Contacts of the helix formed by residues 715 - 731 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674E LEU* 4.2 34.8 - - + +
675E THR* 5.9 0.7 - - - -
678E SER* 3.5 19.5 + - - -
713E SER* 3.0 11.0 + - - +
714E LYS* 1.3 77.5 - - - +
716E LYS* 1.3 61.1 + - - +
717E MET* 3.3 22.4 - - + +
718E ILE* 3.2 43.5 + - + -
719E ALA* 2.9 31.2 + - - +
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Residues in contact with LYS 716 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E LYS 3.5 7.7 + - - +
715E HIS* 1.3 73.8 - - - +
717E MET* 1.3 75.8 + - + +
719E ALA* 3.4 5.1 + - - +
720E MET* 2.9 33.1 + - + +
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Residues in contact with MET 717 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ASP* 4.1 25.1 - - + +
640E ARG* 4.6 16.9 + - - +
678E SER* 3.1 25.9 - - - +
681E CYS* 4.5 2.1 - - - +
715E HIS* 3.3 13.8 - - + +
716E LYS* 1.3 87.2 - - + +
718E ILE* 1.3 55.7 + - - +
720E MET* 4.1 23.6 - - - +
721E GLY* 2.8 32.9 + - - -
497J ARG* 4.4 13.7 - - - +
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Residues in contact with ILE 718 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674E LEU* 3.8 34.1 - - + +
677E VAL* 3.9 17.3 - - + -
678E SER* 3.8 18.6 - - - +
681E CYS* 4.0 8.3 - - - -
710E LEU* 3.9 28.7 - - + +
713E SER* 3.6 20.0 - - - +
715E HIS* 3.2 34.8 - - + +
717E MET* 1.3 77.6 - - - +
719E ALA* 1.3 51.6 + - - +
722E SER* 2.7 40.4 + - - -
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Residues in contact with ALA 719 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710E LEU 3.9 7.0 - - - -
711E ILE 3.8 16.7 - - - +
713E SER* 3.7 18.6 - - - +
715E HIS 2.9 18.3 + - - +
716E LYS* 3.8 5.8 - - - +
718E ILE* 1.3 75.7 - - - +
720E MET* 1.3 62.8 + - - +
722E SER* 3.2 15.6 + - - -
723E ALA* 3.2 16.1 + - - +
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Residues in contact with MET 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS* 6.6 0.2 - - - -
574A GLU* 4.8 13.7 - - - +
640E ARG* 5.7 3.6 - - - +
685E TRP* 4.0 31.6 - - + -
716E LYS 2.9 15.0 + - - +
717E MET* 4.0 26.7 - - + +
719E ALA* 1.3 77.9 - - - +
721E GLY* 1.3 55.1 + - - +
723E ALA* 3.4 4.6 + - - +
724E ALA* 2.9 31.1 + - + +
727E ARG* 5.1 2.2 + - - +
497J ARG* 3.1 38.8 - - + +
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Residues in contact with GLY 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681E CYS* 3.8 22.0 - - - +
682E GLY 4.8 0.4 - - - -
685E TRP* 3.8 20.7 - - - +
717E MET 2.8 21.7 + - - -
720E MET* 1.3 70.5 - - - +
722E SER* 1.3 59.4 + - - +
724E ALA* 3.4 1.9 + - - +
725E ALA* 3.0 30.1 + - - +
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Residues in contact with SER 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681E CYS* 3.8 10.9 - - - +
707E LEU* 3.8 26.1 - - - +
710E LEU* 3.4 37.8 - - - -
711E ILE* 3.5 3.7 + - - -
718E ILE 2.7 24.3 + - - -
719E ALA 3.2 5.4 + - - -
721E GLY* 1.3 73.5 - - - +
723E ALA* 1.3 59.9 + - - +
725E ALA* 3.8 1.7 - - - +
726E LEU* 2.9 30.8 + - - +
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Residues in contact with ALA 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711E ILE* 3.8 19.5 - - + -
719E ALA 3.2 16.8 + - - +
720E MET* 3.7 4.7 - - - +
722E SER* 1.3 79.7 + - - +
724E ALA* 1.3 57.5 + - - +
726E LEU* 3.3 4.8 + - - +
727E ARG* 2.9 49.2 + - + +
