYR* 3.3 49.1 + - + +
598A ASP* 4.8 0.9 - - - +
631A LEU* 2.9 39.4 + - - +
632A LEU* 3.7 16.0 + - - +
634A MSE 3.0 20.8 + - - -
635A PRO* 4.1 3.4 - - - +
636A GLU 4.6 0.4 - - - +
561C LEU* 3.1 41.7 + - + +
562C ASP* 3.7 13.6 + - - +
563C ARG 3.2 0.6 - - - -
564C TYR* 1.3 81.8 - - + +
566C ILE* 1.3 60.9 + - + +
568C ILE* 3.4 17.8 - - + +
569C THR* 3.4 19.8 - - - +
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Residues in contact with ILE 566 (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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562C ASP* 3.3 18.8 + - + +
563C ARG* 3.2 15.6 + - - +
565C ARG* 1.3 75.0 - - + +
567C LEU* 1.3 69.1 + - + +
568C ILE 3.2 1.6 - - - -
569C THR* 2.6 30.2 + - - +
570C LYS* 3.6 14.4 + - + +
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Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ARG* 2.9 57.0 + - + +
564C TYR* 3.3 6.9 + - - +
566C ILE* 1.3 79.9 - - + +
568C ILE* 1.3 61.4 + - - +
570C LYS* 3.2 27.5 + - + +
608C LYS* 4.7 1.4 - - - +
609C ALA* 4.0 17.9 - - + +
612C VAL* 3.6 39.1 - - + +
613C TYR* 3.9 26.9 - - + +
640C PHE* 4.0 18.8 - - + -
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Residues in contact with ILE 568 (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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598A ASP* 3.2 31.1 - - + +
564C TYR* 3.1 52.6 + - + +
565C ARG* 3.4 25.4 - - + +
567C LEU* 1.3 77.5 - - - +
569C THR* 1.3 57.2 + - - +
570C LYS 3.3 0.4 - - - -
605C LYS* 3.7 44.2 - - + +
608C LYS* 3.0 25.1 + - + +
609C ALA* 3.9 3.6 - - + -
636C GLU* 4.7 0.7 - - - +
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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