Contacts of the helix formed by residues 600 - 615 (chain C) in PDB entry 5Y7K
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 THR 600 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ILE* 4.7 0.2 - - - +
597C ARG* 2.7 61.3 + - + +
598C LEU 3.8 5.6 - - - +
599C GLY* 1.3 80.9 - - - +
601C PHE* 1.3 71.8 + - - -
602C GLU* 3.1 4.5 + - - -
603C VAL* 3.1 3.5 + - - +
604C GLU* 2.8 47.8 + - - +
682C HIS* 6.0 3.4 - - + -
686C SER* 5.7 2.5 - - - -
691C ARG* 5.9 0.4 - - - +
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Residues in contact with PHE 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ARG* 3.3 53.2 - - + +
593C ALA* 3.3 26.2 - - + -
594C ILE* 3.9 9.2 - - + -
597C ARG* 3.3 45.8 - - - -
600C THR* 1.3 82.8 + - - +
602C GLU* 1.3 59.6 + - - +
604C GLU* 3.7 16.6 - - - +
605C ASP* 2.8 37.8 + - - -
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Residues in contact with GLU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ALA* 3.9 28.1 - - + +
580C GLY* 5.6 1.1 - - - -
581C ARG 3.4 22.4 - - - +
582C GLY* 5.3 0.9 - - - -
594C ILE* 3.3 20.6 - - + +
598C LEU* 3.5 1.6 - - - +
599C GLY* 2.5 32.1 + - - -
600C THR 3.1 14.6 + - - -
601C PHE* 1.3 74.3 - - - +
603C VAL* 1.3 64.4 + - + +
605C ASP* 4.4 3.3 - - - +
606C GLN* 3.1 31.4 + - - +
631C TYR* 2.9 20.4 + - - +
634C TYR* 4.5 0.3 - - - -
635C VAL* 4.2 10.8 - - + +
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Residues in contact with VAL 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C GLY* 3.5 34.1 - - - +
600C THR 3.1 6.9 + - - +
601C PHE 3.1 0.4 - - - -
602C GLU* 1.3 83.3 - - + +
604C GLU* 1.3 68.2 + - + +
606C GLN* 3.3 5.5 + - - +
607C ILE* 3.3 26.8 + - + +
634C TYR* 4.9 0.4 - - + -
635C VAL* 4.3 17.5 - - + -
638C MET* 3.9 32.8 - - + +
639C VAL* 3.7 20.3 - - + +
642C SER* 5.4 0.2 - - - -
691C ARG* 4.5 7.0 - - - +
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Residues in contact with GLU 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ARG* 4.2 4.8 + - - +
597C ARG* 5.8 0.2 + - - -
600C THR* 2.8 39.4 + - - +
601C PHE* 3.7 23.0 - - - +
603C VAL* 1.3 74.8 - - + +
605C ASP* 1.3 62.4 - - - +
607C ILE* 3.1 15.3 + - + +
608C GLU* 2.9 28.0 + - - +
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Residues in contact with ASP 605 (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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519C LEU* 3.8 18.1 - - + +
524C PHE* 5.3 1.7 - - - -
578C PHE* 3.4 19.8 - - + -
580C GLY* 4.3 7.2 - - - -
581C ARG* 2.8 59.4 + - - +
601C PHE 2.8 22.1 + - - +
602C GLU 4.4 2.5 - - - +
604C GLU* 1.3 72.3 - - - +
606C GLN* 1.3 61.5 + - + +
608C GLU* 3.8 6.7 - - - +
609C ALA* 2.9 29.8 + - - +
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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
----------------------------------------------------------
544C LEU* 3.4 37.8 - - + +
545C ASP 5.1 0.2 - - - +
546C VAL* 3.5 31.0 - - + +
548C ALA* 4.3 12.0 - - + +
578C PHE* 2.8 44.9 + - - +
580C GLY* 4.5 4.2 - - - +
602C GLU 3.1 16.5 + - - +
603C VAL 3.3 8.2 + - - +
605C ASP* 1.3 79.5 - - - +
607C ILE* 1.3 61.9 + - - +
609C ALA* 3.4 3.8 + - - +
610C ALA* 3.1 24.3 + - - +
635C VAL* 4.0 6.1 - - + -
639C VAL* 4.4 10.5 - - + -
647C PHE* 5.1 0.9 - - - -
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Residues in contact with ILE 607 (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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603C VAL* 3.4 18.4 - - + +
604C GLU* 3.1 16.5 + - + +
606C GLN* 1.3 74.7 - - - +
608C GLU* 1.3 59.7 + - - +
610C ALA* 3.4 2.9 + - - +
611C ARG* 2.9 50.3 + - - +
639C VAL* 3.9 24.2 - - + -
642C SER* 3.4 33.2 - - - +
644C SER* 3.7 21.3 - - - +
646C VAL* 4.3 7.5 - - + +
647C PHE* 4.5 7.9 - - + -
