Contacts of the helix formed by residues 596 - 617 (chain C) in PDB entry 3GQL
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 596 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C GLN* 4.1 1.4 - - - +
595C LEU* 1.3 78.8 - - - +
597C SER* 1.3 63.9 + - - +
598C LYS* 2.9 12.4 + - - +
599C ASP* 2.6 44.2 + - - -
600C LEU* 3.4 9.4 + - - +
764C GLN 4.5 2.5 - - - -
765C GLU* 3.5 36.8 - - - +
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Residues in contact with SER 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595C LEU 4.6 0.2 - - - -
596C SER* 1.3 74.5 - - - +
598C LYS* 1.3 58.4 + - - +
600C LEU* 3.8 14.1 + - - +
601C VAL* 3.0 28.2 + - - +
694C PHE* 5.2 1.2 - - - -
724C ASN 5.5 2.4 + - - -
726C THR* 5.4 7.8 - - - +
761C THR* 4.7 3.1 + - - -
764C GLN* 5.2 9.7 + - - +
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Residues in contact with LYS 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C SER* 2.9 11.8 + - - +
597C SER* 1.3 77.8 - - - +
599C ASP* 1.3 69.6 + - - +
601C VAL* 3.0 5.6 + - + +
602C SER* 2.9 25.8 + - - -
758C VAL* 4.8 14.6 - - + +
761C THR* 3.0 45.6 + - + +
764C GLN* 4.6 1.5 - - + +
765C GLU* 4.7 6.5 - - + +
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Residues in contact with ASP 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C GLN 4.2 3.0 - - - +
595C LEU* 3.4 26.1 - - + -
596C SER* 2.6 38.6 + - - +
598C LYS* 1.3 79.7 - - - +
600C LEU* 1.3 52.5 + - - +
602C SER* 2.8 10.5 + - - -
603C CYS* 2.7 37.9 + - - +
765C GLU* 5.6 1.8 - - - +
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Residues in contact with LEU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C LEU* 3.9 23.8 - - + -
595C LEU* 4.3 16.8 - - + +
596C SER 3.4 9.8 + - - +
597C SER* 3.9 12.8 - - - +
598C LYS 3.2 0.8 - - - -
599C ASP* 1.3 78.4 - - - +
601C VAL* 1.3 56.3 + - - +
603C CYS* 3.2 7.4 - - + +
604C ALA* 3.0 27.9 + - - +
693C ILE* 3.8 25.0 - - + +
694C PHE* 3.5 33.8 - - + -
696C LEU* 4.1 22.2 - - + -
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Residues in contact with VAL 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C SER* 3.0 23.6 - - - +
598C LYS* 3.0 7.8 + - - +
600C LEU* 1.3 72.4 - - - +
602C SER* 1.3 53.9 + - - +
604C ALA* 2.9 7.0 + - - +
605C TYR* 2.7 33.3 + - - +
694C PHE* 4.5 8.1 - - + -
729C LEU* 4.6 17.3 - - + -
754C LEU* 4.0 26.7 - - + +
757C ILE* 3.9 37.9 - - + +
758C VAL* 4.1 6.1 - - + -
761C THR* 4.6 6.1 - - - +
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Residues in contact with SER 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C LYS* 2.9 19.8 + - - -
599C ASP* 2.8 21.5 + - - -
601C VAL* 1.3 73.6 - - - +
603C CYS* 1.3 52.3 + - - +
605C TYR* 2.9 15.8 + - - +
606C GLN* 2.8 48.5 + - - +
758C VAL* 4.5 15.8 - - - +
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Residues in contact with CYS 603 (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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569C LEU* 3.8 18.4 - - - -
572C TYR* 5.6 2.2 - - + -
573C LEU* 4.9 7.2 - - - -
599C ASP 2.7 22.7 + - - +
600C LEU* 3.2 9.6 - - + +
602C SER* 1.3 75.5 + - - +
604C ALA* 1.3 62.3 + - - +
606C GLN* 3.5 10.6 + - - +
