Contacts of the helix formed by residues 599 - 612 (chain C) in PDB entry 3HR4
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 599 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544C ALA* 4.5 7.0 - - + -
545C THR 3.7 9.0 - - - +
546C GLU* 2.8 35.2 - - + +
591C SER* 3.6 38.6 - - - +
593C PHE* 4.1 9.4 - - + -
597C ASP 3.9 4.3 - - - +
598C CYS* 1.3 88.2 - - + +
600C GLY* 1.3 57.3 + - - +
601C ASN* 2.9 17.7 - - + +
602C GLY* 2.8 19.9 + - - -
603C GLU 3.0 5.5 + - - -
637C PHE* 4.2 3.8 - - + -
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Residues in contact with GLY 600 (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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546C GLU* 3.5 7.1 + - - -
573C ASP* 4.9 4.5 - - - +
598C CYS 3.6 0.6 + - - -
599C PRO* 1.3 71.7 - - - +
601C ASN* 1.3 62.3 + - - +
602C GLY 3.0 0.9 + - - -
603C GLU* 3.6 24.5 + - - +
604C LYS* 4.4 5.0 + - - +
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Residues in contact with ASN 601 (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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543C PHE* 5.5 1.6 - - - -
544C ALA* 3.8 13.2 - - + -
545C THR* 2.6 43.2 + - - +
546C GLU* 3.4 3.6 - - - +
571C CYS* 3.7 21.8 - - - -
572C MET* 3.5 3.4 - - - +
573C ASP* 2.8 41.3 + - - +
599C PRO* 2.8 12.0 + - - +
600C GLY* 1.3 73.4 + - - +
602C GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C ALA* 4.5 2.9 - - - +
572C MET* 3.6 28.0 - - - -
598C CYS* 4.2 5.6 - - - -
599C PRO 2.8 6.3 + - - -
601C ASN* 1.3 82.0 - - - +
603C GLU* 1.3 51.1 + - - +
604C LYS 3.1 2.7 - - - -
605C LEU* 2.6 25.5 + - - +
606C LYS* 2.6 18.2 + - - +
637C PHE* 4.8 3.8 - - - -
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Residues in contact with GLU 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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630A MET* 4.0 25.2 - - + +
631A TYR* 5.8 0.2 + - - -
597C ASP* 4.6 12.7 - - - +
598C CYS* 3.5 25.8 - - - +
599C PRO 3.0 11.7 + - - +
600C GLY* 3.6 16.2 + - - +
602C GLY* 1.3 77.4 - - - +
604C LYS* 1.3 62.3 - - - +
605C LEU 3.0 1.0 + - - -
606C LYS* 3.7 0.3 - - - +
607C LYS* 3.0 24.9 + - - +
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Residues in contact with LYS 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ASP* 4.1 40.9 + - + +
574C LYS* 6.2 1.8 - - - +
575C TYR 5.8 1.6 - - - -
576C ARG* 5.6 6.1 - - - +
577C LEU* 6.0 3.8 - - - -
600C GLY 4.4 4.1 + - - +
602C GLY* 3.1 0.6 - - - -
603C GLU* 1.3 78.6 - - - +
605C LEU* 1.3 53.1 + - + +
607C LYS* 3.5 26.6 - - - +
608C SER* 2.6 37.1 + - - +
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Residues in contact with LEU 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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542C LEU* 5.0 5.8 - - + -
572C MET* 3.3 65.5 - - + +
573C ASP* 5.1 1.1 - - - +
575C TYR* 4.1 14.8 - - + +
577C LEU* 3.2 44.2 - - + -
602C GLY 2.6 22.3 + - - +
604C LYS* 1.3 74.0 - - + +
606C LYS* 1.3 64.1 + - - +
607C LYS 3.0 1.3 - - - -
608C SER* 4.2 0.7 - - - -
609C LEU* 2.7 38.0 + - + +
641C ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 606 (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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630A MET* 4.5 10.3 - - + -
