Contacts of the helix formed by residues 712 - 726 (chain D) 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 HIS 712 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D ILE* 3.3 39.7 - - + +
238D TYR* 5.1 4.3 - + + -
256D TYR* 3.2 39.0 - + - -
258D LYS* 2.9 29.0 + - - -
661D TYR 4.2 1.8 + - - -
704D HIS* 3.6 1.2 + - - -
708D ASP 3.4 9.9 - - - +
709D ASP* 2.9 34.9 + - - -
710D ASN 3.6 1.3 + - - -
711D VAL* 1.3 74.9 - - - +
713D PHE* 1.3 61.3 + - - +
714D GLN* 4.1 13.5 - - + +
715D GLN* 2.8 33.5 + - + +
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Residues in contact with PHE 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C TYR* 3.3 28.9 - + - +
706C THR* 4.8 6.7 - - + -
713C PHE* 6.0 3.6 - + - -
734C TRP* 3.5 49.1 - + - -
238D TYR* 6.1 3.3 - - + +
704D HIS* 3.7 38.0 + - + -
705D GLY 3.9 16.2 - - - +
706D THR* 4.1 24.7 + - + +
708D ASP* 4.1 5.1 + - - +
711D VAL 3.5 1.4 + - - -
712D HIS* 1.3 71.7 - - - +
714D GLN* 1.3 63.0 + - - +
715D GLN 2.9 0.9 + - - -
716D SER* 3.1 4.3 + - - -
717D ALA* 2.8 33.3 + - + -
734D TRP* 4.3 11.7 - - + -
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Residues in contact with GLN 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C TYR* 3.6 25.8 + - + -
246C LEU 3.2 17.0 + - - -
247C GLN 2.9 23.7 + - - +
249C PRO* 3.6 31.0 - - + +
258D LYS* 3.1 28.2 + - - -
661D TYR* 3.4 27.0 + - + +
712D HIS* 4.1 10.3 + - + +
713D PHE* 1.3 76.4 - - - +
715D GLN* 1.3 56.9 + - - +
717D ALA* 3.2 2.0 + - - +
718D GLN* 2.9 36.6 + - + +
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Residues in contact with GLN 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D PRO 3.6 16.2 - - - +
656D VAL* 3.4 22.4 - - - +
657D SER* 2.7 54.9 + - - +
658D ARG 3.3 9.2 - - - +
661D TYR* 3.3 39.5 + - + +
662D TYR* 3.9 11.3 - - - +
704D HIS* 4.5 0.4 - - + -
711D VAL* 4.5 6.3 - - - +
712D HIS* 2.8 30.8 + - + +
714D GLN* 1.3 73.7 - - + +
716D SER* 1.3 61.0 + - - +
718D GLN* 3.3 1.0 + - - +
719D ILE* 3.2 19.7 + - - +
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Residues in contact with SER 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734C TRP* 3.9 8.0 - - - -
655D PRO* 3.2 17.8 - - - +
702D LEU* 3.6 21.2 - - - +
704D HIS* 2.6 42.8 + - - +
713D PHE* 3.1 4.8 + - - -
715D GLN* 1.3 75.1 - - - +
717D ALA* 1.3 65.9 + - - +
719D ILE* 3.2 9.6 + - - +
720D SER* 3.1 23.7 + - - -
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Residues in contact with ALA 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C TYR* 4.0 21.3 - - + -
734C TRP* 4.0 6.0 - - - +
736C THR* 2.6 35.1 + - + +
713D PHE* 2.8 32.2 + - + +
714D GLN* 3.2 11.4 + - - +
716D SER* 1.3 78.4 - - - +
718D GLN* 1.3 58.5 + - - +
720D SER* 3.1 10.3 + - - -
721D LYS* 3.3 6.1 + - - +
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Residues in contact with GLN 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C TYR* 3.4 18.1 + - + +
242C SER 3.2 21.6 + - - -
243C ASP 3.4 12.3 + - - -
244C GLU* 3.9 12.0 - - - +
246C LEU 5.1 1.2 + - - -
661D TYR* 3.4 30.9 + - + +
689D MET* 3.5 19.4 - - + +
714D GLN* 2.9 23.7 + - + +
715D GLN 3.7 5.2 - - - +
716D SER 3.2 0.2 - - - -
717D ALA* 1.3 75.5 - - - +
719D ILE* 1.3 64.8 + - - +
721D LYS* 3.0 25.9 + - - -
722D ALA* 3.1 24.1 + - - +
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Residues in contact with ILE 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D SER* 4.7 1.8 - - - +
