Contacts of the helix formed by residues 598 - 618 (chain C) in PDB entry 2R17
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 598 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C GLN* 4.7 12.1 - - + +
596C PHE* 3.5 2.4 + - + -
597C GLU* 1.3 82.1 + - + +
599C HIS* 1.3 67.0 + - - +
600C GLU* 3.2 4.3 - - - +
601C THR* 3.1 40.5 + - - +
602C VAL* 3.1 16.8 + - - +
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Residues in contact with HIS 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C ALA* 3.2 28.0 + - - +
592C GLY* 3.9 4.1 + - - -
595C GLY* 3.4 19.0 + - - -
596C PHE* 2.9 50.9 - - + +
597C GLU* 3.1 3.0 + - - -
598C ASN* 1.3 80.0 - - - +
600C GLU* 1.3 73.8 + - + +
602C VAL* 3.4 2.3 + - - +
603C ALA* 2.8 29.8 + - - +
640C CYS* 3.7 30.5 + - + +
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Residues in contact with GLU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C ASN 3.2 0.8 - - - -
599C HIS* 1.3 97.0 - - + +
601C THR* 1.3 65.8 + - - +
603C ALA* 3.3 6.6 + - - +
604C TYR* 2.9 28.4 + - - +
640C CYS* 3.7 17.1 - - - +
641C PHE* 3.2 11.1 - - + -
642C SER* 2.8 31.4 + - - -
645C ASN* 2.7 31.8 + - - +
683C THR* 5.4 0.9 + - - +
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Residues in contact with THR 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C ASN* 3.1 34.4 + - - +
600C GLU* 1.3 82.1 - - - +
602C VAL* 1.3 64.1 + - - +
604C TYR* 3.3 6.7 + - - +
605C GLU* 3.0 23.0 + - + +
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Residues in contact with VAL 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C GLN* 5.7 5.4 - - + +
561C PHE* 4.0 27.4 - - + -
591C ALA* 4.1 6.5 - - + -
596C PHE* 4.1 17.5 - - + -
598C ASN* 3.1 24.1 + - + +
599C HIS 3.5 7.4 - - - +
601C THR* 1.3 75.6 - - + +
603C ALA* 1.3 59.8 + - - +
605C GLU* 3.1 6.9 + - - +
606C PHE* 2.9 52.1 + - + -
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Residues in contact with ALA 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C ALA* 4.0 6.5 - - - +
591C ALA* 4.0 16.4 - - + -
592C GLY 4.5 0.9 - - - +
599C HIS 2.8 17.9 + - - +
600C GLU* 3.6 7.6 - - - +
602C VAL* 1.3 76.6 - - - +
604C TYR* 1.3 61.8 + - - +
606C PHE* 3.4 2.9 + - - +
607C MSE 3.0 28.8 + - - +
638C MSE 3.9 15.7 - - + -
640C CYS* 4.3 5.6 - - - -
641C PHE* 3.9 17.7 - - + -
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Residues in contact with TYR 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C GLU 2.9 17.8 + - - +
601C THR* 3.7 7.2 - - - +
603C ALA* 1.3 74.1 - - - +
605C GLU* 1.3 68.3 + - - +
607C MSE 3.3 2.3 + - - +
608C SER* 3.0 40.0 + - - -
641C PHE* 3.6 10.3 - + + -
645C ASN* 3.7 43.5 - - + +
648C PRO* 4.0 18.2 - - + +
649C LEU* 3.7 38.0 - - + +
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Residues in contact with GLU 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C HIS* 3.7 25.1 + - + +
601C THR* 3.0 14.9 + - + +
602C VAL* 3.1 11.6 + - - +
604C TYR* 1.3 79.8 - - - +
606C PHE* 1.3 58.6 + - + +
608C SER* 3.3 9.7 + - - -
609C GLN* 2.9 54.1 + - - +
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Residues in contact with PHE 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C TYR* 3.5 22.7 - + - -
561C PHE* 3.6 34.3 - + - -
564C ALA* 4.3 2.2 - - + -
565C HIS* 3.9 32.5 - + - -
568C ILE* 4.3 10.5 - - + -
584C PHE* 3.3 49.1 - + - +
587C GLY* 3.5 13.7 - - - -
588C ALA* 3.8 9.6 - - - +
602C VAL* 2.9 41.4 + - + +
603C ALA* 3.7 5.4 - - - +
604C TYR 3.3 0.2 - - - -
605C GLU* 1.3 77.4 - - + +
607C MSE 1.3 62.1 + - - +
609C GLN* 3.8 5.3 - - - +
610C ALA* 3.3 15.4 + - - +
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Residues in contact with MSE 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C LEU* 4.0 17.7 - - + -
588C ALA* 3.7 22.2 - - + -
603C ALA 3.0 18.8 + - - +
604C TYR* 3.7 6.1 - - - +
605C GLU 3.2 0.4 - - - -
606C PHE* 1.3 74.4 - - - +
608C SER* 1.3 61.8 + - - +
609C GLN 3.1 0.9 - - - -
610C ALA* 2.9 7.8 + - + +
611C PHE* 2.9 32.8 + - + +
631C ILE* 3.9 27.8 - - + +
634C THR* 4.5 5.4 - - - -
635C PHE* 4.5 17.3 - - + -
638C MSE 4.0 12.8 - - - +
641C PHE* 4.0 18.2 - - + -
649C LEU* 4.1 23.3 - - + -
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Residues in contact with SER 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C TYR* 3.0 35.1 + - - -
605C GLU* 3.3 15.6 + - - -
607C MSE 1.3 77.2 - - - +
609C GLN* 1.3 57.0 + - - +
611C PHE* 3.1 11.9 + - - +