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Residues in contact with GLU 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LYS* 4.4 8.3 - - - +
519C LEU* 3.8 30.5 - - + -
604C GLU 2.9 16.2 + - - +
605C ASP* 3.9 6.3 - - - +
606C GLN 3.4 0.2 - - - -
607C ILE* 1.3 77.1 - - - +
609C ALA* 1.3 62.4 + - - +
611C ARG* 3.2 29.7 + - - +
612C GLN* 3.1 46.5 + - - +
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Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C ILE* 4.1 11.7 - - + -
519C LEU* 5.4 0.4 - - - +
544C LEU* 5.7 0.9 - - + -
578C PHE* 3.4 43.1 - - + -
605C ASP 2.9 18.7 + - - +
606C GLN* 3.7 4.0 - - - +
607C ILE 3.2 0.2 - - - -
608C GLU* 1.3 74.5 - - - +
610C ALA* 1.3 61.6 + - - +
612C GLN* 3.1 4.9 + - - +
613C PHE* 2.9 39.4 + - + -
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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
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542C LEU* 5.5 1.6 - - + -
544C LEU* 4.4 7.8 - - + +
606C GLN 3.1 12.4 + - - +
607C ILE 3.8 2.9 - - - +
609C ALA* 1.3 75.7 - - - +
611C ARG* 1.3 56.8 + - - +
613C PHE* 3.1 15.8 + - + +
614C SER* 2.8 31.2 + - - -
624C ILE* 4.3 8.8 - - + +
646C VAL* 4.2 9.4 - - + -
647C PHE* 3.5 35.9 - - + -
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Residues in contact with ARG 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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342B ALA* 5.9 0.4 - - - +
390B ASP* 3.6 48.0 + - + +
391B LYS* 3.6 29.2 - - - +
392B LYS 5.2 1.8 - - - +
607C ILE* 2.9 40.1 + - - +
608C GLU* 3.2 33.8 + - - +
609C ALA 3.1 0.2 - - - -
610C ALA* 1.3 75.5 - - - +
612C GLN* 1.3 61.7 + - + +
614C SER* 2.6 25.6 + - - +
615C LYS* 3.4 21.7 + - + +
644C SER* 5.1 4.4 + - - -
646C VAL* 4.1 23.2 - - + +
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Residues in contact with GLN 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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517C ILE* 3.7 32.7 - - + +
518C ILE 3.7 20.0 + - - +
519C LEU* 4.2 6.7 - - - +
608C GLU* 3.1 32.9 + - - +
609C ALA 3.1 7.4 + - - +
611C ARG* 1.3 74.0 - - + +
613C PHE* 1.3 65.5 + - + +
615C LYS* 3.5 26.7 + - - +
616C MET* 3.4 20.7 - - + +
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Residues in contact with PHE 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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517C ILE* 4.8 8.1 - - + -
526C TYR* 3.6 44.6 - + + -
528C MET* 3.4 25.4 - - + -
542C LEU* 3.8 29.2 - - + -
544C LEU* 4.5 9.9 - - + -
576C ALA* 4.2 16.2 - - + -
577C SER 5.3 0.2 - - - -
578C PHE* 4.6 4.7 - + + -
609C ALA* 2.9 39.6 + - + -
610C ALA* 3.1 12.8 + - - +
612C GLN* 1.3 75.4 - - + +
614C SER* 1.3 64.4 + - - +
615C LYS 3.3 1.0 + - - -
616C MET* 3.3 25.5 - - + +
619C VAL* 3.2 20.4 - - + +
624C ILE* 5.7 0.2 - - + -
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Residues in contact with SER 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C LYS* 5.8 0.5 + - - -
610C ALA 2.8 12.4 + - - -
611C ARG* 2.6 27.4 + - - +
613C PHE* 1.3 73.1 - - - +
615C LYS* 1.3 63.5 + - - +
616C MET 3.4 2.5 + - - -
617C GLY 4.9 0.9 + - - -
619C VAL* 3.4 28.1 - - - +
621C ASN* 3.7 24.5 + - - +
624C ILE* 3.5 23.3 - - - -
646C VAL* 5.2 4.0 - - - +
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Residues in contact with LYS 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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390B ASP* 4.4 25.1 - - - +
611C ARG* 3.4 24.2 + - + +
612C GLN* 3.6 15.2 - - - +
613C PHE 3.2 0.6 - - - -
614C SER* 1.3 90.0 + - - +
616C MET* 1.3 56.9 + - - +
617C GLY 3.7 1.3 - - - -
621C ASN* 5.5 5.4 - - - +
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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
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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