Contacts of the helix formed by residues 713 - 728 (chain A) in PDB entry 3OSE
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 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A SER 3.8 1.2 + - - -
712A MET* 1.3 75.4 - - - +
714A PRO* 1.3 75.7 - - - +
715A ASN* 2.8 42.3 + - - +
716A ASP* 3.0 25.6 + - - +
717A MET* 2.9 18.9 + - - +
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Residues in contact with PRO 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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697A PRO* 3.6 25.4 - - + -
712A MET 3.4 3.5 - - - +
713A ASP* 1.3 91.9 - - - +
715A ASN* 1.3 57.2 + - - +
717A MET* 3.2 14.6 + - - +
718A MET* 3.0 31.2 + - - +
738A PHE* 3.5 22.2 - - + -
759A VAL* 3.8 7.4 - - + +
761A LYS* 4.1 14.6 - - - +
768A ASN* 3.9 17.3 - - - +
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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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713A ASP* 2.8 19.3 + - - +
714A PRO* 1.3 71.5 - - - +
716A ASP* 1.3 68.6 + - - +
718A MET* 3.3 7.8 + - - +
719A ARG* 3.1 21.5 + - - +
722A ARG* 4.8 1.7 + - - -
737A ARG* 3.2 32.4 + - - +
738A PHE* 3.6 24.5 - - - -
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Residues in contact with ASP 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 MET* 3.5 22.6 - - + +
713A ASP* 3.0 27.4 + - - +
715A ASN* 1.3 75.5 - - - +
717A MET* 1.3 66.1 + - - +
719A ARG* 3.3 10.2 + - - +
720A GLU* 3.0 22.7 + - - +
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Residues in contact with MET 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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708A THR 5.5 0.2 - - - +
710A SER* 4.0 17.7 - - - +
712A MET* 3.5 39.3 - - + +
713A ASP 2.9 13.3 + - - +
714A PRO* 3.2 15.7 + - - +
716A ASP* 1.3 77.0 - - - +
718A MET* 1.3 57.1 + - - +
720A GLU* 3.2 3.1 + - - +
721A ILE* 2.9 35.0 + - + +
759A VAL* 3.9 13.2 - - + -
768A ASN* 3.5 22.9 - - + +
769A GLY 3.8 15.5 - - - +
770A VAL* 3.7 29.2 - - + -
795A LEU* 4.1 11.8 - - + +
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Residues in contact with MET 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 PRO 3.0 17.9 + - - +
715A ASN* 3.6 10.5 - - - +
717A MET* 1.3 75.0 - - - +
719A ARG* 1.3 63.0 + - - +
721A ILE* 3.3 8.6 + - - +
722A ARG* 3.0 48.4 + - - +
734A GLN* 3.7 16.6 - - - +
737A ARG 3.4 20.6 - - - +
738A PHE* 3.6 36.3 - - + +
740A LEU* 3.8 26.0 - - + -
757A MET 5.8 0.7 - - - +
759A VAL* 3.5 23.8 - - + -
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Residues in contact with ARG 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 ASN 3.1 12.7 + - - +
716A ASP* 3.5 13.7 - - - +
717A MET 3.2 0.2 - - - -
718A MET* 1.3 77.7 - - - +
720A GLU* 1.3 61.7 + - - +
722A ARG* 3.5 16.5 + - - +
723A LYS* 3.1 24.5 + - + +
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Residues in contact with GLU 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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712A MET* 4.9 3.6 - - + -
716A ASP 3.0 12.1 + - - +
717A MET 3.6 7.2 - - - +
719A ARG* 1.3 72.5 - - - +
721A ILE* 1.3 67.5 + - - +
723A LYS* 3.2 22.5 + - - +
724A VAL* 3.0 39.4 + - - +
793A LEU* 4.3 4.5 - - + -
794A LYS* 2.9 54.9 + - - +
795A LEU* 3.7 18.8 - - + -