607C VAL* 3.4 23.0 + - - +
637C MET* 3.6 32.6 - - + +
693C ILE* 4.2 17.5 - - - -
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Residues in contact with ALA 604 (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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600C LEU 3.0 10.2 + - - +
601C VAL* 2.9 10.6 + - - +
603C CYS* 1.3 73.5 - - - +
605C TYR* 1.3 64.7 + - - +
607C VAL* 3.5 2.9 + - - +
608C ALA* 3.2 22.2 + - - +
686C PHE* 3.6 6.1 - - + -
690C LEU* 3.6 24.7 - - + -
693C ILE* 3.5 26.0 - - + -
694C PHE* 4.7 3.8 - - + -
754C LEU* 3.6 12.4 - - + +
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Residues in contact with TYR 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C VAL 2.7 12.4 + - - +
602C SER* 2.9 21.1 + - - +
604C ALA* 1.3 74.7 - - - +
606C GLN* 1.3 68.4 + - + +
608C ALA* 3.0 6.2 + - - +
609C ARG* 2.9 62.3 + - + +
751C VAL* 3.7 26.4 - - + +
754C LEU* 4.1 13.0 - - + +
755C ASP* 3.6 52.6 + - + -
758C VAL* 4.3 13.0 - - + -
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Residues in contact with GLN 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LYS* 4.7 4.2 + - - -
543C ASN* 2.8 39.3 + - - +
602C SER* 2.8 33.0 + - - +
603C CYS* 3.7 12.0 - - - +
604C ALA 3.4 0.2 - - - -
605C TYR* 1.3 83.5 - - + +
607C VAL* 1.3 63.4 + - - +
609C ARG* 2.9 12.7 + - - +
610C GLY 3.0 5.4 + - - -
635C ASN 4.3 10.3 + - - -
636C VAL* 3.6 13.5 - - - +
637C MET* 2.9 40.8 + - + +
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Residues in contact with VAL 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C ASN* 5.4 0.4 - - - -
569C LEU* 4.7 4.7 - - + -
603C CYS 3.4 14.9 + - - +
604C ALA* 3.9 7.9 - - - +
605C TYR 3.3 0.6 - - - -
606C GLN* 1.3 76.0 - - - +
608C ALA* 1.3 61.1 + - - +
611C MET* 3.2 24.0 + - + +
624C LEU* 4.4 4.0 - - + -
629C VAL* 3.9 31.2 - - + -
637C MET* 4.0 9.9 - - + -
639C ILE* 3.5 20.2 - - + +
686C PHE* 4.0 14.6 - - + -
689C LEU* 4.0 31.6 - - + -
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Residues in contact with ALA 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C ALA 3.2 12.6 + - - +
605C TYR 3.0 11.5 + - - +
607C VAL* 1.3 76.8 - - - +
609C ARG* 1.3 64.8 + - - +
611C MET* 3.4 5.4 + - - +
612C GLU* 2.9 23.6 + - - +
686C PHE* 4.0 12.5 - - + -
747C PHE* 4.3 5.5 - - + +
750C LEU* 4.7 4.0 - - + -
751C VAL* 3.7 20.9 - - + +
754C LEU* 3.5 20.9 - - + -
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Residues in contact with ARG 609 (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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541C HIS* 4.0 17.7 + - + +
543C ASN* 3.1 19.2 + - - +
605C TYR* 2.9 62.0 + - + +
606C GLN* 2.9 3.0 + - - +
608C ALA* 1.3 73.4 - - - +
610C GLY* 1.3 69.8 + - - +
612C GLU* 2.7 41.7 + - - +
613C TYR* 3.0 4.9 + - - +
751C VAL* 4.2 4.4 - - + +
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Residues in contact with GLY 610 (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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541C HIS* 3.8 8.3 - - - -
543C ASN* 3.5 30.1 - - - +
544C ILE* 4.0 4.2 - - - +
606C GLN 3.0 8.6 + - - -
609C ARG* 1.3 78.4 - - - +
611C MET* 1.3 59.9 + - - +
