Contacts of the helix formed by residues 846 - 860 (chain A) in PDB entry 1PD0
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 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A PHE* 6.4 1.8 - - - -
823A ASP* 3.0 36.7 + - - -
843A VAL* 3.3 29.2 + - - +
844A GLU 3.2 1.2 - - - -
845A ASN* 1.3 78.2 - - - +
847A GLU* 1.3 63.2 + - - +
848A PHE 3.7 1.6 + - - -
849A ASN* 3.1 22.0 + - - +
850A GLN* 3.2 11.6 + - - +
853A ARG* 5.4 0.2 + - - -
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Residues in contact with GLU 847 (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 LEU* 5.5 7.1 - - + +
845A ASN 3.8 3.0 + - - -
846A SER* 1.3 73.1 - - - +
848A PHE* 1.3 71.0 + - - +
850A GLN* 3.2 10.0 + - - +
851A ARG* 2.9 65.1 + - + +
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Residues in contact with PHE 848 (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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759A LEU 3.7 25.6 - - - -
760A HIS* 4.6 5.4 - - - -
762A MET* 4.2 12.1 - - + -
799A LEU* 4.1 6.7 - - + -
820A LEU* 3.6 29.2 - - + -
823A ASP* 3.5 36.3 - - + +
824A VAL* 3.6 17.7 - - + -
846A SER* 3.0 1.7 - - - +
847A GLU* 1.3 88.4 - - + +
849A ASN* 1.3 59.2 + - - +
851A ARG* 3.1 25.1 + - - +
852A VAL* 2.9 43.3 + - + +
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Residues in contact with ASN 849 (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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823A ASP 3.0 18.3 + - - +
824A VAL* 3.1 23.5 + - - +
840A ILE* 4.0 5.3 - - - +
841A PRO 2.7 22.4 + - - -
843A VAL* 3.2 23.1 + - + +
846A SER* 3.1 20.9 + - - +
848A PHE* 1.3 77.7 - - - +
850A GLN* 1.3 58.3 + - - +
852A VAL* 3.4 7.0 + - - +
853A ARG* 2.5 60.0 + - - +
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Residues in contact with GLN 850 (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 LEU* 5.9 2.9 - - + -
846A SER 3.2 8.9 + - - +
847A GLU* 3.4 11.9 - - - +
848A PHE 3.2 0.4 - - - -
849A ASN* 1.3 78.3 + - - +
851A ARG* 1.3 60.9 + - + +
853A ARG* 2.6 46.1 + - - +
854A ASN* 2.8 56.1 + - - +
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Residues in contact with ARG 851 (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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762A MET* 4.1 20.0 + - - +
763A ALA 2.7 31.1 + - - -
764A ASP* 3.3 22.3 + - - +
766A ALA 2.9 18.9 + - - -
767A GLY* 3.4 26.4 - - - +
768A LEU* 4.1 15.2 - - + +
847A GLU* 2.9 51.5 + - + +
848A PHE* 3.1 24.4 + - + +
850A GLN* 1.3 78.3 - - + +
852A VAL* 1.3 61.3 + - - +
854A ASN* 3.2 2.6 + - - +
855A ILE* 3.0 30.4 + - - +
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Residues in contact with VAL 852 (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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759A LEU* 4.2 25.1 - - + -
762A MET* 4.6 3.8 - - + -
799A LEU* 4.5 3.6 - - + -
810A LEU* 4.9 4.3 - - + -
824A VAL* 4.9 7.2 - - + -
840A ILE* 3.4 34.8 - - + -
848A PHE* 2.9 49.6 + - + +
849A ASN* 3.8 6.7 - - - +
851A ARG* 1.3 74.2 - - - +
853A ARG* 1.3 63.4 + - - +
855A ILE* 3.4 8.5 + - - +
856A ILE* 3.1 25.8 + - + +
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Residues in contact with ARG 853 (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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840A ILE* 4.1 26.9 - - + +
841A PRO 3.9 12.6 - - - -
842A VAL* 4.0 32.9 - - - +
843A VAL 5.2 2.0 + - - +
846A SER 5.4 0.4 + - - -
849A ASN* 2.5 35.2 + - - +
850A GLN* 2.6 49.3 + - - +
852A VAL* 1.3 78.1 - - - +
854A ASN* 1.3 61.4 + - - +
856A ILE* 3.4 6.8 + - - +
857A ASN* 2.8 42.2 + - - +
