Contacts of the helix formed by residues 821 - 833 (chain A) in PDB entry 4FYT
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 LEU 821 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A HIS* 3.8 20.0 - - + +
368A LEU* 5.6 11.0 - - + -
369A PHE* 5.5 1.3 - - - -
370A ASP* 3.2 43.5 - - + +
373A SER* 3.5 9.9 - - - +
374A SER* 4.4 1.3 - - - +
819A ALA* 3.5 1.9 - - - +
820A THR* 1.3 83.8 - - - +
822A VAL* 1.3 67.6 + - + +
823A ASN* 3.2 24.0 - - + +
824A GLU* 3.1 19.2 + - + +
825A ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO 6.2 0.2 - - - +
363A ARG* 6.3 0.4 - - + -
364A GLU* 3.3 37.7 - - + +
365A ASN* 3.4 35.0 - - + +
821A LEU* 1.3 75.8 - - + +
823A ASN* 1.3 53.6 + - - +
825A ALA* 3.2 7.0 + - + +
826A ASP* 2.8 47.3 + - - +
857A GLN* 5.4 11.4 - - - +
858A ASP* 6.0 0.2 - - - +
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Residues in contact with ASN 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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365A ASN* 3.6 32.2 + - - +
368A LEU 4.4 11.0 + - - +
369A PHE* 4.8 0.2 - - - -
373A SER 5.4 1.3 - - - +
374A SER* 2.7 33.0 + - - +
378A ASN* 3.4 38.0 - - - +
821A LEU* 4.2 11.1 - - + +
822A VAL* 1.3 77.8 - - - +
824A GLU* 1.3 62.6 + - - +
826A ASP* 3.6 6.9 + - - +
827A LYS* 3.1 32.3 + - - +
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Residues in contact with GLU 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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373A SER* 4.7 8.7 + - - +
779A TRP* 3.9 12.1 - - - -
786A ASN* 4.0 1.7 + - - -
793A ARG* 3.1 32.4 + - - -
797A TYR* 2.5 35.2 + - - -
819A ALA* 5.2 5.8 - - + -
821A LEU* 3.1 22.1 + - + +
823A ASN* 1.3 74.3 - - - +
825A ALA* 1.3 66.7 + - - +
827A LYS* 3.2 9.5 + - - +
828A LEU* 3.1 32.9 + - + +
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Residues in contact with ALA 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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816A PHE* 3.3 27.5 - - + +
819A ALA* 3.8 20.8 - - + +
821A LEU 2.9 15.9 + - - +
822A VAL* 3.7 8.3 - - + +
824A GLU* 1.3 76.6 - - - +
826A ASP* 1.3 58.9 + - - +
828A LEU* 3.3 3.8 + - - -
829A ARG* 2.8 31.7 + - - +
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Residues in contact with ASP 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASN* 2.7 35.8 + - - +
822A VAL* 2.8 33.4 + - - +
823A ASN* 3.8 8.2 + - - +
825A ALA* 1.3 76.5 - - - +
827A LYS* 1.3 62.0 + - + +
829A ARG* 2.9 35.1 + - - +
830A ALA* 3.1 24.6 + - - +
858A ASP* 4.8 4.7 - - - +
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Residues in contact with LYS 827 (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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373A SER 4.6 7.4 + - - -
375A SER* 4.3 3.9 - - - +
378A ASN* 2.8 28.1 + - - +
790A PRO 3.9 14.4 - - - -
793A ARG* 3.7 21.8 - - + +
794A SER* 3.2 28.1 - - - +
797A TYR* 4.1 15.7 - - + +
823A ASN* 3.1 25.5 + - - +
824A GLU* 3.2 14.8 + - - +
826A ASP* 1.3 76.7 - - + +
828A LEU* 1.3 58.2 + - - +
830A ALA* 3.5 4.5 + - - +
831A ALA* 3.0 28.9 + - - +
1017A SO4 3.6 27.4 - - - +
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Residues in contact with LEU 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A TRP* 4.1 12.8 - - + -
797A TYR* 3.7 27.1 - - + -
812A ALA* 3.9 31.2 - - + +
815A GLN* 3.8 13.7 - - + +
816A PHE* 3.6 36.6 - - + +
819A ALA* 5.2 0.2 - - + -
824A GLU* 3.1 37.8 + - + +
825A ALA* 3.7 5.6 - - - +
827A LYS* 1.3 77.5 - - - +
829A ARG* 1.3 61.5 + - - +
831A ALA* 3.1 5.4 + - + +
832A LEU* 3.0 31.7 + - + +
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Residues in contact with ARG 829 (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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363A ARG* 5.6 0.4 - - - +
365A ASN* 5.6 0.4 - - - +
816A PHE* 3.8 28.2 - - + -
825A ALA* 2.8 19.4 + - - +
826A ASP* 2.9 36.1 + - - +
828A LEU* 1.3 74.5 - - - +
830A ALA* 1.3 62.9 + - - +
832A LEU* 3.7 6.1 + - - -
833A ALA* 4.5 1.0 - - - +
844A TYR* 2.7 41.0 + - - +
854A ILE* 4.3 7.2 - - + -
858A ASP* 3.6 37.4 + - - +
861A SER* 3.2 24.5 + - - -
862A THR* 2.9 35.5 + - + +
865A SER* 5.2 1.8 + - - -
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Residues in contact with ALA 830 (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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794A SER* 6.2 2.0 - - - +
826A ASP 3.1 16.7 + - - +
827A LYS* 3.9 5.2 - - - +
829A ARG* 1.3 76.7 - - - +
831A ALA* 1.3 64.8 + - - +
833A ALA* 3.1 19.6 + - - +
834A CYS* 3.9 8.0 - - - -
865A SER* 4.3 19.4 - - - +
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Residues in contact with ALA 831 (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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794A SER 4.8 1.1 - - - +
797A TYR* 3.4 31.0 - - + -
798A CYS* 3.6 18.8 - - + +
801A ILE* 3.5 17.6 - - + +
827A LYS 3.0 18.6 + - - +
828A LEU* 3.1 7.1 + - + +
830A ALA* 1.3 76.8 - - - +
832A LEU* 1.3 57.8 + - - +
834A CYS* 2.8 28.8 + - - +
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Residues in contact with LEU 832 (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* 3.9 4.0 - - + -
809A TRP* 2.8 71.5 + - + +
812A ALA* 3.7 17.9 - - + +
813A TRP* 3.7 36.8 - - + +
816A PHE* 4.4 6.7 - - + -
828A LEU 3.0 25.1 + - - +
829A ARG* 4.2 1.8 - - - -
830A ALA 3.2 0.6 - - - -
831A ALA* 1.3 77.5 - - - +
833A ALA* 1.3 59.7 + - - +
834A CYS 3.1 1.3 + - - -
835A SER* 3.7 5.7 + - - -
841A LEU* 4.2 1.9 - - - +
844A TYR* 3.5 30.6 - - + +
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Residues in contact with ALA 833 (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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829A ARG 4.5 0.2 - - - +
830A ALA 3.1 12.4 + - - +
831A ALA 3.0 1.2 - - - -
832A LEU* 1.3 78.1 - - - +
834A CYS* 1.3 58.1 + - - +
835A SER 3.3 1.1 - - - -
841A LEU* 3.6 12.5 - - - +
844A TYR* 3.6 11.4 - - + -
865A SER* 3.6 38.9 - - - +
866A ILE* 3.8 12.3 - - + +
869A ASN* 2.9 26.9 + - - +
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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