Contacts of the helix formed by residues 708 - 723 (chain A) in PDB entry 4PK7
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 LEU 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A ILE* 6.2 1.3 - - + -
662A ALA* 5.2 6.1 - - + -
665A PHE* 5.6 4.3 - - + -
694A ILE* 3.9 35.4 - - + -
698A HIS* 3.2 36.3 - - + +
703A LEU* 4.4 7.6 - - + +
706A TRP* 2.7 38.0 + - + +
707A ASP* 1.3 70.2 - - - +
709A PHE* 1.3 66.8 + - - +
710A ALA 3.1 1.3 - - - -
711A CYS* 3.3 20.4 + - + -
712A ASN* 3.2 34.4 + - - +
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Residues in contact with PHE 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A ASP* 3.3 14.8 + - - +
708A LEU* 1.3 80.1 - - - +
710A ALA* 1.3 56.0 + - - +
712A ASN* 4.0 5.8 - - + +
713A TYR* 2.8 76.3 + + + +
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Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ASP* 3.8 22.3 + - - +
709A PHE* 1.3 83.9 - - - +
711A CYS* 1.3 56.5 + - - +
713A TYR* 3.6 5.2 - - - +
714A LYS* 2.8 49.3 + - - +
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Residues in contact with CYS 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A PHE* 4.0 15.3 - - + -
666A ASN* 3.8 22.4 - - - +
669A LEU* 3.7 28.7 - - + +
707A ASP 4.3 4.5 - - - -
708A LEU* 3.3 30.3 + - - +
710A ALA* 1.3 77.3 - - - +
712A ASN* 1.3 62.0 + - - +
714A LYS* 3.7 14.4 + - - +
715A LEU* 3.3 22.5 + - - +
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Residues in contact with ASN 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A PHE* 4.6 8.0 - - - -
691A LEU* 3.8 24.9 - - - +
694A ILE* 5.6 4.8 - - - +
698A HIS* 5.8 2.4 - - - -
708A LEU* 3.2 30.1 + - - +
709A PHE* 4.0 6.4 - - + +
711A CYS* 1.3 75.8 - - - +
713A TYR* 1.3 68.1 + - - +
715A LEU* 2.9 12.6 + - - +
716A LEU* 2.9 33.3 + - + +
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Residues in contact with TYR 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A PHE* 2.8 55.2 + + + +
710A ALA* 3.6 5.4 - - - +
712A ASN* 1.3 71.7 - - - +
714A LYS* 1.3 58.9 + - + +
715A LEU 2.9 6.4 + - - -
716A LEU* 2.9 11.0 + - + -
717A LYS* 2.9 65.7 + - + +
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Residues in contact with LYS 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ASN* 5.7 2.4 + - - -
669A LEU* 5.9 6.1 - - + +
673A LEU* 4.0 23.4 - - + +
710A ALA* 2.8 31.8 + - - +
711A CYS* 3.8 13.9 - - - +
713A TYR* 1.3 77.7 - - + +
715A LEU* 1.3 55.3 + - - +
716A LEU 3.5 0.2 - - - -
717A LYS* 4.3 18.8 - - - +
718A THR* 3.0 26.4 + - - +
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A PHE* 4.4 11.4 - - + -
669A LEU* 4.4 21.8 - - + -
672A PHE* 4.0 17.5 - - + -
673A LEU* 4.6 2.7 - - + -
687A VAL* 4.8 3.8 - - + -
691A LEU* 4.3 15.5 - - + -
711A CYS 3.3 15.3 + - - +
712A ASN* 2.9 11.8 + - - +
714A LYS* 1.3 76.8 - - - +
716A LEU* 1.3 64.4 + - + +
718A THR* 3.1 19.6 - - + +
719A GLY* 3.6 5.5 + - - -
725A MET* 3.7 31.7 - - + +
729A ILE* 3.8 25.4 - - + +
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Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ASN* 2.9 24.7 + - + +
713A TYR* 3.7 9.9 - - + +
715A LEU* 1.3 78.7 - - + +
717A LYS* 1.3 63.2 + - - +
718A THR 3.2 1.1 - - - -
719A GLY* 3.2 2.9 + - - +
720A ILE* 3.2 28.9 + - + +
729A ILE 5.6 0.2 - - - +
730A VAL* 4.0 38.6 - - + +
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Residues in contact with LYS 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A TYR* 2.9 56.2 + - + +
714A LYS* 4.3 18.6 - - - +
716A LEU* 1.3 78.2 - - - +
718A THR* 1.3 66.0 + - - +
720A ILE* 3.4 12.5 + - + +
721A GLU* 3.3 30.8 + - + +
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Residues in contact with THR 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A LEU* 3.8 22.5 - - + +
714A LYS 3.0 24.8 + - - +
715A LEU* 3.1 21.5 - - - +
717A LYS* 1.3 82.3 - - - +
719A GLY* 1.3 60.6 + - - +
721A GLU* 4.2 6.0 - - - +
722A ASN* 3.3 28.2 + - - +
725A MET* 3.5 16.2 - - + +
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Residues in contact with GLY 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A LEU 3.6 3.0 + - - -
716A LEU* 3.2 7.7 + - - -
717A LYS 3.2 0.4 - - - -
718A THR* 1.3 81.3 - - - +
720A ILE* 1.3 58.0 + - - +
722A ASN* 5.0 0.7 - - - -
723A GLY* 2.7 34.9 + - - -
724A ASP 4.0 0.4 + - - -
725A MET* 3.6 29.5 - - - +
730A VAL* 5.8 1.6 - - - -
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Residues in contact with ILE 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A LEU* 3.2 15.2 + - + +
717A LYS* 3.6 15.3 - - - +
719A GLY* 1.3 79.3 - - - +
721A GLU* 1.3 73.4 + - + +
723A GLY* 3.4 7.6 + - - -
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Residues in contact with GLU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A LYS* 3.3 21.1 + - + +
718A THR* 4.6 4.7 - - - +
720A ILE* 1.3 84.5 - - + +
722A ASN* 1.3 61.1 + - + +
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Residues in contact with ASN 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A THR* 3.3 22.5 + - - +
720A ILE 3.3 0.2 - - - -
721A GLU* 1.3 81.2 - - + +
723A GLY* 1.3 58.4 + - - +
724A ASP* 2.9 45.5 + - - +
725A MET* 5.7 1.2 - - + +
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Residues in contact with GLY 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A GLY 2.7 19.3 + - - -
720A ILE 3.4 7.6 + - - -
722A ASN* 1.3 76.6 - - - +
724A ASP* 1.3 58.3 + - - +
725A MET 4.1 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
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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