Contacts of the helix formed by residues 802 - 821 (chain A) in PDB entry 6AH0
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 THR 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799A PRO* 4.0 8.8 + - - +
800A TYR 3.5 3.4 + - - -
801A ILE* 1.3 84.2 - - - +
803A ALA* 1.3 65.3 + - - +
804A GLU 3.4 2.2 - - - -
805A GLU 4.0 1.1 - - - +
806A ALA* 3.2 13.0 + - - -
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Residues in contact with ALA 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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802A THR* 1.3 70.9 - - - +
804A GLU* 1.3 65.8 + - - +
806A ALA* 3.3 1.4 + - - +
807A VAL* 3.1 21.1 + - - -
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Residues in contact with GLU 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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802A THR 3.4 0.2 - - - -
803A ALA* 1.3 77.4 - - - +
805A GLU* 1.3 58.9 + - - +
807A VAL* 3.6 1.3 + - - +
808A ALA* 3.2 17.8 + - - -
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Residues in contact with GLU 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A ILE 4.0 10.7 + - - -
802A THR* 3.6 4.8 + - - +
803A ALA 3.2 0.4 - - - -
804A GLU* 1.3 74.8 - - - +
806A ALA* 1.3 64.5 + - - +
808A ALA* 3.1 2.9 + - - +
809A VAL* 2.9 21.1 + - - -
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Residues in contact with ALA 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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801A ILE* 4.0 3.0 + - - +
802A THR 3.2 15.6 + - - -
803A ALA 3.3 2.9 + - - -
805A GLU* 1.3 75.4 - - - +
807A VAL* 1.3 62.3 + - - +
809A VAL* 3.3 2.1 + - - +
810A TYR* 3.0 20.1 + - - -
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Residues in contact with VAL 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 ALA 3.1 14.8 + - - -
804A GLU 4.1 1.3 - - - -
806A ALA* 1.3 76.3 - - - +
808A ALA* 1.3 52.9 + - - +
810A TYR* 3.7 0.8 - - - +
811A THR* 2.8 33.3 + - - -
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Residues in contact with ALA 808 (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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804A GLU 3.2 11.6 + - - -
805A GLU* 3.1 7.4 + - - +
807A VAL* 1.3 76.9 - - - +
809A VAL* 1.3 60.4 + - - +
811A THR* 3.5 1.0 + - - +
812A THR* 3.0 21.5 + - - -
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLU 2.9 13.9 + - - -
806A ALA* 3.8 2.9 - - - +
808A ALA* 1.3 76.1 - - - +
810A TYR* 1.3 63.2 + - - +
812A THR* 3.4 1.2 + - - -
813A THR* 3.2 18.2 + - - -
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Residues in contact with TYR 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 ALA 3.0 14.8 + - - -
807A VAL* 3.2 3.1 + - - +
809A VAL* 1.3 77.6 - - - +
811A THR* 1.3 56.2 + - - +
813A THR* 3.2 3.7 + - - +
814A VAL* 2.9 25.6 + - - -
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Residues in contact with THR 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 VAL 2.8 17.4 + - - -
808A ALA* 3.9 1.6 - - - +
810A TYR* 1.3 75.9 - - - +
812A THR* 1.3 60.0 + - - +
814A VAL* 3.2 3.5 + - - +
815A HIS* 3.0 19.6 + - - -
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Residues in contact with THR 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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808A ALA 3.0 16.9 + - - -
809A VAL* 3.9 1.8 - - - +
811A THR* 1.3 74.3 - - - +
813A THR* 1.3 57.3 + - - +
815A HIS* 3.2 2.9 + - - +
816A TRP* 2.9 25.6 + - - -
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Residues in contact with THR 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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809A VAL 3.2 13.5 + - - -
810A TYR 3.2 4.2 + - - -
812A THR* 1.3 75.6 - - - +
814A VAL* 1.3 56.9 + - - +
816A TRP* 3.2 2.2 + - - +
817A LEU* 2.9 27.4 + - - -
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Residues in contact with VAL 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 TYR 2.9 14.1 + - - -
811A THR* 3.2 4.5 + - - +
813A THR* 1.3 76.7 - - - +
815A HIS* 1.3 56.7 + - - +
817A LEU* 3.5 1.1 + - - +
818A GLU* 2.9 25.6 + - - -
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Residues in contact with HIS 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 THR 3.0 13.7 + - - -
812A THR* 3.2 3.1 + - - +
814A VAL* 1.3 73.2 - - - +
816A TRP* 1.3 64.8 + - - +
818A GLU* 4.4 1.6 - - - +
819A SER* 2.9 22.3 + - - -
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Residues in contact with TRP 816 (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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812A THR 2.9 14.6 + - - -
813A THR* 3.6 3.8 - - - +
815A HIS* 1.3 77.0 - - - +
817A LEU* 1.3 53.2 + - - +
819A SER* 3.6 0.4 - - - +
820A ARG* 2.6 35.9 + - - -
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Residues in contact with LEU 817 (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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813A THR 2.9 14.3 + - - -
814A VAL* 3.9 1.3 - - - +
816A TRP* 1.3 74.3 - - - +
818A GLU* 1.3 63.5 + - - +
820A ARG* 5.2 0.7 - - - +
821A ARG* 3.4 16.8 + - - -
822A PHE 4.5 7.4 + - - +
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Residues in contact with GLU 818 (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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814A VAL 2.9 16.8 + - - -
815A HIS* 3.7 2.7 - - - +
817A LEU* 1.3 79.3 - - - +
819A SER* 1.3 58.6 + - - +
821A ARG* 3.7 8.3 + - - -
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Residues in contact with SER 819 (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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815A HIS 2.9 14.4 + - - -
816A TRP 3.6 1.6 - - - -
818A GLU* 1.3 73.9 - - - +
820A ARG* 1.3 63.4 + - - +
821A ARG* 3.2 1.5 + - - -
1065A PRO 5.5 1.9 - - - -
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Residues in contact with ARG 820 (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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816A TRP 2.6 21.3 + - - -
817A LEU* 4.3 1.1 - - - +
819A SER* 1.3 72.9 - - - +
821A ARG* 1.3 59.0 + - - +
822A PHE 3.2 7.6 + - - +
1065A PRO* 3.4 28.0 - - - +
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Residues in contact with ARG 821 (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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817A LEU 3.4 12.2 + - - -
818A GLU 3.7 6.5 + - - -
819A SER 3.2 3.7 - - - -
820A ARG* 1.3 77.0 - - - +
822A PHE* 1.3 66.2 + - - +
823A SER* 3.5 1.7 + - - -
1065A PRO* 5.6 2.5 - - - -
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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