Contacts of the helix formed by residues 711 - 727 (chain A) in PDB entry 5QSY
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 ASP 711 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A ASN* 5.7 0.2 - - - +
708A THR 4.2 3.6 - - - +
709A LYS 3.9 2.5 + - - +
710A TRP* 1.3 70.7 - - - +
712A LEU* 1.3 62.3 + - - +
713A PHE* 4.1 8.3 + - - +
714A GLY* 3.6 25.0 + - - -
715A ASN* 4.3 9.4 + - - -
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Residues in contact with LEU 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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666A VAL* 4.1 21.5 - - + -
669A PHE* 3.8 30.9 - - + -
670A ASN* 5.0 2.5 - - - +
695A LEU* 6.2 0.2 - - + -
698A LEU* 4.1 26.7 - - + -
702A HIS* 4.0 26.0 - - + +
707A LEU* 4.4 17.7 - - + +
710A TRP* 2.9 18.4 + - + +
711A ASP* 1.3 69.7 - - - +
713A PHE* 1.3 67.2 + - - +
714A GLY 3.1 2.8 + - - -
715A ASN* 3.3 4.0 + - - +
716A CYS* 3.1 26.7 + - - -
740A CYS* 4.2 20.4 - - - -
744A SER* 5.8 0.8 + - - -
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Residues in contact with PHE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ASP* 3.4 8.6 + - - +
712A LEU* 1.3 77.7 - - - +
714A GLY* 1.3 59.6 + - - +
716A CYS* 3.4 5.1 + - - +
717A TYR* 2.8 63.7 + + + +
741A SER* 3.7 39.7 - - - +
744A SER* 3.8 23.5 + - - +
745A ILE* 4.2 5.4 - - + -
748A GLN* 4.8 3.8 - - - +
768A THR* 3.8 40.6 - - + -
771A SER* 4.0 7.0 - - - -
772A PHE* 3.9 19.7 - + + -
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Residues in contact with GLY 714 (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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711A ASP* 3.6 22.9 + - - -
712A LEU 3.1 1.6 + - - -
713A PHE* 1.3 82.4 - - - +
715A ASN* 1.3 61.3 + - - +
717A TYR* 3.3 8.3 + - - +
718A ARG* 3.2 29.1 + - - +
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Residues in contact with ASN 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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669A PHE* 3.8 18.4 - - + -
670A ASN* 2.7 38.6 + - - +
673A VAL* 3.5 15.1 - - + +
674A GLU* 5.8 1.0 + - - +
711A ASP 4.3 7.2 + - - +
712A LEU* 3.3 5.0 + - - +
714A GLY* 1.3 70.6 - - - +
716A CYS* 1.3 66.6 + - - +
717A TYR 3.1 1.3 - - - -
718A ARG* 2.5 40.1 + - - +
719A LEU* 3.1 28.9 + - - +
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Residues in contact with CYS 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 4.4 5.4 - - - -
695A LEU* 3.9 19.7 - - - -
712A LEU* 3.1 21.3 + - - +
713A PHE* 3.7 1.6 - - - +
715A ASN* 1.3 77.9 - - - +
717A TYR* 1.3 63.5 + - - +
719A LEU* 3.2 10.1 + - - +
720A LEU* 3.1 28.5 + - - +
737A ALA* 3.8 12.1 - - + +
740A CYS* 3.7 34.1 - - - -
741A SER* 3.2 21.5 - - - +
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Residues in contact with TYR 717 (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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713A PHE* 2.8 43.9 + + + +
714A GLY* 3.4 8.5 - - - +
715A ASN 3.1 0.2 - - - -
716A CYS* 1.3 76.7 - - - +
718A ARG* 1.3 61.1 + - + +
720A LEU* 3.4 9.5 + - + +
721A LYS* 2.8 65.0 + - + +
741A SER* 4.6 1.1 + - - -
771A SER* 3.8 34.7 + - - -
772A PHE* 5.5 1.6 - + - -
775A VAL* 3.5 27.1 - - + -
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Residues in contact with ARG 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A VAL* 4.0 2.2 - - - +
674A GLU* 3.3 38.5 + - - -
677A LEU* 3.3 37.6 - - + +
678A GLN* 5.2 4.2 - - - +
714A GLY 3.2 16.2 + - - +
715A ASN* 2.5 37.2 + - - +
717A TYR* 1.3 77.7 - - + +
719A LEU* 1.3 56.0 + - - +
721A LYS* 3.7 5.8 - - - +
722A THR* 2.8 42.4 + - - +
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Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 4.1 11.4 - - + -
