Contacts of the helix formed by residues 802 - 815 (chain A) in PDB entry 3SPY
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 PRO 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791A TYR* 3.6 31.2 - - + -
800A LYS 3.2 9.2 - - - +
801A CYS* 1.3 89.3 - - - +
803A PHE* 1.3 61.0 + - - +
804A HIS* 3.3 25.1 - - + +
805A ILE* 3.2 13.3 + - + -
806A ARG* 2.9 26.5 + - - +
110P G 4.0 24.5 - - - +
12T G 6.2 0.2 - - - -
13T T 4.9 3.8 - - - -
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Residues in contact with PHE 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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801A CYS 3.7 2.3 + - - -
802A PRO* 1.3 72.4 - - - +
804A HIS* 1.3 60.4 + - + +
806A ARG* 3.3 5.4 - - - +
807A GLY 3.1 20.1 + - - -
832A VAL* 3.8 19.3 - - + -
834A PRO* 4.7 10.3 - - + -
844A LYS* 3.9 45.5 - - + -
845A CYS* 3.3 40.3 - - + -
874A LYS* 3.4 27.6 - - - -
12T G 3.7 43.1 + - - +
13T T 4.1 6.1 - - - -
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Residues in contact with HIS 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A SER* 3.5 15.2 + - - -
784A SER 3.0 21.2 + - - -
785A ALA* 4.1 4.9 - - + -
802A PRO* 3.6 24.7 - - + +
803A PHE* 1.3 79.0 + - + +
805A ILE* 1.3 83.1 + - + +
807A GLY* 3.2 2.6 + - - +
808A ILE* 3.2 25.5 + - - +
830A VAL* 4.7 3.6 - - + -
832A VAL* 3.9 30.5 - - + -
847A ALA* 3.9 3.5 - - - +
110P G 3.7 4.3 - - - -
111P C 2.9 42.4 + - - -
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Residues in contact with ILE 805 (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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785A ALA* 4.2 8.7 - - + -
786A ASN 3.4 25.8 - - - +
788A ILE* 4.1 37.9 - - + +
791A TYR* 4.0 17.0 - - + -
801A CYS* 4.0 14.1 - - - -
802A PRO* 3.2 30.8 + - + +
804A HIS* 1.3 94.5 - - + +
806A ARG* 1.3 66.1 + - - +
808A ILE* 3.1 6.4 + - + +
809A LEU* 3.1 25.3 + - + +
111P C 5.0 0.2 - - - +
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Residues in contact with ARG 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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797A PRO* 3.5 29.3 - - + +
798A GLY 5.6 0.6 + - - -
801A CYS* 3.5 22.9 + - - +
802A PRO 2.9 13.1 + - - +
803A PHE* 3.3 11.6 - - - +
805A ILE* 1.3 76.1 - - - +
807A GLY* 1.3 56.7 + - - +
809A LEU* 3.3 8.5 + - - +
810A THR* 2.9 30.8 + - - -
843A ASP* 3.1 42.8 + - - +
844A LYS* 3.7 37.0 - - - +
845A CYS* 3.9 7.6 - - - -
13T T 4.4 9.3 + - - -
14T C 5.4 7.1 + - - -
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Residues in contact with GLY 807 (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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803A PHE 3.1 11.2 + - - -
804A HIS* 3.2 5.8 + - - -
805A ILE 3.2 0.6 - - - -
806A ARG* 1.3 76.2 - - - +
808A ILE* 1.3 56.6 + - - +
810A THR 3.5 0.7 + - - -
811A TYR* 3.0 20.6 + - - +
832A VAL* 5.4 0.4 - - - -
845A CYS* 3.4 19.0 - - - -
846A ILE* 3.4 8.4 - - - -
847A ALA* 2.9 30.3 + - - -
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Residues in contact with ILE 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A ALA* 3.5 31.9 - - + -
788A ILE* 3.8 34.3 - - + -
804A HIS 3.2 14.8 + - - +
805A ILE* 3.1 14.0 + - + +
807A GLY* 1.3 72.9 - - - +
809A LEU* 1.3 56.0 + - - +
811A TYR* 3.2 6.9 + - - +
812A ASN* 2.7 53.4 + - - +
824A VAL* 3.8 17.9 - - + -
830A VAL* 3.9 13.9 - - + -
847A ALA* 3.8 14.1 - - + -
