Contacts of the helix formed by residues 790 - 806 (chain A) in PDB entry 1Q1O
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 ASN 790 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A VAL 4.0 5.5 - - - +
789A TRP* 1.3 85.5 + - - +
791A PHE* 1.3 62.6 + - - +
792A ASP* 3.3 22.4 - - - +
793A ASP* 3.7 17.0 - - - +
794A LEU* 2.9 29.3 + - - +
834A TRP* 3.9 14.1 + - - -
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Residues in contact with PHE 791 (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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790A ASN* 1.3 76.2 - - - +
792A ASP* 1.3 68.7 + - + +
794A LEU* 3.4 7.3 + - + +
795A ILE* 3.2 36.3 + - + +
814A THR 4.6 12.3 - - - -
816A ILE* 5.8 0.4 - - + -
828A LEU* 3.5 37.9 - - + -
829A GLY* 3.5 33.2 - - - -
830A SER 3.8 11.4 - - - +
831A ASP* 3.7 36.5 - - + +
834A TRP* 3.9 14.0 - - + -
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Residues in contact with ASP 792 (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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790A ASN* 3.5 16.6 - - - +
791A PHE* 1.3 82.8 + - + +
793A ASP* 1.3 89.6 + - - +
794A LEU 3.1 0.2 - - - -
795A ILE* 3.1 12.6 - - + +
796A MET* 3.0 29.8 + - + +
831A ASP* 5.5 1.7 - - - +
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Residues in contact with ASP 793 (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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789A TRP* 3.8 29.4 + - + -
790A ASN* 3.4 30.8 + - - +
791A PHE 3.4 0.2 - - - -
792A ASP* 1.3 95.8 + - - +
794A LEU* 1.3 61.1 + - - +
796A MET* 3.7 22.5 - - - +
797A ALA* 3.3 21.5 + - - +
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Residues in contact with LEU 794 (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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764A PHE* 3.8 18.4 - - + -
785A VAL* 4.0 12.8 - - + -
789A TRP* 4.2 11.0 - - + -
790A ASN 2.9 19.1 + - - +
791A PHE* 3.5 11.0 - - + +
792A ASP 3.1 0.2 - - - -
793A ASP* 1.3 74.2 - - - +
795A ILE* 1.3 69.4 + - + +
796A MET 3.1 2.6 + - - -
797A ALA* 3.2 12.8 + - - +
798A ILE* 3.2 23.2 + - + +
816A ILE* 3.6 31.0 - - + -
828A LEU* 4.3 11.7 - - + -
834A TRP* 3.5 42.2 - - + -
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Residues in contact with ILE 795 (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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791A PHE* 3.2 25.1 + - + +
792A ASP* 3.1 21.1 - - + +
794A LEU* 1.3 81.5 - - + +
796A MET* 1.3 62.9 + - + +
798A ILE* 3.6 14.1 + - + +
799A ASN* 3.2 23.1 + - - +
813A ILE* 3.3 30.5 - - + +
814A THR* 3.6 30.7 - - + +
815A LYS 4.0 2.2 - - - +
816A ILE* 4.2 25.1 - - + -
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Residues in contact with MET 796 (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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792A ASP* 3.0 20.1 + - + +
793A ASP* 3.7 28.7 - - - +
794A LEU 3.1 0.2 - - - -
795A ILE* 1.3 78.2 - - + +
797A ALA* 1.3 64.5 + - - +
799A ASN* 3.3 15.8 + - + +
800A SER* 3.2 21.7 + - - +
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Residues in contact with ALA 797 (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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783A LEU* 3.7 16.7 - - + +
789A TRP* 3.4 39.7 - - + -
793A ASP 3.3 2.9 + - - +
794A LEU 3.2 7.4 + - - +
796A MET* 1.3 78.6 - - - +
798A ILE* 1.3 62.2 + - - +
800A SER* 3.5 8.9 + - - -
801A LYS* 3.2 22.3 + - - +
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Residues in contact with ILE 798 (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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764A PHE* 5.2 6.5 - - + -
766A ILE* 3.8 37.5 - - + -
781A PHE* 5.8 0.7 - - + -
783A LEU* 4.8 14.1 - - + -
