Contacts of the helix formed by residues 702 - 722 (chain A) in PDB entry 5WRZ
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 SER 702 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A LYS 3.4 5.8 + - - -
701A LEU* 1.3 79.5 - - - +
703A LYS* 1.3 64.8 + - - +
704A ARG* 3.7 21.2 + - - +
705A GLN* 3.0 32.3 + - - +
706A ILE* 3.2 29.2 + - - +
772A GLU* 4.1 8.7 - - - -
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Residues in contact with LYS 703 (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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702A SER* 1.3 74.9 - - - +
704A ARG* 1.3 58.4 + - - +
705A GLN 3.3 0.2 + - - -
706A ILE* 3.3 5.8 + - - +
707A GLN* 2.8 47.8 + - - +
769A LEU* 4.3 20.5 - - + +
772A GLU* 3.7 29.3 + - - +
773A VAL* 5.9 4.9 - - + -
878A ARG* 6.1 2.5 - - - +
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A SER* 3.7 20.2 + - - +
703A LYS* 1.3 78.2 - - - +
705A GLN* 1.3 67.7 + - + +
707A GLN* 3.7 12.4 - - - +
708A ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A MET* 3.6 31.2 - - + +
700A LYS 4.4 6.7 + - - -
702A SER* 3.0 28.5 + - - +
703A LYS 3.3 0.8 - - - -
704A ARG* 1.3 78.1 - - + +
706A ILE* 1.3 62.4 + - + +
708A ALA* 3.3 7.5 + - - +
709A ALA* 2.9 26.7 + - - +
739A LEU* 4.7 19.5 + - + +
740A ILE* 4.3 6.7 - - + +
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Residues in contact with ILE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A LEU* 4.4 18.8 - - + -
702A SER 3.2 20.0 + - - +
703A LYS 3.8 3.1 - - - +
705A GLN* 1.3 74.2 - - + +
707A GLN* 1.3 59.0 + - + +
709A ALA* 2.9 8.8 + - - +
710A TYR* 2.8 44.0 + - + -
740A ILE* 4.8 5.2 - - + -
765A LEU* 3.8 28.3 - - + +
768A LEU* 3.7 43.5 - - + +
769A LEU* 3.7 20.4 - - + +
772A GLU* 4.5 3.8 - - + -
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Residues in contact with GLN 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LYS* 2.8 40.9 + - - +
704A ARG* 3.7 9.7 - - - +
706A ILE* 1.3 76.1 - - + +
708A ALA* 1.3 62.2 + - - +
710A TYR* 3.3 12.1 + - + +
711A SER* 3.1 23.8 + - - -
769A LEU* 6.0 4.3 - - + +
881A PRO* 5.1 11.2 - - + -
883A GLU* 3.1 37.1 - - - +
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Residues in contact with ALA 708 (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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704A ARG 2.9 18.7 + - - +
705A GLN* 3.7 6.3 - - - +
706A ILE 3.3 0.2 - - - -
707A GLN* 1.3 75.7 - - - +
709A ALA* 1.3 62.3 + - - +
711A SER* 3.2 9.5 + - - +
712A ILE* 3.1 25.3 + - - +
739A LEU* 3.7 21.5 - - + -
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Residues in contact with ALA 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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705A GLN 2.9 13.2 + - - +
706A ILE 2.9 7.8 + - - +
708A ALA* 1.3 74.3 - - - +
710A TYR* 1.3 65.3 + - - +
712A ILE* 3.2 3.9 + - - +
713A LEU* 3.0 23.4 + - - +
736A PHE* 3.8 11.7 - - + -
739A LEU* 3.9 12.8 - - + +
740A ILE* 3.6 33.2 - - + -
765A LEU* 3.8 13.9 - - + -
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Residues in contact with TYR 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ILE* 2.8 38.2 + - + -
707A GLN* 3.3 11.2 + - + +
709A ALA* 1.3 76.3 - - - +
711A SER* 1.3 56.6 + - - +
713A LEU* 3.1 7.2 + - + +
714A SER* 2.9 23.4 + - - -
762A ALA* 3.9 5.8 - - + -
765A LEU* 3.5 27.9 + - + +
766A ASP* 2.4 43.0 + - - -
769A LEU* 4.3 9.2 - - + +
880A ALA* 4.7 0.2 - - - +
881A PRO* 3.6 35.2 - - + +
883A GLU* 3.3 9.7 - - + +
884A ALA* 3.4 36.6 - - + +
885A PRO* 4.0 8.0 - - + +
889A TYR* 3.8 4.0 - - - -
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Residues in contact with SER 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLN 3.1 9.0 + - - -
708A ALA* 3.2 11.9 + - - -
710A TYR* 1.3 74.5 - - - +
712A ILE* 1.3 67.1 + - - +
714A SER* 3.1 8.4 + - - -
715A GLU* 3.0 19.1 + - - +
883A GLU* 3.5 30.0 + - - +
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Residues in contact with ILE 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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708A ALA 3.1 4.7 + - - +
709A ALA 3.7 6.3 - - - +
711A SER* 1.3 79.0 - - - +
713A LEU* 1.3 58.0 + - - +
715A GLU* 3.1 23.5 + - + +
716A VAL* 2.8 26.1 + - + +
732A LEU* 3.5 15.7 - - - +
735A ARG* 3.9 17.5 - - + +
736A PHE* 3.5 33.9 - - + +
739A LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 713 (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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709A ALA 3.0 9.6 + - - +
