Contacts of the helix formed by residues 715 - 731 (chain F) in PDB entry 4YJL
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 715 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674F LEU* 4.3 29.9 - - + +
675F THR* 6.1 0.2 - - - -
678F SER* 3.6 14.3 + - - -
713F SER* 2.9 12.6 + - - +
714F LYS* 1.3 77.9 - - - +
716F LYS* 1.3 67.3 + - - +
717F MET* 3.3 34.4 - - + +
718F ILE* 3.2 46.6 + - + +
719F ALA* 2.9 26.1 + - - +
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Residues in contact with LYS 716 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F LYS 3.5 6.3 + - - +
715F HIS* 1.3 73.7 - - - +
717F MET* 1.3 65.4 + - + +
719F ALA* 3.4 4.7 + - - +
720F MET* 3.0 36.5 + - + +
497L ARG* 6.2 0.9 - - - +
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Residues in contact with MET 717 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640F ARG* 3.4 41.9 + - - +
678F SER* 3.4 23.6 - - - +
681F CYS* 4.5 3.1 - - - +
715F HIS* 3.3 14.0 - - - +
716F LYS* 1.3 78.4 - - + +
718F ILE* 1.3 60.6 + - - +
720F MET* 4.4 13.2 - - + -
721F GLY* 2.9 27.9 + - - -
497L ARG* 4.6 21.5 - - + +
498L ASP 4.7 4.0 - - - +
499L SER* 5.0 5.2 - - - -
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Residues in contact with ILE 718 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674F LEU* 3.9 34.8 - - + +
677F VAL* 3.9 21.8 - - + -
678F SER* 3.7 19.5 - - - +
681F CYS* 4.0 7.4 - - - -
710F LEU* 4.0 22.0 - - + +
713F SER* 3.7 24.2 - - - +
715F HIS* 3.2 33.3 + - + +
717F MET* 1.3 74.1 - - - +
719F ALA* 1.3 61.6 + - - +
722F SER* 2.8 33.1 + - - -
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Residues in contact with ALA 719 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710F LEU 3.9 7.2 - - - -
711F ILE 3.6 19.5 - - - +
713F SER* 3.7 16.8 - - - +
715F HIS 2.9 17.6 + - - +
716F LYS* 3.8 5.2 - - - +
718F ILE* 1.3 75.5 - - - +
720F MET* 1.3 61.8 + - - +
722F SER* 3.3 5.9 + - - -
723F ALA* 3.2 25.8 + - - +
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Residues in contact with MET 720 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685F TRP* 3.8 28.7 - - + -
716F LYS* 3.0 23.8 + - + +
717F MET* 4.0 13.2 - - + +
719F ALA* 1.3 74.3 - - - +
721F GLY* 1.3 60.6 + - - +
723F ALA* 3.4 4.9 + - - +
724F ALA* 3.0 30.7 + - + +
727F ARG* 4.7 3.5 + - - +
497L ARG* 3.4 43.1 - - - +
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Residues in contact with GLY 721 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F CYS* 3.9 20.3 - - - +
682F GLY* 4.8 0.9 - - - -
685F TRP* 3.7 21.7 - - - +
717F MET 2.9 21.5 + - - -
720F MET* 1.3 69.2 - - - +
722F SER* 1.3 64.9 + - - +
724F ALA* 3.3 2.1 + - - +
725F ALA* 3.0 25.8 + - - +
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Residues in contact with SER 722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F CYS* 3.8 11.9 - - - +
707F LEU* 3.9 25.3 - - - +
710F LEU* 3.4 38.2 - - - -
711F ILE* 3.4 4.7 + - - -
718F ILE 2.8 24.3 + - - -
719F ALA 3.3 5.2 + - - -
721F GLY* 1.3 74.0 - - - +
723F ALA* 1.3 59.8 + - - +
725F ALA* 3.5 1.6 + - - +
726F LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 723 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711F ILE* 3.8 20.6 - - + +
719F ALA 3.2 17.2 + - - +
720F MET* 3.8 4.5 - - - +