655D PRO* 3.9 29.2 - - + -
656D VAL 4.7 1.1 - - - +
657D SER* 3.5 11.4 - - - -
688D VAL* 3.3 33.4 - - + -
689D MET* 4.0 6.7 - - - +
695D PHE* 5.7 3.6 - - + -
700D TYR* 4.0 17.5 - - + +
702D LEU* 3.8 13.9 - - + -
715D GLN 3.2 17.3 + - - +
716D SER* 3.2 10.6 + - - +
718D GLN* 1.3 75.3 - - - +
720D SER* 1.3 63.5 + - - +
722D ALA* 3.1 4.5 + - - +
723D LEU* 3.0 41.7 + - + +
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Residues in contact with SER 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734C TRP* 3.1 37.9 + - - -
735C TYR* 6.3 0.2 - - - -
736C THR* 3.3 4.3 + - - -
702D LEU* 4.5 2.0 - - - -
716D SER 3.1 9.4 + - - -
717D ALA 3.1 8.7 + - - -
719D ILE* 1.3 76.0 - - - +
721D LYS* 1.3 59.2 + - - +
723D LEU* 3.2 5.2 + - - +
724D VAL* 2.8 36.0 + - - +
730D PHE* 3.6 31.1 - - - -
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Residues in contact with LYS 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C SER 3.1 23.8 + - - -
243C ASP* 4.4 6.3 + - - +
244C GLU* 4.4 2.2 - - - +
736C THR* 3.7 42.4 - - - +
737C ASP* 3.8 7.4 - - + +
717D ALA 3.3 11.1 + - - +
718D GLN* 3.0 28.4 + - - +
719D ILE 3.3 0.4 - - - -
720D SER* 1.3 82.0 + - - +
722D ALA* 1.3 56.8 + - - +
724D VAL* 3.8 7.3 - - + +
725D ASP* 2.9 49.0 + - - +
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Residues in contact with ALA 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLU* 5.4 0.4 - - - +
689D MET* 3.4 44.2 - - + +
692D ALA* 3.6 11.3 - - + +
718D GLN 3.1 7.6 + - - +
719D ILE 3.5 3.8 - - - +
721D LYS* 1.3 76.1 - - - +
723D LEU* 1.3 64.3 + - - +
725D ASP* 3.4 17.6 + - - +
726D VAL* 3.4 17.3 + - - +
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Residues in contact with LEU 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692D ALA* 3.7 27.8 - - + +
695D PHE* 3.8 19.5 - - + -
700D TYR* 3.9 30.5 - - + -
719D ILE* 3.0 27.2 + - + +
720D SER* 3.6 5.8 - - - +
722D ALA* 1.3 72.8 - - - +
724D VAL* 1.3 64.6 + - - +
726D VAL* 3.4 1.3 + - - -
727D GLY 3.1 3.3 + - - -
728D VAL* 3.0 53.1 + - + +
730D PHE* 3.6 33.0 - - + -
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Residues in contact with VAL 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C TRP 6.0 0.4 - - - +
735C TYR* 4.0 15.9 - - + -
746C THR* 3.4 36.4 - - - +
747C ALA* 3.6 20.4 - - + +
750C HIS* 3.8 36.1 - - + +
720D SER* 2.8 24.4 + - - +
721D LYS* 3.8 8.1 - - + +
723D LEU* 1.3 74.3 - - - +
725D ASP* 1.3 66.5 + - - +
727D GLY* 3.1 12.6 + - - -
730D PHE* 4.3 4.9 - - + -
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Residues in contact with ASP 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C THR* 3.3 33.2 + - + +
721D LYS* 2.9 43.7 + - - +
722D ALA* 3.7 10.5 - - - +
723D LEU 3.3 0.4 - - - -
724D VAL* 1.3 77.7 - - - +
726D VAL* 1.3 64.1 + - + +
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Residues in contact with VAL 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692D ALA* 3.8 22.7 - - + +
693D GLU* 3.7 21.8 - - + +
696D LYS* 2.8 26.4 + - - -
722D ALA 3.4 16.6 - - - +
723D LEU 3.5 7.4 - - - +
725D ASP* 1.3 82.7 - - + +
727D GLY* 1.3 56.9 + - - +
728D VAL* 3.7 15.0 - - + -
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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
------------------------------------------------------------
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