Contacts of the helix formed by residues 549 - 569 (chain C) in PDB entry 4IVE
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 PRO 549 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C SER 4.7 0.7 - - - +
548C ALA* 1.4 88.3 - - + +
550C PRO* 1.4 74.8 - - + +
551C GLN* 4.7 1.6 - - + +
552C LYS* 3.1 23.7 + - + +
553C GLN* 3.0 18.9 + - - +
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Residues in contact with PRO 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ALA 3.8 1.5 - - - +
549C PRO* 1.4 85.6 - - + +
551C GLN* 1.4 61.1 + - - +
553C GLN* 3.3 28.6 - - + +
554C LYS* 3.6 12.0 + - - +
585C ASN* 4.9 2.1 + - - +
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Residues in contact with GLN 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG* 4.8 3.2 - - - +
547B SER* 3.7 22.3 + - - +
548B ALA* 5.4 1.0 - - - +
549B PRO* 6.1 1.0 - - - +
549C PRO* 3.4 1.8 - - + +
550C PRO* 1.4 74.6 - - - +
552C LYS* 1.4 63.7 + - - +
553C GLN 3.2 0.4 - - - -
554C LYS* 3.2 27.7 + - - +
555C GLN* 3.2 34.8 + - - +
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Residues in contact with LYS 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ALA* 3.8 18.6 - - + -
549C PRO* 3.1 29.5 + - + +
551C GLN* 1.4 77.0 - - - +
553C GLN* 1.4 55.6 + - - +
555C GLN* 3.3 16.3 + - + +
556C MSE 3.0 50.0 + - + +
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Residues in contact with GLN 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C LEU* 3.1 45.8 + - + +
546C ALA* 4.1 10.8 + - - +
548C ALA 3.0 18.3 + - - +
549C PRO 3.0 13.2 + - - +
550C PRO* 3.3 22.7 - - - +
551C GLN 3.2 0.2 - - - -
552C LYS* 1.4 76.0 - - - +
554C LYS* 1.3 56.6 + - - +
556C MSE 3.3 10.0 + - + -
557C LEU* 3.1 34.4 + - - +
585C ASN* 3.0 31.7 + - - +
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Residues in contact with LYS 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B SER* 4.7 4.9 - - - +
550C PRO 3.6 11.2 + - - +
551C GLN* 3.2 26.9 + - - +
553C GLN* 1.3 72.9 - - - +
555C GLN* 1.3 61.1 + - - +
557C LEU* 3.4 2.0 + - - -
558C GLY* 2.8 25.3 + - - -
581C LEU* 2.9 45.7 + - + +
582C GLU* 4.4 3.2 + - - +
583C ILE 2.8 27.7 + - - -
584C ASP* 4.5 1.6 - - - +
585C ASN* 2.8 32.0 + - - +
588C LEU* 4.1 2.4 - - + +
575D LYS* 5.4 4.1 - - - +
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Residues in contact with GLN 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B SER 5.5 1.6 - - - +
544B ARG* 3.5 37.2 + - - +
547B SER* 3.3 27.3 - - - +
551C GLN* 3.2 32.5 + - - +
552C LYS* 3.3 16.7 + - + +
554C LYS* 1.3 76.4 - - - +
556C MSE 1.4 56.7 + - + +
558C GLY* 3.3 1.4 + - - -
559C GLU* 2.9 39.3 + - + +
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Residues in contact with MSE 556 (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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540C LEU* 4.4 17.2 - - + +
544C ARG 5.1 2.7 - - - +
545C LEU* 3.6 23.8 - - + +
548C ALA* 3.3 31.9 - - + -
552C LYS* 3.0 29.5 + - + +
553C GLN* 3.3 33.0 - - + +
554C LYS 3.3 0.2 - - - -
555C GLN* 1.4 75.0 - - + +
557C LEU* 1.3 61.5 + - - +
559C GLU* 3.5 22.1 + - - +
560C ARG* 3.4 22.6 + - - +
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Residues in contact with LEU 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU* 3.9 15.0 - - + -
545C LEU* 3.8 11.2 - - + -
553C GLN 3.1 22.4 + - - +
554C LYS* 3.8 5.4 - - - +
556C MSE 1.3 72.3 - - - +
558C GLY* 1.3 61.0 + - - +
560C ARG* 3.2 5.7 + - - +
561C LEU* 2.9 36.0 + - + +
581C LEU* 4.0 8.1 - - + -
585C ASN* 3.4 35.9 - - + +
588C LEU* 3.9 24.0 - - + -
589C LEU* 3.9 17.9 - - + -
592C LEU* 3.8 23.1 - - + -
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Residues in contact with GLY 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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543B SER* 4.0 11.2 - - - -
554C LYS 2.8 15.8 + - - -
555C GLN* 3.3 4.5 + - - -
557C LEU* 1.3 75.2 - - - +
559C GLU* 1.4 54.1 + - - +
561C LEU* 4.4 1.1 - - - -
562C PHE* 2.9 37.1 + - - +
577C THR* 4.1 7.2 - - - +
581C LEU* 3.7 21.2 - - - +
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Residues in contact with GLU 559 (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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541B THR* 5.7 0.9 - - - +
543B SER* 3.8 24.7 - - - +
544B ARG* 5.8 0.9 - - + +
555C GLN* 2.9 24.9 + - + +
556C MSE 3.7 20.5 - - - +
557C LEU 3.3 0.4 - - - -
558C GLY* 1.4 73.6 - - - +
560C ARG* 1.3 62.2 + - + +
563C PRO* 3.2 22.9 - - - +