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Residues in contact with ALA 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685E TRP* 3.3 44.2 - - + +
720E MET* 2.9 17.4 + - + +
721E GLY 3.7 0.7 - - - +
723E ALA* 1.3 76.7 - - - +
725E ALA* 1.3 62.1 + - - +
727E ARG* 3.3 26.1 + - - +
728E ASN* 3.1 28.8 + - - -
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Residues in contact with ALA 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681E CYS 4.7 0.2 - - - +
684E LEU* 3.9 8.3 - - + -
685E TRP* 3.8 23.9 - - - +
688E SER* 3.5 16.1 + - - +
698E LEU* 6.4 0.2 - - + -
707E LEU* 3.9 23.6 - - + -
721E GLY 3.0 17.1 + - - +
722E SER 3.9 0.9 - - - +
724E ALA* 1.3 72.3 - - - +
726E LEU* 1.3 65.8 - - - +
728E ASN* 3.3 4.9 + - - +
729E LEU* 3.1 26.0 + - + +
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Residues in contact with LEU 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704E VAL* 3.7 40.4 - - + +
707E LEU* 3.8 13.1 - - + +
708E LYS* 3.7 25.6 - - + -
711E ILE* 4.0 26.5 - - + -
722E SER 2.9 18.8 + - - +
723E ALA* 3.6 4.9 - - - +
725E ALA* 1.3 77.2 - - - +
727E ARG* 1.3 57.5 + - + +
729E LEU* 3.2 3.1 + - - -
730E MET* 2.8 52.6 + - + +
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Residues in contact with ARG 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A LEU* 3.5 33.3 - - + +
534A LYS* 3.7 52.3 + - - +
808A EDO 5.7 3.4 - - - +
685E TRP* 5.5 2.4 - - - -
720E MET* 5.1 2.2 + - - +
723E ALA* 2.9 33.8 + - + +
724E ALA* 3.6 30.1 + - - +
725E ALA 3.3 0.2 - - - -
726E LEU* 1.3 76.3 - - + +
728E ASN* 1.3 59.9 + - - +
730E MET* 3.9 5.8 - - - +
731E ALA* 2.9 34.5 + - - +
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Residues in contact with ASN 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A GLU* 4.6 15.0 - - - +
685E TRP* 3.3 22.2 + - - +
688E SER* 3.1 41.5 + - - +
689E ALA* 3.6 18.0 - - - +
690E ARG 5.4 0.2 - - - -
695E GLN* 4.2 2.9 - - - +
724E ALA 3.1 13.7 + - - +
725E ALA 3.4 2.9 - - - +
727E ARG* 1.3 79.9 - - - +
729E LEU* 1.3 62.4 + - - +
731E ALA* 4.8 1.8 - - - -
732E ASN* 2.8 30.7 + - - +
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Residues in contact with LEU 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688E SER* 4.2 4.5 - - - -
695E GLN* 3.7 37.0 - - + +
698E LEU* 3.8 25.8 - - + -
699E TRP* 2.9 30.3 + - + +
703E ALA* 3.9 20.2 - - + -
704E VAL* 4.1 19.3 - - + -
707E LEU* 3.7 29.4 - - + -
725E ALA 3.1 10.5 + - - +
726E LEU* 3.7 5.4 - - - +
728E ASN* 1.3 73.5 - - - +
730E MET* 1.3 61.8 + - - +
732E ASN* 3.0 18.9 + - - -
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Residues in contact with MET 730 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699E TRP* 4.3 12.5 - - - -
704E VAL* 4.1 24.5 - - - -
708E LYS* 4.8 14.4 - - - +
726E LEU* 2.8 40.8 + - + +
727E ARG* 3.9 5.8 - - - +
729E LEU* 1.3 73.0 - - - +
731E ALA* 1.3 60.1 + - - +
732E ASN 3.1 0.9 + - - -
733E ARG* 3.7 35.7 + - - +
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Residues in contact with ALA 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A LEU 3.3 25.5 + - - +
489A THR* 4.8 4.3 + - - +
490A ASN* 3.4 38.6 + - - +
536A GLU* 4.8 0.2 - - - +
808A EDO 3.9 7.0 - - - +
727E ARG 2.9 17.6 + - - +
728E ASN* 4.1 2.0 - - - +
730E MET* 1.3 75.8 - - - +
732E ASN* 1.3 65.7 + - - +
733E ARG 3.8 0.8 + - - -
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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