Contacts of the helix formed by residues 558 - 581 (chain C) in PDB entry 4PE5
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 PHE 558 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C GLN* 3.1 6.3 - - + -
557C PRO* 1.3 81.1 - - + +
559C GLN* 1.3 73.4 + - - +
562C LEU* 3.2 28.8 - - + +
563C TRP* 5.1 4.3 - - + +
647C TYR* 5.5 8.1 - - + -
811D SER 3.2 11.7 - - - +
812D GLN* 3.8 5.0 - - - -
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Residues in contact with GLN 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C GLN* 3.4 17.0 + - - +
557C PRO 3.1 6.3 - - - +
558C PHE* 1.3 89.6 - - - +
560C SER* 1.3 60.5 + - - +
561C CYS* 3.1 8.5 + - + +
563C TRP* 2.9 24.7 + - - +
810D SER* 6.4 0.4 - - - -
812D GLN* 3.7 21.1 - - + -
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Residues in contact with SER 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C GLN* 1.3 70.5 - - - +
561C CYS* 1.3 60.7 + - - +
563C TRP* 3.7 9.0 - - - -
564C LEU* 2.9 32.2 + - - +
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Residues in contact with CYS 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C GLN* 3.1 9.1 - - + +
560C SER* 1.3 78.2 - - - +
562C LEU* 1.3 59.9 + - - +
564C LEU* 3.9 2.2 - - - +
565C LEU* 2.9 30.4 + - - +
812D GLN* 5.1 6.3 - - + +
814D ASP 3.9 7.0 - - - -
815D CYS* 2.0 47.1 - - - -
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Residues in contact with LEU 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C PHE* 3.2 28.1 + - + +
559C GLN 3.4 1.6 + - - -
561C CYS* 1.3 77.6 - - - +
563C TRP* 1.3 59.2 + - - +
565C LEU* 3.7 8.8 - - - +
566C VAL* 2.9 28.4 + - - +
812D GLN* 3.9 17.9 - - - +
813D LEU* 5.7 2.2 - - + -
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Residues in contact with TRP 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C GLN* 5.2 11.2 - - + -
558C PHE* 4.9 4.2 - - + +
559C GLN 2.9 18.9 + - - +
560C SER* 3.8 9.4 - - - +
562C LEU* 1.3 75.5 - - - +
564C LEU* 1.3 59.9 + - - +
566C VAL* 3.1 7.7 + - - +
567C GLY* 2.9 24.4 + - - -
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Residues in contact with LEU 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C SER 2.9 19.1 + - - +
561C CYS* 4.1 2.0 - - - +
563C TRP* 1.3 74.6 - - - +
565C LEU* 1.3 59.2 + - - +
567C GLY* 4.4 2.0 - - - +
568C LEU* 2.9 31.5 + - - +
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Residues in contact with LEU 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C CYS* 2.9 21.0 + - - +
562C LEU* 3.7 10.5 - - - +
563C TRP 3.1 0.2 - - - -
564C LEU* 1.3 76.7 - - - +
566C VAL* 1.3 56.9 + - - +
568C LEU* 3.8 4.8 - - - +
569C SER* 2.9 31.2 + - - -
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Residues in contact with VAL 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C LEU 2.9 18.3 + - - +
563C TRP* 3.1 6.9 + - - +
565C LEU* 1.3 75.0 - - - +
567C GLY* 1.3 60.3 + - - +
569C SER* 3.4 6.6 + - - -
570C VAL* 2.9 28.9 + - - +
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Residues in contact with GLY 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C TRP 2.9 14.7 + - - -
564C LEU* 3.9 2.5 - - - -
565C LEU 3.3 0.2 - - - -
566C VAL* 1.3 77.4 - - - +
568C LEU* 1.3 54.8 - - - +
570C VAL* 3.1 8.5 + - - +
571C HIS* 2.9 28.7 + - - +
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Residues in contact with LEU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C LEU 2.9 19.5 + - - +
565C LEU* 3.9 5.2 - - - +
567C GLY* 1.3 75.7 - - - +
569C SER* 1.3 57.6 + - - +
571C HIS* 3.5 6.7 + - - +
572C VAL* 2.9 29.6 + - - +
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Residues in contact with SER 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C LEU 2.9 19.1 + - - -
566C VAL* 3.6 7.9 - - - -
567C GLY 3.2 0.2 - - - -
568C LEU* 1.3 76.5 - - - +
570C VAL* 1.3 59.6 + - - +
572C VAL* 3.8 5.8 - - - +
573C VAL* 2.9 29.6 + - - +