721F GLY 3.3 0.2 - - - -
722F SER* 1.3 80.0 + - - +
724F ALA* 1.3 57.3 + - - +
726F LEU* 3.7 4.0 - - - +
727F ARG* 2.8 40.9 + - - +
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Residues in contact with ALA 724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F TRP* 3.3 47.1 - - + +
720F MET 3.0 15.5 + - - +
721F GLY 3.7 0.9 - - - +
723F ALA* 1.3 74.3 - - - +
725F ALA* 1.3 59.5 + - - +
727F ARG* 3.4 27.4 + - - +
728F ASN* 3.0 34.2 + - - +
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Residues in contact with ALA 725 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681F CYS 4.7 0.2 - - - +
684F LEU* 4.0 7.9 - - + -
685F TRP* 3.9 17.9 - - - +
688F SER* 3.5 21.2 + - - +
698F LEU* 6.4 0.2 - - + -
707F LEU* 3.9 22.0 - - + -
721F GLY 3.0 16.5 + - - +
722F SER 3.9 2.9 - - - +
724F ALA* 1.3 73.1 - - - +
726F LEU* 1.3 66.8 + - - +
728F ASN* 3.1 4.3 + - - +
729F LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 726 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704F VAL* 3.8 41.3 - - + +
707F LEU* 3.9 13.2 - - + +
708F LYS* 3.9 24.7 - - + -
711F ILE* 4.0 27.4 - - + -
722F SER 2.9 18.9 + - - +
723F ALA* 3.7 4.5 - - - +
725F ALA* 1.3 75.3 - - - +
727F ARG* 1.3 56.9 + - - +
729F LEU* 3.2 2.4 + - - +
730F MET* 2.8 53.7 + - + +
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Residues in contact with ARG 727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F TRP* 5.6 4.0 - - - +
720F MET* 4.7 3.8 + - - +
723F ALA* 2.8 21.9 + - - +
724F ALA* 3.4 39.8 + - - +
725F ALA 3.2 0.2 - - - -
726F LEU* 1.3 77.6 - - - +
728F ASN* 1.3 65.0 + - - +
730F MET* 3.5 5.4 + - - +
731F ALA* 3.1 29.1 + - + +
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Residues in contact with ASN 728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685F TRP* 3.2 22.2 + - - -
688F SER* 3.0 42.3 + - - +
689F ALA* 3.5 17.8 - - - +
695F GLN* 4.3 2.6 - - - +
724F ALA 3.0 17.9 + - - +
725F ALA 3.1 2.2 + - - +
727F ARG* 1.3 81.3 + - - +
729F LEU* 1.3 62.4 - - - +
731F ALA* 4.2 1.5 - - - +
732F ASN* 2.9 31.6 + - - +
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Residues in contact with LEU 729 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688F SER* 4.0 11.2 - - - -
695F GLN* 4.0 22.9 - - + +
698F LEU* 3.9 35.7 - - + -
699F TRP* 2.9 30.1 + - + +
703F ALA* 3.9 20.4 - - + -
704F VAL* 4.1 20.2 - - + -
707F LEU* 3.8 26.0 - - + -
725F ALA 3.0 14.7 + - - +
726F LEU* 3.2 5.4 + - - +
728F ASN* 1.3 75.7 - - - +
730F MET* 1.3 63.7 + - - +
732F ASN* 3.0 14.7 + - - -
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Residues in contact with MET 730 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699F TRP* 4.2 20.9 - - - -
704F VAL* 4.4 9.4 - - - -
708F LYS* 5.0 13.7 - - - +
726F LEU* 2.8 48.8 + - + +
727F ARG* 4.0 5.4 - - - +
729F LEU* 1.3 71.7 - - - +
731F ALA* 1.3 60.8 + - - +
732F ASN 3.1 1.3 + - - -
733F ARG* 3.5 36.1 + - - +
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Residues in contact with ALA 731 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727F ARG* 3.1 20.0 + - + +
728F ASN* 4.2 1.8 - - - +
730F MET* 1.3 76.0 - - - +
732F ASN* 1.3 73.5 + - - +
733F ARG 3.8 1.2 + - - -
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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