710A TYR 3.3 9.9 - - - +
712A ILE* 1.3 78.2 - - - +
714A SER* 1.3 55.7 + - - +
716A VAL* 3.4 9.6 + - + +
717A GLN* 2.9 26.7 + - - +
736A PHE* 3.8 21.7 - - + -
752A LEU* 4.6 8.7 - - + -
757A SER 5.0 0.2 - - - +
758A VAL* 4.1 19.9 - - + +
761A LYS* 3.7 20.6 - - + -
762A ALA* 3.4 42.4 - - + +
765A LEU* 3.9 16.2 - - + -
885A PRO* 4.3 13.1 - - + +
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Residues in contact with SER 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A TYR 2.9 7.1 + - - -
711A SER* 3.2 13.2 - - - -
713A LEU* 1.3 73.3 - - - +
715A GLU* 1.3 57.6 + - - +
717A GLN* 3.3 17.7 + - - +
718A GLN* 3.0 27.5 + - - +
883A GLU 2.6 28.5 + - - -
884A ALA 3.7 1.0 + - - -
885A PRO* 3.5 17.3 - - - +
981B ASP* 4.4 11.7 + - - -
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Residues in contact with GLU 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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711A SER 3.0 11.7 + - - +
712A ILE* 3.1 27.1 + - + +
714A SER* 1.3 71.9 - - - +
716A VAL* 1.3 67.3 + - - +
718A GLN* 3.1 11.8 + - + +
719A ALA 3.0 19.4 + - - -
732A LEU* 3.6 38.3 - - + +
735A ARG* 3.8 12.1 + - - -
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Residues in contact with VAL 716 (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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712A ILE* 2.8 21.3 + - + +
713A LEU* 3.6 12.8 - - + +
715A GLU* 1.3 76.9 - - - +
717A GLN* 1.3 59.8 + - - +
719A ALA* 3.5 2.0 + - - +
720A VAL* 3.2 28.5 + - + +
729A ILE* 5.2 4.0 - - + -
732A LEU* 3.7 41.3 - - + +
733A SER* 4.1 5.6 - - - +
736A PHE* 5.3 0.7 - - + -
752A LEU* 3.7 35.9 - - + +
754A ASN 5.7 0.4 - - - +
758A VAL* 4.0 17.4 - - + +
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Residues in contact with GLN 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 LEU 2.9 15.3 + - - +
714A SER* 3.4 16.8 + - - +
715A GLU 3.2 0.2 - - - -
716A VAL* 1.3 76.1 - - - +
718A GLN* 1.3 64.7 + - - +
720A VAL* 3.4 4.7 + - - +
721A SER* 3.1 31.5 + - - +
758A VAL* 4.3 15.5 - - + +
885A PRO* 3.0 32.8 - - + +
886A VAL* 4.3 2.6 - - - +
887A THR* 2.9 42.9 + - + +
934B HIS* 3.3 27.5 + - + +
981B ASP* 5.6 5.5 + - - +
982B THR 5.9 0.2 - - - -
983B SER* 5.1 1.3 - - - +
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Residues in contact with GLN 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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714A SER 3.0 13.7 + - - +
715A GLU* 3.2 16.6 - - + +
717A GLN* 1.3 79.9 - - - +
719A ALA* 1.3 63.4 + - - +
721A SER* 3.5 6.0 + - - -
722A GLN* 3.2 45.4 + - - +
953B LYS* 2.9 30.8 + - - +
981B ASP* 5.8 0.5 - - - -
982B THR 2.6 30.8 + - - +
983B SER* 3.9 13.4 - - - +
985B LEU* 5.0 5.1 - - + +
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Residues in contact with ALA 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 GLU 3.0 6.8 + - - +
716A VAL 3.9 2.0 - - - +
717A GLN 3.3 0.4 - - - -
718A GLN* 1.3 78.6 - - - +
720A VAL* 1.3 59.4 + - - +
722A GLN* 3.4 9.1 + - - +
723A GLY 3.0 31.8 + - - +
728A GLN* 5.3 8.5 - - + +
729A ILE* 3.4 25.1 - - + +
732A LEU* 3.5 25.8 - - + -
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Residues in contact with VAL 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 VAL* 3.2 20.8 + - + +
717A GLN* 3.4 4.0 + - - +
719A ALA* 1.3 75.2 - - - +
721A SER* 1.3 67.5 + - - +
723A GLY* 3.3 11.9 + - - +
729A ILE* 3.7 17.3 - - + -
753A ASN* 3.2 35.2 - - - +
754A ASN* 4.1 14.8 - - - +
755A ALA* 4.3 10.3 - - + +
758A VAL* 5.8 0.7 - - + -
756B ASP* 5.5 9.0 - - - +
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Residues in contact with SER 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN* 3.1 18.7 + - - +
718A GLN* 3.6 11.4 - - - -
720A VAL* 1.3 78.3 - - - +
722A GLN* 1.3 59.0 + - - +
723A GLY 3.6 0.3 + - - -
887A THR* 5.5 3.3 + - - +
890B MET* 6.2 1.1 - - - -
983B SER* 3.8 34.8 + - - -
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Residues in contact with GLN 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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718A GLN* 3.2 41.2 + - - +
719A ALA* 3.7 8.1 - - - +
720A VAL 3.2 0.2 - - - -
721A SER* 1.3 78.4 - - - +
723A GLY* 1.3 59.9 + - - +
983B SER 4.5 8.4 - - - +
985B LEU* 4.0 33.8 - - + +
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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
------------------------------------------------------------
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