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Residues in contact with ARG 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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538C GLU* 2.9 40.0 + - - +
539C THR* 4.0 1.6 - - - +
540C LEU* 3.5 45.3 - - + +
556C MSE 3.4 17.4 + - - +
557C LEU 3.2 4.1 + - - +
559C GLU* 1.3 81.0 - - - +
561C LEU* 1.3 63.5 + - - +
562C PHE 3.5 0.2 - - - -
563C PRO* 3.4 9.6 - - - +
564C LEU* 3.8 18.2 - - - +
592C LEU* 3.7 28.5 - - + -
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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
----------------------------------------------------------
557C LEU* 2.9 23.4 + - + +
558C GLY* 3.9 3.6 - - - +
560C ARG* 1.3 76.5 - - - +
562C PHE* 1.3 63.8 + - - +
564C LEU* 3.2 7.0 + - - +
565C ILE* 3.0 36.2 + - + +
577C THR* 4.5 3.4 - - + -
580C LEU* 5.0 8.1 - - + -
581C LEU* 3.9 23.1 - - + -
588C LEU* 3.8 27.4 - - + +
591C MSE 4.7 9.6 - - + -
592C LEU* 3.7 24.7 - - + -
598C LEU* 3.7 29.6 - - + -
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Residues in contact with PHE 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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542B ALA* 3.4 34.8 - - + -
543B SER* 3.7 24.7 - - - -
546B ALA* 4.7 0.2 - - + -
558C GLY 2.9 22.1 + - - +
561C LEU* 1.3 71.3 - - - +
563C PRO* 1.4 65.6 - - + +
565C ILE* 3.4 0.9 + - - +
566C GLN* 2.8 66.4 + - - +
570C PRO 5.8 0.2 - - - -
573C ALA* 3.7 22.4 - - + -
574C GLY* 3.7 14.8 - - - -
577C THR* 3.6 27.7 + - + +
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Residues in contact with PRO 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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543B SER* 5.8 0.2 - - - -
559C GLU 3.2 26.5 - - - +
560C ARG* 3.4 12.1 - - - +
562C PHE* 1.4 96.9 - - + +
564C LEU* 1.3 57.1 + - + +
566C GLN* 3.5 11.6 + - + +
567C ALA* 3.1 27.4 + - - +
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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
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560C ARG 3.8 17.5 - - - +
561C LEU 3.2 6.1 + - - +
563C PRO* 1.3 74.9 - - + +
565C ILE* 1.3 63.6 + - - +
567C ALA* 3.3 16.6 + - + +
568C MSE 3.4 22.3 - - + +
592C LEU* 4.1 24.0 - - + +
598C LEU* 3.8 26.9 - - + -
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Residues in contact with ILE 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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561C LEU* 3.0 32.6 + - + +
562C PHE 3.9 2.9 - - - +
564C LEU* 1.3 72.0 - - - +
566C GLN* 1.3 60.8 + - - +
568C MSE 3.1 10.8 + - - +
569C HIS 2.9 26.5 + - - +
573C ALA* 3.8 16.6 - - - +
576C ILE* 3.7 31.6 - - + -
577C THR* 3.4 26.9 - - - +
580C LEU* 3.8 25.6 - - + -
598C LEU* 4.2 8.7 - - + -
602C VAL* 3.8 17.7 - - + -
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Residues in contact with GLN 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 PHE* 2.8 47.1 + - + +
563C PRO* 3.7 11.6 + - - +
565C ILE* 1.3 77.2 - - - +
567C ALA* 1.3 59.1 + - - +
569C HIS 4.2 0.4 - - - -
570C PRO* 3.1 43.4 - - + +
573C ALA* 3.6 17.7 - - + +
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Residues in contact with ALA 567 (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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563C PRO 3.1 14.5 + - - +
564C LEU* 3.4 14.8 - - + +
565C ILE 3.2 0.4 - - - -
566C GLN* 1.3 76.2 - - - +
568C MSE 1.3 61.7 + - + +
570C PRO* 4.7 2.8 - - - +
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Residues in contact with MSE 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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564C LEU* 3.4 15.5 - - + +
565C ILE* 3.1 7.1 + - - +
567C ALA* 1.3 80.3 - - + +
569C HIS* 1.3 77.8 + - + +
570C PRO* 3.9 4.7 - - - +
595C PRO* 4.8 3.6 - - + +
598C LEU* 3.9 34.3 - - + -
599C ARG* 3.7 50.9 + - + +
602C VAL* 3.8 30.1 - - + -
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Residues in contact with HIS 569 (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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565C ILE 2.9 10.4 + - - +
566C GLN 3.6 1.8 - - - -
568C MSE 1.3 83.5 + - + +
570C PRO* 1.3 62.8 - - - +
571C THR 3.3 3.1 + - - -
572C LEU* 4.4 8.1 - - + +
573C ALA* 3.0 27.4 + - - +
576C ILE* 3.8 15.0 - - + -
599C ARG* 5.4 4.6 + - - -
602C VAL* 3.5 29.2 - - + +
603C ASP* 4.4 10.3 + - - -
606C VAL* 3.7 31.8 - - + +
701C CL 3.5 17.1 - - + +
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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
------------------------------------------------------------
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