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Residues in contact with LEU 809 (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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788A ILE* 4.4 16.6 - - + +
791A TYR 3.7 13.7 - - - +
792A ASP* 3.5 34.3 - - + +
795A GLY* 3.9 13.3 - - - +
796A PHE 3.7 3.4 - - - +
797A PRO* 3.6 37.5 - - + -
801A CYS* 4.3 8.5 - - - -
805A ILE* 3.1 21.0 + - + +
806A ARG* 3.7 6.5 - - - +
808A ILE* 1.3 72.3 - - - +
810A THR* 1.3 66.3 + - - +
812A ASN* 3.6 11.1 - - + +
813A ARG* 3.0 34.0 + - - +
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Residues in contact with THR 810 (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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806A ARG 2.9 15.8 + - - -
807A GLY 3.5 4.7 - - - -
809A LEU* 1.3 77.3 - - - +
811A TYR* 1.3 62.2 + - - +
813A ARG* 3.4 15.1 + - - +
814A ALA* 3.1 21.0 + - - +
835A LEU* 4.7 0.7 - - + -
841A PHE* 3.6 41.0 - - + +
843A ASP* 3.4 21.5 + - + +
845A CYS 3.0 26.9 + - - +
846A ILE* 4.4 8.5 - - + -
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Residues in contact with TYR 811 (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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807A GLY 3.0 9.0 + - - +
808A ILE 3.2 6.7 + - - +
810A THR* 1.3 75.0 - - - +
812A ASN* 1.3 74.8 + - - +
814A ALA* 3.0 13.2 + - - +
815A ILE* 3.0 40.4 + - + +
822A PRO* 2.6 41.6 + - - +
823A GLN* 5.0 0.2 - - - -
824A VAL* 3.9 23.6 - - + -
846A ILE* 3.8 13.0 - - + +
847A ALA 3.0 24.7 - - - +
848A TRP* 4.0 13.9 - - + +
849A PRO* 4.3 7.3 - - + +
854A ILE* 4.3 2.5 - - + -
855A THR* 4.0 17.4 + - + +
858A ILE* 3.8 22.2 - - + -
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Residues in contact with ASN 812 (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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788A ILE* 4.7 5.7 - - - +
792A ASP* 5.0 3.8 + - - -
795A GLY* 6.5 1.3 - - - -
808A ILE* 2.7 40.9 + - - +
809A LEU* 3.2 18.8 + - + +
811A TYR* 1.3 86.1 - - - +
813A ARG* 1.3 61.4 + - + +
815A ILE* 3.6 10.2 + - - +
816A LYS* 3.1 24.8 + - - +
823A GLN* 5.1 8.6 + - - +
824A VAL* 4.6 6.3 + - - +
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Residues in contact with ARG 813 (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 GLY* 3.0 34.3 + - - +
796A PHE* 3.5 45.8 - - - +
797A PRO* 4.4 4.8 - - - +
809A LEU* 3.0 26.6 + - - +
810A THR* 3.7 22.8 + - - +
812A ASN* 1.3 76.4 - - + +
814A ALA* 1.3 62.5 + - - +
816A LYS* 3.3 26.8 + - + +
841A PHE 3.2 26.6 + - - +
842A GLY 4.0 5.7 + - - -
843A ASP* 4.0 12.5 + - - +
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Residues in contact with ALA 814 (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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810A THR 3.1 13.2 + - - +
811A TYR* 3.0 12.4 + - - +
813A ARG* 1.3 76.4 - - - +
815A ILE* 1.3 60.8 + - - +
816A LYS 3.5 0.2 - - - -
841A PHE* 3.8 31.9 - - + -
857A LEU* 5.9 1.0 - - - +
858A ILE* 4.2 19.8 - - + +
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Residues in contact with ILE 815 (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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811A TYR* 3.0 57.1 + - + +
812A ASN* 3.8 10.8 - - - +
814A ALA* 1.3 79.1 - - - +
816A LYS* 1.3 67.0 + - - +
818A ASN* 3.0 28.7 + - + +
821A ALA* 3.8 18.4 - - + -
822A PRO 3.8 7.9 - - - +
823A GLN* 3.5 28.5 - - - +
855A THR* 4.0 17.0 - - + -
857A LEU* 4.4 7.0 - - + -
858A ILE* 4.5 6.7 - - + -
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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