Contacts of the helix formed by residues 711 - 729 (chain D) in PDB entry 4YFI
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 GLU 711 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578D HIS* 5.5 3.8 + - - +
644D ILE* 4.2 19.0 - - - +
645D LYS* 4.1 20.6 + - - +
648D VAL* 5.1 1.3 - - - -
709D ARG 3.9 0.4 + - - -
710D PRO* 1.3 76.5 - - - +
712D PHE* 1.3 65.3 + - - +
713D SER* 3.2 17.7 - - - +
714D GLU* 3.0 18.1 + - + +
715D VAL* 3.4 10.0 + - - +
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Residues in contact with PHE 712 (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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571D ALA* 3.7 22.7 - - + -
574D MET* 3.5 28.9 - - + +
575D GLU* 3.8 22.4 - - + +
578D HIS* 3.5 33.9 + + + +
579D ASN* 5.8 1.1 - - - +
647D ASP 4.0 3.4 - - - -
648D VAL* 3.6 29.6 - - + +
651D TYR* 3.5 49.6 - + + -
711D GLU* 1.3 71.6 + - - +
713D SER* 1.3 65.4 + - - +
714D GLU 3.2 0.2 - - - -
715D VAL* 3.3 12.6 + - + +
716D VAL* 3.0 28.5 + - - +
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Residues in contact with SER 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D GLU* 3.3 30.4 + - - +
579D ASN* 5.3 6.2 + - - +
711D GLU* 3.7 15.1 - - - +
712D PHE* 1.3 75.6 - - - +
714D GLU* 1.3 63.3 + - - +
716D VAL* 3.4 2.6 + - - +
717D MET* 3.2 29.2 + - - +
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Residues in contact with GLU 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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697D LEU* 5.2 0.9 - - + -
700D ARG* 2.8 43.1 + - - -
710D PRO* 3.6 10.8 - - + +
711D GLU* 3.0 14.9 + - + +
713D SER* 1.3 79.6 + - - +
715D VAL* 1.3 65.7 + - - +
717D MET* 3.4 6.2 + - + +
718D LYS* 3.2 48.2 + - + +
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Residues in contact with VAL 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D ALA* 3.9 8.3 - - + -
648D VAL* 5.3 4.5 - - + -
651D TYR* 3.7 24.2 - - + -
697D LEU* 4.0 19.0 - - + +
710D PRO* 4.2 20.6 - - + +
711D GLU 3.4 12.8 + - - +
712D PHE* 3.3 23.4 + - + +
714D GLU* 1.3 77.4 - - - +
716D VAL* 1.3 62.1 + - - +
718D LYS* 4.1 0.7 - - - +
719D LEU* 3.0 46.7 + - + +
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Residues in contact with VAL 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D VAL* 4.7 2.8 - - + +
571D ALA* 3.5 39.7 - - + +
572D LYS* 3.7 22.7 - - + +
575D GLU* 3.7 19.5 - - - +
712D PHE 3.0 21.2 + - - +
713D SER 3.8 3.8 - - - +
714D GLU 3.2 0.4 - - - -
715D VAL* 1.3 76.3 - - - +
717D MET* 1.3 59.0 + - + +
719D LEU* 4.0 2.3 - - - +
720D GLU* 2.9 48.2 + - + +
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Residues in contact with MET 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713D SER* 3.2 17.5 + - - +
714D GLU* 4.0 6.1 - - + +
715D VAL 3.3 0.2 - - - -
716D VAL* 1.3 76.8 - - + +
718D LYS* 1.3 66.6 + - + +
720D GLU* 3.7 11.5 - - - +
721D GLU* 3.0 24.7 + - - +
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Residues in contact with LYS 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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693D PRO* 5.6 6.5 - - + +
697D LEU* 4.3 21.5 - - + -
700D ARG* 4.8 6.1 - - - +
714D GLU* 3.2 46.8 + - + +
715D VAL 4.1 2.2 - - - +
717D MET* 1.3 77.0 - - + +
719D LEU* 1.3 62.9 + - + +
721D GLU* 3.4 17.1 + - - +
722D CYS* 3.1 29.2 + - - -
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Residues in contact with LEU 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D LEU* 4.3 20.5 - - + +
567D ALA* 4.1 19.5 - - + +
568D VAL* 3.5 18.3 - - + +
571D ALA* 4.6 1.1 - - + -
651D TYR* 3.1 28.5 - - + +
655D LEU* 4.5 11.4 - - + -
694D ILE* 4.4 17.7 - - + -
697D LEU* 4.1 15.3 - - + -
715D VAL* 3.0 32.8 + - + +
716D VAL* 4.0 2.0 - - - +
718D LYS* 1.3 79.4 - - - +