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Residues in contact with ASN 854 (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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767A GLY 2.6 29.5 + - - +
768A LEU* 4.6 6.1 - - - +
769A PRO* 5.1 4.7 - - - +
781A ILE* 3.6 26.1 - - + +
850A GLN* 2.8 55.6 + - - +
851A ARG* 3.2 2.8 + - - +
853A ARG* 1.3 73.1 - - - +
855A ILE* 1.3 58.2 + - - +
857A ASN* 3.1 9.8 + - - +
858A GLN* 2.8 29.8 + - - +
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Residues in contact with ILE 855 (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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757A TYR* 5.2 2.0 - - + -
759A LEU* 4.0 6.5 - - + -
762A MET* 3.5 40.8 - - + -
767A GLY* 3.8 14.8 - - - +
781A ILE* 4.3 1.5 - - - +
782A VAL 4.4 5.4 - - - +
783A LEU* 3.7 17.5 - - + -
784A PRO* 3.8 21.1 - - + -
801A LEU* 3.6 24.9 - - + -
851A ARG 3.0 17.2 + - - +
852A VAL* 3.7 7.4 - - - +
853A ARG 3.4 0.2 - - - -
854A ASN* 1.3 73.9 - - - +
856A ILE* 1.3 64.9 + - - +
858A GLN* 3.1 8.1 + - - +
859A LEU* 2.9 26.8 + - + +
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Residues in contact with ILE 856 (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 LEU* 4.3 23.3 - - + -
808A LEU* 4.1 10.9 - - + +
810A LEU* 5.4 0.2 - - + -
839A GLU* 5.2 0.9 - - - +
840A ILE* 3.2 37.9 - - + +
852A VAL* 3.1 19.1 + - + +
853A ARG* 3.7 6.3 - - - +
855A ILE* 1.3 77.0 - - - +
857A ASN* 1.3 67.7 + - - +
859A LEU* 3.3 9.9 + - - +
860A ARG* 3.2 50.9 + - - +
871A LEU* 4.0 20.9 - - + -
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Residues in contact with ASN 857 (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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781A ILE* 5.7 3.4 - - + -
853A ARG* 2.8 38.4 + - - +
854A ASN* 3.7 9.6 + - - +
856A ILE* 1.3 82.8 - - - +
858A GLN* 1.3 62.3 + - - +
860A ARG* 3.1 28.9 + - - +
861A ASN* 3.5 10.2 + - - +
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Residues in contact with GLN 858 (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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779A GLY 4.2 0.9 - - - +
780A THR* 3.5 16.5 - - - +
781A ILE* 2.8 58.4 + - + +
783A LEU* 4.0 19.1 - - + -
854A ASN 2.8 13.7 + - - +
855A ILE 3.4 9.0 - - - +
857A ASN* 1.3 73.6 - - - +
859A LEU* 1.3 62.4 + - - +
860A ARG 2.9 4.7 + - - -
861A ASN* 3.0 42.1 + - - +
862A HIS* 5.0 1.0 - - - -
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Residues in contact with LEU 859 (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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750A LYS* 5.3 0.2 + - - -
757A TYR* 3.5 37.7 - - + +
783A LEU* 3.9 19.5 - - + -
801A LEU* 3.5 32.8 - - + -
803A ASP* 3.8 17.5 - - + +
808A LEU* 4.1 23.6 - - + -
855A ILE* 2.9 20.1 + - + +
856A ILE* 3.8 5.8 - - - +
858A GLN* 1.3 75.8 - - - +
860A ARG* 1.3 53.8 + - - +
861A ASN 3.5 0.2 - - - -
862A HIS* 2.7 30.3 + - - -
869A GLN* 3.4 10.6 + - - -
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Residues in contact with ARG 860 (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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546A LYS* 4.5 7.6 + - - -
808A LEU* 4.3 7.3 - - + +
839A GLU* 2.7 43.4 + - - -
856A ILE* 3.2 33.4 + - - +
857A ASN* 3.4 21.1 + - - +
858A GLN 2.9 1.8 - - - -
859A LEU* 1.3 79.9 - - - +
861A ASN* 1.3 59.6 + - - +
862A HIS* 3.8 9.8 + - - -
867A THR 4.4 8.3 - - - +
868A TYR* 3.2 38.5 + - + -
869A GLN* 3.0 41.3 + - + +
870A SER* 3.9 1.4 - - - +
871A LEU* 3.6 15.4 - - - +
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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