Contacts of the helix formed by residues 813 - 825 (chain A) in PDB entry 4REC
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 813 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812A CYS* 1.3 74.9 - - - +
814A VAL* 1.3 66.2 + - - +
815A GLU* 3.4 11.8 + - - +
816A GLU* 3.4 33.0 + - - +
817A LEU* 3.1 21.3 + - - +
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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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812A CYS 3.3 6.9 + - - +
813A SER* 1.3 71.6 + - - +
815A GLU* 1.3 85.9 + - + +
817A LEU* 3.3 8.1 + - + +
818A ALA 3.1 17.2 + - - -
976A VAL* 3.6 23.4 - - + +
978A GLY* 4.0 27.8 - - - +
979A PRO* 5.0 4.3 - - + -
1006A VAL* 4.0 20.9 - - + +
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Residues in contact with GLU 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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813A SER* 3.3 10.7 - - - +
814A VAL* 1.3 89.6 - - + +
816A GLU* 1.3 59.8 + - - +
818A ALA* 3.2 4.9 + - - +
819A LEU* 2.8 33.5 + - - +
832A HIS* 3.2 49.6 + - + +
834A GLU* 4.8 1.9 - - - +
960A ALA* 3.6 11.3 - - - +
961A LEU* 4.0 5.8 - - + +
976A VAL* 3.2 33.0 - - - +
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Residues in contact with GLU 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 CYS* 6.2 1.3 - - + -
813A SER* 3.2 28.3 + - - +
815A GLU* 1.3 78.7 - - + +
817A LEU* 1.3 61.4 + - - +
819A LEU* 3.4 23.5 + - - +
820A ALA* 3.1 23.2 + - - +
823A ARG* 4.9 3.8 + - - -
832A HIS* 4.7 13.9 + - - +
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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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782A ILE* 3.9 13.3 - - + +
783A THR 4.3 3.6 - - - +
784A GLY* 4.0 2.5 - - - -
785A ARG* 3.7 57.0 - - + +
812A CYS* 4.5 17.5 - - + +
813A SER 3.1 16.5 + - - +
814A VAL* 3.6 7.9 - - - +
815A GLU 3.2 0.2 - - - -
816A GLU* 1.3 76.5 - - - +
818A ALA* 1.3 63.1 + - - +
820A ALA* 3.3 10.6 + - + +
821A HIS* 3.1 21.3 + - - +
824A ARG* 5.2 1.4 + - - -
1006A VAL* 3.8 24.0 - - + -
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Residues in contact with ALA 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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782A ILE* 4.0 12.7 - - + +
814A VAL 3.1 13.0 + - - +
815A GLU 3.2 8.0 + - - +
817A LEU* 1.3 77.1 - - - +
819A LEU* 1.3 63.0 + - - +
821A HIS* 3.0 3.7 + - - +
822A TYR* 3.0 32.1 + - + -
961A LEU* 3.7 18.6 - - + -
976A VAL* 3.8 14.4 - - + -
1004A CYS* 4.1 16.6 - - - -
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Residues in contact with LEU 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 GLU 2.8 22.7 + - - +
816A GLU* 3.7 29.6 - - - +
817A LEU 3.3 0.2 - - - -
818A ALA* 1.3 72.2 - - - +
820A ALA* 1.3 56.5 + - - +
822A TYR* 3.3 5.0 + - - +
823A ARG* 3.0 47.7 + - - +
830A GLY* 4.1 22.2 - - - +
831A ILE 4.3 0.9 - - - +
832A HIS* 4.3 21.5 - - + +
961A LEU* 3.7 24.2 - - + -
963A VAL* 3.8 20.0 - - + -
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Residues in contact with ALA 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 GLU 3.1 12.1 + - - +
817A LEU* 3.5 13.9 - - + +
818A ALA 3.2 0.2 - - - -
819A LEU* 1.3 76.0 - - - +
821A HIS* 1.3 62.4 + - - +
823A ARG* 3.3 29.1 + - - +
824A ARG* 3.1 40.2 + - - +
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Residues in contact with HIS 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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780A VAL* 5.2 7.2 - - + +
782A ILE* 3.5 35.9 - - + +
817A LEU 3.1 11.2 + - - +
818A ALA 3.0 7.4 + - - +
820A ALA* 1.3 76.3 - - - +
822A TYR* 1.3 96.3 + + - +
824A ARG* 3.0 31.2 + - - +
825A SER* 2.9 44.2 + - - -
1002A GLU* 5.3 0.4 + - - -
1004A CYS* 5.0 1.8 - - - -
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Residues in contact with TYR 822 (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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780A VAL* 3.9 3.3 - - - +
818A ALA* 3.0 35.2 + - + +
819A LEU 4.0 2.9 - - - +
821A HIS* 1.3 95.2 - + - +
823A ARG* 1.3 55.0 + - - +
825A SER* 2.9 16.0 + - - +
826A GLY 3.1 0.7 + - - -
827A PHE* 2.7 54.3 + + + +
961A LEU* 4.8 1.6 - - + -
963A VAL* 4.1 31.6 - - + -
972A LYS* 4.5 8.3 - - + -
974A VAL* 3.6 31.0 - - + +
1002A GLU* 2.6 33.5 + - - +
1004A CYS* 3.5 27.9 - - - +
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Residues in contact with ARG 823 (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 GLU* 4.9 3.8 + - - -
819A LEU* 3.0 32.2 + - - +
820A ALA* 3.3 35.3 - - - +
821A HIS 3.2 0.2 - - - -
822A TYR* 1.3 77.6 - - - +
824A ARG* 1.3 58.3 + - + +
826A GLY* 3.4 10.4 + - - -
827A PHE 3.3 20.1 + - - +
828A ASP* 4.0 19.9 + - - +
829A GLN 5.7 1.6 - - - +
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Residues in contact with ARG 824 (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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782A ILE* 5.6 4.8 - - - +
817A LEU 5.2 1.6 + - - -
820A ALA* 3.1 34.2 + - - +
821A HIS* 3.0 39.1 + - - +
823A ARG* 1.3 77.7 - - + +
825A SER* 1.3 58.6 + - - +
826A GLY 3.1 3.4 + - - -
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Residues in contact with SER 825 (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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821A HIS* 2.9 32.5 + - - -
822A TYR* 2.9 17.4 + - - -
824A ARG* 1.3 78.3 - - - +
826A GLY* 1.3 59.5 + - - +
827A PHE* 3.5 20.1 - - - -
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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