720D GLU* 1.3 55.3 + - - +
722D CYS* 3.4 7.1 + - - +
723D LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D VAL* 4.0 17.6 - - + +
572D LYS* 4.4 16.8 + - - +
716D VAL* 2.9 38.2 + - - +
717D MET* 3.7 11.0 - - - +
719D LEU* 1.3 72.6 - - - +
721D GLU* 1.3 59.9 + - - +
723D LEU* 3.1 12.5 + - + +
724D CYS* 2.9 34.7 + - - -
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Residues in contact with GLU 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717D MET 3.0 15.1 + - - +
718D LYS* 3.5 20.2 - - - +
720D GLU* 1.3 74.4 - - - +
722D CYS* 1.3 63.8 + - - +
724D CYS* 3.2 10.0 + - + +
725D ASN* 3.1 42.8 + - - +
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Residues in contact with CYS 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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564D LEU* 4.3 15.5 - - + -
691D PRO* 6.3 0.4 - - - -
693D PRO* 4.2 22.4 - - - -
694D ILE* 4.0 25.8 - - + -
718D LYS* 3.1 23.1 + - - -
719D LEU* 3.5 11.0 - - - +
720D GLU 3.3 0.2 - - - -
721D GLU* 1.3 75.9 - - - +
723D LEU* 1.3 58.0 + - - +
725D ASN* 3.4 8.7 + - - +
726D ILE* 3.0 39.8 + - + +
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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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561D GLN* 3.8 40.6 - - + +
564D LEU* 4.1 17.3 - - + -
565D ILE* 4.3 18.8 - - + -
568D VAL* 4.9 16.6 - - + -
719D LEU 3.0 14.3 + - - +
720D GLU* 3.1 14.3 + - + +
722D CYS* 1.3 76.9 - - - +
724D CYS* 1.3 62.2 + - - +
726D ILE* 4.0 2.4 - - + +
727D GLU* 3.1 40.9 + - - +
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Residues in contact with CYS 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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720D GLU* 2.9 18.5 + - - -
721D GLU* 3.2 11.6 + - - +
723D LEU* 1.3 75.0 - - - +
725D ASN* 1.3 63.8 + - - +
727D GLU* 3.0 13.2 + - - +
728D LEU* 2.8 41.1 + - + +
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Residues in contact with ASN 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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721D GLU* 3.1 34.0 + - - +
722D CYS* 3.9 7.6 - - - +
724D CYS* 1.3 78.2 - - - +
726D ILE* 1.3 57.9 + - + +
728D LEU* 3.5 15.9 + - - +
729D MET* 3.0 46.2 + - + +
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Residues in contact with ILE 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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560D LEU* 3.2 28.9 - - + -
561D GLN* 4.4 30.9 - - + +
564D LEU* 3.2 33.9 - - + -
691D PRO* 6.0 1.3 - - + -
694D ILE* 6.0 1.1 - - + -
722D CYS* 3.0 23.9 + - + +
723D LEU* 4.2 4.0 - - - +
725D ASN* 1.3 75.7 - - + +
727D GLU* 1.3 65.3 + - - +
729D MET* 3.7 21.4 + - - +
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Residues in contact with GLU 727 (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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561D GLN* 4.0 31.4 + - + +
565D ILE* 5.4 1.4 - - - +
723D LEU* 3.1 40.3 + - - +
724D CYS* 3.0 11.8 + - - +
726D ILE* 1.3 75.4 - - - +
728D LEU* 1.3 65.6 + - + +
729D MET 3.4 7.4 - - - +
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Residues in contact with LEU 728 (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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724D CYS* 2.8 31.6 + - + +
725D ASN* 3.7 16.6 - - - +
727D GLU* 1.3 77.6 - - + +
729D MET* 1.3 62.9 + - + +
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Residues in contact with MET 729 (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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725D ASN* 3.0 32.5 + - - +
726D ILE* 3.7 17.8 + - + +
727D GLU 3.4 9.4 - - - +
728D LEU* 1.3 83.3 - - + +
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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