794A LEU* 3.2 22.9 - - + +
795A ILE* 3.7 22.9 - - + +
796A MET 3.2 0.4 - - - -
797A ALA* 1.3 74.7 - - - +
799A ASN* 1.3 66.2 + - - +
801A LYS* 3.0 21.5 + - + +
802A ILE* 3.2 20.8 - - + +
813A ILE* 6.0 2.2 - - + -
816A ILE* 3.8 31.4 - - + -
851A ILE* 6.0 0.2 - - + -
853A LEU* 4.6 9.0 - - + -
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Residues in contact with ASN 799 (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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795A ILE* 3.2 16.1 + - - +
796A MET* 3.3 14.3 + - + +
798A ILE* 1.3 79.2 - - - +
800A SER* 1.3 62.6 + - - +
802A ILE* 3.0 23.7 + - - +
803A SER* 3.3 11.7 + - - -
812A PRO* 3.9 26.9 - - - +
813A ILE* 3.4 31.4 + - - +
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Residues in contact with SER 800 (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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796A MET* 3.2 15.8 + - - +
797A ALA* 3.8 9.3 - - - -
798A ILE 3.3 0.4 - - - -
799A ASN* 1.3 77.3 - - - +
801A LYS* 1.3 51.9 + - - +
803A SER* 3.2 7.6 + - - +
804A ASN* 2.8 42.3 + - - +
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Residues in contact with LYS 801 (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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766A ILE* 4.7 4.7 - - + -
781A PHE* 3.5 43.4 - - + -
782A THR 4.2 10.6 + - - +
783A LEU* 4.0 26.4 - - + +
797A ALA 3.2 12.7 + - - +
798A ILE* 3.0 18.0 + - - +
800A SER* 1.3 78.2 - - - +
802A ILE* 1.3 59.6 + - - +
804A ASN* 3.4 26.6 + - + +
805A THR* 3.4 18.7 - - - +
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Residues in contact with ILE 802 (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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766A ILE* 6.4 0.4 - - + -
768A TYR* 3.7 40.4 - - + +
781A PHE* 4.4 15.5 - - + -
798A ILE* 3.2 25.4 - - + +
799A ASN* 3.0 14.7 + - - +
801A LYS* 1.3 78.0 - - - +
803A SER* 1.3 58.4 + - - +
805A THR* 3.8 2.2 - - + +
806A HIS* 3.1 38.6 + - + +
808A ASN 5.7 0.2 - - - -
810A ILE* 3.9 23.1 - - + -
813A ILE* 3.8 28.3 - - + -
853A LEU* 5.3 2.5 - - + -
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Residues in contact with SER 803 (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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799A ASN 3.3 7.9 + - - -
800A SER* 3.2 9.7 + - - -
802A ILE* 1.3 76.5 - - - +
804A ASN* 1.3 63.0 + - - +
805A THR 3.3 1.1 - - - -
806A HIS 3.3 19.0 + - - +
807A ASN* 5.1 1.4 + - - -
808A ASN 4.7 2.2 + - - -
809A ASN* 4.1 18.9 + - - -
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Residues in contact with ASN 804 (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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800A SER* 2.8 22.5 + - - +
801A LYS* 3.5 27.5 - - + +
802A ILE 3.3 0.4 - - - -
803A SER* 1.3 80.1 - - - +
805A THR* 1.3 58.8 + - + +
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Residues in contact with THR 805 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779A GLU* 4.3 15.2 + - - +
781A PHE* 3.7 28.5 - - + -
801A LYS 3.4 17.3 - - - +
802A ILE 3.8 4.9 - - - +
803A SER 4.5 0.2 - - - -
804A ASN* 1.3 80.0 - - + +
806A HIS* 1.3 73.6 + - + +
807A ASN* 3.5 12.5 + - - +
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Residues in contact with HIS 806 (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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768A TYR* 4.0 34.8 + + - -
770A ASN* 4.9 10.5 + - - -
779A GLU* 5.0 10.9 + - - -
802A ILE* 3.1 19.5 + - + +
803A SER* 3.3 20.0 + - - +
805A THR* 1.3 85.4 + - + +
807A ASN* 1.3 68.7 + - - +
808A ASN* 3.2 22.8 + - + +
810A ILE* 5.2 7.0 - - + -
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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