613C TYR* 3.3 3.7 + - - +
614C LEU* 3.1 28.0 + - - +
639C ILE* 3.9 8.3 - - - -
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Residues in contact with MET 611 (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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607C VAL 3.2 23.7 + - - +
608C ALA 3.6 1.3 - - - +
609C ARG 2.8 1.4 + - - -
610C GLY* 1.3 75.6 - - - +
612C GLU* 1.3 63.1 + - - +
614C LEU* 3.3 28.3 + - + +
615C ALA* 3.1 22.3 + - - +
621C HIS* 3.6 24.9 - - + -
624C LEU* 3.5 32.3 - - + -
639C ILE* 3.2 35.6 - - + +
682C ASP* 4.5 4.9 - - - +
747C PHE* 3.6 33.9 - - + -
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Residues in contact with GLU 612 (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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541C HIS* 5.7 1.0 + - - +
608C ALA 2.9 10.4 + - - +
609C ARG* 2.7 42.4 + - - +
611C MET* 1.3 70.1 - - - +
613C TYR* 1.3 54.6 + - + +
615C ALA* 3.1 6.5 + - - +
616C SER* 2.8 33.8 + - - -
747C PHE* 3.8 21.7 - - + +
748C LYS* 3.8 20.2 - - + +
751C VAL* 3.5 30.9 - - - +
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Residues in contact with TYR 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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538C ILE* 2.8 33.5 + - + -
539C GLY* 3.5 23.9 - - - -
540C LYS 3.5 10.3 + - - -
541C HIS* 3.4 45.5 - + + -
544C ILE* 4.3 7.2 - - + -
609C ARG 3.0 5.5 + - - +
610C GLY 3.4 8.1 - - - +
612C GLU* 1.3 75.1 - - + +
614C LEU* 1.3 64.5 + - + +
615C ALA 2.9 1.1 - - - -
616C SER* 2.5 40.5 + - - -
617C LYS* 3.0 26.2 + - - +
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Residues in contact with LEU 614 (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 ILE* 4.0 22.0 - - + -
544C ILE* 3.9 24.2 - - + -
610C GLY 3.1 12.5 + - - +
611C MET* 3.3 36.8 - - + +
613C TYR* 1.3 80.7 - - + +
615C ALA* 1.3 53.3 + - - +
617C LYS* 3.4 8.0 + - - +
619C CYS* 2.7 54.1 + - + +
621C HIS* 4.7 1.3 - - + +
639C ILE* 4.3 3.6 - - + -
642C PHE* 3.5 39.5 - - + -
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Residues in contact with ALA 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 MET 3.1 16.3 + - - +
612C GLU* 3.2 15.9 - - - +
613C TYR 2.9 0.8 - - - -
614C LEU* 1.3 76.2 - - - +
616C SER* 1.3 62.4 + - - +
618C LYS* 3.3 8.8 + - - +
619C CYS 3.8 0.9 - - - -
679C HIS* 3.6 38.2 + - + +
747C PHE* 4.6 11.4 - - + -
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Residues in contact with SER 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C GLU 2.8 11.1 + - - -
613C TYR* 2.5 36.0 + - - -
615C ALA* 1.3 68.8 - - - +
617C LYS* 1.3 68.0 + - - +
618C LYS* 3.0 16.5 + - - +
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Residues in contact with LYS 617 (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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537C MET 3.8 11.6 + - - +
538C ILE* 3.3 56.1 + - + +
539C GLY* 5.3 0.6 - - - -
613C TYR* 3.0 32.1 + - + +
614C LEU 3.8 7.2 - - - +
615C ALA 3.3 0.4 - - - -
616C SER* 1.3 87.9 + - - +
618C LYS* 1.3 69.9 + - - +
619C CYS* 2.9 6.6 + - + +
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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