631A TYR* 3.4 32.2 + - + -
999A FMN 4.0 8.5 - - - +
596C GLY 4.1 1.8 + - - -
597C ASP* 2.7 38.1 + - - +
598C CYS* 3.0 33.6 - - + +
602C GLY 2.6 10.1 + - - +
603C GLU 3.2 3.8 + - - +
605C LEU* 1.3 73.4 - - - +
607C LYS* 1.3 67.2 + - - +
609C LEU* 3.1 23.0 - - - +
610C PHE* 3.3 35.6 - - + -
637C PHE* 4.3 14.7 - - + -
640C ASP* 4.5 13.7 - - - -
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Residues in contact with LYS 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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630A MET* 4.4 23.0 - - + +
603C GLU 3.0 11.7 + - - +
604C LYS* 3.5 35.4 - - - +
606C LYS* 1.3 82.3 - - - +
608C SER* 1.3 72.5 + - - +
609C LEU 2.8 1.9 + - - -
610C PHE* 5.3 0.7 - - - -
611C MET* 3.1 32.6 - - + +
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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
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577C LEU* 3.3 40.5 - - - +
604C LYS* 2.6 27.2 + - - +
605C LEU 3.3 4.0 + - - -
607C LYS* 1.3 84.2 - - - +
609C LEU* 1.3 65.9 + - - +
611C MET* 3.4 16.2 - - - +
612C LEU* 3.9 4.0 + - - +
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Residues in contact with LEU 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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572C MET* 5.9 1.3 - - + -
577C LEU* 4.4 10.3 - - + +
580C LEU* 5.4 8.7 - - + -
605C LEU* 2.7 34.3 + - + +
606C LYS* 3.1 19.7 - - - +
607C LYS 2.8 3.2 + - - -
608C SER* 1.3 71.8 - - - +
610C PHE* 1.3 66.9 + - + +
611C MET 2.5 19.2 + - - -
612C LEU* 2.9 17.2 + - - +
637C PHE* 5.6 6.5 - - + -
641C ILE* 4.3 36.3 - - + -
644C LYS* 4.5 18.3 - - + -
645C LEU* 5.0 8.5 - - + -
648C LEU* 6.0 2.0 - - + +
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Residues in contact with PHE 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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595A ASN* 5.3 11.0 - - - -
630A MET 5.8 0.7 - - - -
631A TYR* 5.3 8.3 - + - -
632A PRO* 4.1 24.5 - - + -
606C LYS* 3.3 53.6 + - + -
607C LYS* 5.3 0.7 - - - -
609C LEU* 1.3 86.6 - - + +
611C MET* 1.3 81.0 + - + +
612C LEU 3.2 9.6 - - - +
613C LYS* 4.2 1.6 + - - -
637C PHE* 6.2 0.7 - + - -
640C ASP* 4.4 27.1 - - + -
644C LYS* 4.0 45.0 + - + +
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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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630A MET 4.3 17.9 - - - +
632A PRO* 4.4 9.2 - - + -
607C LYS* 3.1 34.5 - - + +
608C SER* 3.4 12.8 - - - +
609C LEU 2.5 4.6 + - - -
610C PHE* 1.3 94.9 - - + +
612C LEU* 1.3 52.0 + - - +
613C LYS* 2.5 25.5 + - - +
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Residues in contact with LEU 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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580C LEU* 6.6 0.2 - - + -
608C SER 3.9 3.5 + - - +
609C LEU* 2.9 15.2 + - - +
610C PHE 3.2 9.0 - - - +
611C MET* 1.3 69.2 - - - +
613C LYS* 1.3 52.9 + - - +
614C GLU* 2.6 20.4 + - - +
615C LEU* 5.0 14.6 - - + +
644C LYS* 4.0 10.6 - - - -
648C LEU* 4.2 7.0 - - + +
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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