612C SER* 2.8 33.8 + - - -
649C LEU* 4.9 4.4 - - - +
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Residues in contact with GLN 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C HIS* 3.4 27.1 + - - +
569C SER* 3.9 6.9 + - - -
572C ILE* 4.6 8.8 - - + +
584C PHE* 3.0 39.2 - - + -
605C GLU* 2.9 36.5 + - - +
606C PHE* 3.8 6.5 - - - +
608C SER* 1.3 77.5 + - - +
610C ALA* 1.3 62.4 + - - +
612C SER* 3.3 11.6 + - - -
613C LEU* 3.2 23.3 + - + +
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Residues in contact with ALA 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C LEU* 3.6 20.8 - - + +
584C PHE* 3.8 18.5 - - + +
585C LEU* 3.8 27.8 - - + -
606C PHE 3.3 11.4 + - - +
607C MSE 2.9 10.2 + - + +
609C GLN* 1.3 80.7 - - - +
611C PHE* 1.3 61.0 + - - +
613C LEU* 3.3 5.8 + - - +
614C TYR* 3.1 17.5 + - - +
631C ILE* 4.8 4.0 - - + -
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Residues in contact with PHE 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C MSE 2.9 17.6 + - + +
608C SER* 3.5 12.6 - - - +
610C ALA* 1.3 73.8 - - - +
612C SER* 1.3 64.8 + - - +
614C TYR* 3.0 18.1 + + - +
615C GLU* 3.0 35.5 + - + +
628C ILE* 5.8 1.8 - - + -
631C ILE* 3.9 32.3 - - + +
649C LEU* 4.3 21.5 - - + -
652C GLN* 3.8 35.2 - - + -
653C CYS* 3.6 38.6 - - - -
656C ALA* 4.2 14.6 - - + -
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Residues in contact with SER 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C SER* 2.8 21.3 + - - -
609C GLN* 3.4 16.4 + - - -
610C ALA 3.2 0.2 - - - -
611C PHE* 1.3 74.0 - - - +
613C LEU* 1.3 62.3 + - - +
615C GLU* 3.3 12.1 + - - +
616C ASP* 3.1 38.9 + - - +
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Residues in contact with LEU 613 (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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572C ILE* 3.9 31.2 - - + -
576C LEU 4.5 7.0 - - - +
577C ALA* 4.0 6.6 - - + +
580C PRO* 3.6 16.8 - - + -
581C LEU* 3.4 41.1 - - + +
584C PHE* 3.7 17.9 - - + -
609C GLN* 3.2 8.3 + - + +
610C ALA 3.3 6.3 + - - +
612C SER* 1.3 79.0 - - - +
614C TYR* 1.3 63.7 + - - +
616C ASP* 5.1 1.1 - - + -
617C GLU* 2.9 41.8 + - + +
618C ILE* 3.4 6.8 + - - +
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Residues in contact with TYR 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C LEU* 4.1 9.8 - - + +
610C ALA 3.1 8.9 + - - +
611C PHE* 3.0 27.9 + + - +
613C LEU* 1.3 78.5 - - - +
615C GLU* 1.3 73.5 + - + +
618C ILE* 2.6 47.4 + - + +
624C GLN* 3.8 35.9 + - + -
627C ALA* 3.9 15.3 - - + -
628C ILE* 4.0 16.5 - - + +
631C ILE* 4.2 8.7 - - + -
656C ALA* 3.7 29.7 + - + -
660C LEU* 3.2 28.2 - - - +
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Residues in contact with GLU 615 (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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611C PHE* 3.0 24.3 + - + +
612C SER* 3.3 11.5 + - - +
614C TYR* 1.3 91.0 - - + +
616C ASP* 1.3 74.2 + - - +
618C ILE 4.0 7.6 - - - +
652C GLN* 4.0 18.4 + - - -
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Residues in contact with ASP 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C SER* 3.1 26.2 + - - +
613C LEU* 5.1 0.4 - - + -
615C GLU* 1.3 90.2 - - - +
617C GLU* 1.3 77.3 + - + +
618C ILE 5.1 0.9 - - - -
619C SER* 6.0 0.7 - - - -
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Residues in contact with GLU 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ILE* 5.7 4.9 - - + -
575C GLU* 3.4 27.3 - - - +
576C LEU 5.2 2.5 - - - +
577C ALA* 3.6 28.7 - - + +
613C LEU* 2.9 30.8 + - + +
616C ASP* 1.3 89.6 - - + +
618C ILE* 1.3 58.1 + - - -
619C SER* 3.7 5.5 + - - -
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Residues in contact with ILE 618 (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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577C ALA* 5.7 2.7 - - + -
578C GLU* 3.2 31.4 - - - +
581C LEU* 5.1 3.6 - - + -
613C LEU 3.4 5.3 + - - +
614C TYR* 2.6 56.5 + - + +
615C GLU 4.0 6.0 - - - +
616C ASP 3.7 1.4 - - - -
617C GLU* 1.3 76.1 - - - +
619C SER* 1.3 59.7 + - - +
620C ASP 4.5 1.3 - - - +
623C ALA* 3.0 44.4 - - + +
624C GLN* 3.6 15.8 + - + +
627C ALA* 3.6 14.4 - - + -
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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) + - + + + + + -
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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