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Residues in contact with ILE 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 MET* 2.9 18.8 + - + +
718A MET* 3.7 10.5 - - - +
720A GLU* 1.3 76.5 - - - +
722A ARG* 1.3 58.3 + - - +
724A VAL* 3.2 3.1 + - - +
725A LEU* 2.9 48.7 + - + +
740A LEU* 3.7 14.1 - - + -
757A MET* 3.7 22.9 - - + -
758A GLU 5.8 0.4 - - - -
759A VAL* 3.5 32.5 - - + -
770A VAL* 4.0 23.1 - - + -
789A ILE* 5.6 0.4 - - + +
793A LEU* 3.8 23.8 - - + -
795A LEU* 5.1 2.5 - - + -
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Residues in contact with ARG 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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715A ASN 4.8 1.8 + - - -
718A MET* 3.0 36.2 + - - +
719A ARG* 3.8 27.1 - - - +
721A ILE* 1.3 74.6 - - - +
723A LYS* 1.3 57.5 + - - +
725A LEU* 3.8 2.4 - - - +
726A ASP* 2.9 38.3 + - - +
732A TYR* 3.4 44.2 - - + +
734A GLN* 3.0 33.8 + - - +
737A ARG 4.8 1.0 + - - -
740A LEU* 4.2 11.2 - - + -
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Residues in contact with LYS 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 ARG* 3.1 16.6 + - + +
720A GLU* 3.5 26.7 + - - +
721A ILE 3.2 0.2 - - - -
722A ARG* 1.3 77.3 - - - +
724A VAL* 1.3 60.4 + - + +
726A ASP* 3.4 9.6 + - - +
727A ALA* 3.0 28.5 + - + +
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Residues in contact with VAL 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 GLU* 3.0 37.8 + - - +
721A ILE 3.9 2.7 - - - +
723A LYS* 1.3 75.3 - - + +
725A LEU* 1.3 66.2 + - - +
727A ALA* 3.3 5.7 + - - +
728A ASN* 2.9 43.5 + - - +
789A ILE* 3.9 25.8 - - + +
792A GLU* 3.8 32.8 - - + +
793A LEU* 3.9 10.8 - - + -
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Residues in contact with LEU 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 ILE* 2.9 42.5 + - + +
722A ARG 3.8 2.9 - - - +
724A VAL* 1.3 76.5 - - - +
726A ASP* 1.3 62.6 + - - +
728A ASN 3.1 7.4 + - - -
730A CYS* 2.9 49.9 + - + +
732A TYR* 3.6 29.4 - - + -
740A LEU* 3.7 13.0 - - + -
742A CYS* 3.9 13.7 - - - -
755A TRP* 3.9 21.1 - - + -
757A MET* 4.1 9.6 - - - -
789A ILE* 3.9 13.0 - - + -
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Residues in contact with ASP 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 ARG* 2.9 23.3 + - - +
723A LYS* 3.5 8.7 - - - +
725A LEU* 1.3 74.9 - - - +
727A ALA* 1.3 61.0 + - - +
729A ASN* 3.1 14.6 + - - +
730A CYS 4.6 4.4 - - - +
732A TYR* 2.7 31.4 + - - -
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Residues in contact with ALA 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 LYS* 3.0 17.9 + - + +
724A VAL* 3.6 8.7 - - - +
725A LEU 3.3 0.4 - - - -
726A ASP* 1.3 75.5 - - - +
728A ASN* 1.3 64.1 + - - +
729A ASN 3.4 0.8 + - - -
792A GLU* 5.3 2.9 - - - +
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Residues in contact with ASN 728 (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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724A VAL* 2.9 25.0 + - - +
725A LEU 3.1 3.9 + - - +
727A ALA* 1.3 82.2 - - - +
729A ASN* 1.3 67.0 + - - +
730A CYS* 3.2 4.5 - - - -
744A HIS* 3.2 20.1 + - - -
785A ILE* 4.5 5.5 - - + +
788A LYS* 2.8 37.9 + - - +
789A ILE* 3.6 25.9 - - + +
792A GLU* 2.9 24.2 + - - -
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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