673A VAL* 4.1 22.7 - - + -
676A LEU* 3.7 29.6 - - + -
677A LEU* 4.3 10.1 - - + -
691A VAL* 3.8 24.9 - - + -
695A LEU* 4.2 8.5 - - + -
715A ASN 3.1 17.4 + - - +
716A CYS* 3.4 10.1 - - - +
718A ARG* 1.3 77.4 - - - +
720A LEU* 1.3 57.3 + - - +
722A THR* 4.6 0.9 - - - -
723A GLY* 3.1 22.9 + - - -
729A MET* 3.1 27.9 - - + +
733A ILE* 4.2 13.0 - - + -
737A ALA* 4.7 3.8 - - + -
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Residues in contact with LEU 720 (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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716A CYS 3.1 20.0 + - - +
717A TYR* 3.7 9.4 - - + +
719A LEU* 1.3 73.9 - - - +
721A LYS* 1.3 60.4 + - - +
723A GLY* 3.1 3.0 + - - +
724A ILE* 3.0 34.8 + - - +
734A VAL* 3.7 45.3 - - + +
737A ALA* 3.8 27.6 - - + +
738A LEU* 4.0 14.4 - - + +
741A SER* 4.2 6.7 - - - +
772A PHE* 4.3 5.2 - - + -
775A VAL* 3.8 29.8 - - + -
779A CYS* 4.7 3.4 - - - -
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Residues in contact with LYS 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 TYR* 2.8 62.6 + - + +
718A ARG* 3.8 6.1 - - - +
720A LEU* 1.3 72.2 - - - +
722A THR* 1.3 59.2 + - - +
724A ILE* 3.6 7.6 + - + +
725A GLU* 3.1 45.4 + - - +
774A ALA* 5.9 3.0 - - - +
775A VAL* 4.6 8.5 - - + +
778A GLN* 3.3 30.5 + - - +
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Residues in contact with THR 722 (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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677A LEU* 3.4 27.2 - - + +
718A ARG* 2.8 21.5 + - - +
719A LEU 3.7 4.9 - - - -
721A LYS* 1.3 75.4 - - - +
723A GLY* 1.3 59.2 + - - +
724A ILE 3.3 0.2 - - - -
725A GLU* 3.8 5.6 - - - +
726A HIS* 3.1 45.7 + - + +
727A GLY 4.0 0.3 + - - -
728A ALA 4.9 0.7 + - - -
729A MET* 4.1 10.3 + - + +
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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 LEU 3.1 10.6 + - - -
720A LEU* 3.1 4.9 + - - -
722A THR* 1.3 74.0 - - - +
724A ILE* 1.3 60.6 + - - +
727A GLY* 3.0 29.3 + - - -
729A MET* 3.5 32.1 - - - -
734A VAL* 5.4 2.9 - - - -
782A ASN* 5.5 5.8 + - - -
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Residues in contact with ILE 724 (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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720A LEU 3.0 21.4 + - - +
721A LYS* 3.8 10.1 - - + +
723A GLY* 1.3 76.8 - - - +
725A GLU* 1.3 73.6 + - - +
727A GLY* 3.7 4.3 + - - -
775A VAL* 4.1 26.5 - - + +
778A GLN* 3.6 57.9 - - + +
779A CYS* 4.5 11.2 - - - -
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Residues in contact with GLU 725 (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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721A LYS* 3.1 34.9 + - - +
722A THR* 4.0 5.2 - - - +
723A GLY 3.5 0.2 - - - -
724A ILE* 1.3 86.5 - - - +
726A HIS* 1.3 84.8 + - + +
727A GLY 3.6 0.2 + - - -
778A GLN* 5.9 0.3 + - - -
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Residues in contact with HIS 726 (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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722A THR* 3.1 29.8 + - + +
725A GLU* 1.3 97.7 + - + +
727A GLY* 1.3 55.6 + - - +
728A ALA* 3.2 19.5 + - + +
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Residues in contact with GLY 727 (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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723A GLY 3.0 21.0 + - - -
724A ILE 4.3 3.6 - - - -
725A GLU 3.3 3.8 + - - -
726A HIS* 1.3 75.3 - - - +
728A ALA* 1.3 56.1 - - - +
729A MET 3.7 2.2 + - - +
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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