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Residues in contact with VAL 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C VAL 2.9 14.3 + - - +
567C GLY* 3.1 12.3 + - - +
569C SER* 1.3 75.8 - - - +
571C HIS* 1.3 58.1 + - - +
573C VAL* 3.3 6.8 + - - +
574C ALA* 2.9 28.4 + - - +
610C SER* 4.5 17.4 - - - +
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Residues in contact with HIS 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C GLY 2.9 15.2 + - - +
568C LEU* 3.8 7.6 - - - +
570C VAL* 1.3 75.8 - - - +
572C VAL* 1.3 58.8 + - - +
574C ALA* 3.3 8.3 + - - +
575C VAL* 2.9 28.3 + - - +
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Residues in contact with VAL 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C LEU 2.9 18.6 + - - +
569C SER* 3.8 6.7 - - - +
571C HIS* 1.3 74.0 - - - +
573C VAL* 1.3 61.8 + - - +
575C VAL* 3.4 7.0 + - - +
576C MET* 2.9 29.1 + - - +
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Residues in contact with VAL 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C SER 2.9 17.9 + - - +
570C VAL* 3.6 7.2 - - - +
572C VAL* 1.3 76.2 - - - +
574C ALA* 1.3 58.5 + - - +
576C MET* 3.7 6.4 - - - +
577C LEU* 2.9 29.6 + - - +
610C SER* 6.1 2.5 - - - -
636C TRP* 5.3 13.9 - - + -
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Residues in contact with ALA 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C VAL 2.9 17.2 + - - +
571C HIS* 3.5 9.2 - - - +
572C VAL 3.2 0.2 - - - -
573C VAL* 1.3 76.3 - - - +
575C VAL* 1.3 59.0 + - - +
577C LEU* 3.4 6.1 + - - +
578C TYR* 2.9 28.9 + - - +
606C ALA* 4.0 26.3 - - + +
607C MET* 5.1 3.6 - - - +
610C SER* 4.7 9.1 - - - -
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Residues in contact with VAL 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C HIS 2.9 17.0 + - - +
572C VAL* 3.7 7.6 - - - +
574C ALA* 1.3 75.8 - - - +
576C MET* 1.3 58.7 - - - +
578C TYR* 3.3 7.5 + - - +
579C LEU* 2.9 28.8 + - - +
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Residues in contact with MET 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C VAL 2.9 17.5 + - - +
573C VAL* 3.7 8.1 - - - +
574C ALA 3.3 0.2 - - - -
575C VAL* 1.3 76.2 - - - +
577C LEU* 1.3 59.4 + - - +
579C LEU* 3.3 7.0 + - - +
580C LEU* 2.9 29.9 + - - +
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Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C VAL 2.9 17.7 + - - +
574C ALA* 3.7 8.1 - - - +
575C VAL 3.3 0.2 - - - -
576C MET* 1.3 75.4 - - - +
578C TYR* 1.3 59.3 + - - +
580C LEU* 3.4 6.6 + - - +
581C ASP* 3.1 28.1 + - - +
606C ALA* 4.6 10.5 - - + -
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Residues in contact with TYR 578 (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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574C ALA 2.9 17.7 + - - +
575C VAL* 3.7 8.5 - - - +
576C MET 3.3 0.2 - - - -
577C LEU* 1.3 77.2 - - - +
579C LEU* 1.3 59.9 + - - +
581C ASP* 3.8 11.9 + - - +
582C ARG* 4.0 12.5 + - - +
606C ALA* 4.9 9.1 - - + +
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Residues in contact with LEU 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C VAL 2.9 16.3 + - - +
576C MET* 3.7 8.1 - - - +
577C LEU 3.2 0.2 - - - -
578C TYR* 1.3 77.5 - - - +
580C LEU* 1.3 60.2 + - - +
581C ASP 3.4 0.9 - - - -
582C ARG* 3.9 17.0 + - - +
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Residues in contact with LEU 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C MET 2.9 15.9 + - - +
577C LEU* 3.4 8.0 + - - +
578C TYR 3.3 0.2 - - - -
579C LEU* 1.3 75.1 - - - +
581C ASP* 1.3 63.3 + - - +
582C ARG 3.2 4.5 + - - -
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Residues in contact with ASP 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LEU 3.1 16.0 + - - +
578C TYR* 3.8 9.4 + - - +
579C LEU 3.4 0.4 - - - -
580C LEU* 1.3 77.9 - - - +
582C ARG* 1.3 59.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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