Contacts of the helix formed by residues 871 - 883 (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 ILE 871 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A LYS* 3.8 33.2 - - + +
838A LEU* 3.5 45.5 - - + +
841A LEU* 3.9 9.6 - - + -
869A ASN* 3.0 11.8 + - - +
870A VAL* 1.3 90.7 - - + +
872A GLY* 1.3 59.2 + - - +
873A GLN 3.4 0.6 + - - -
874A GLY 4.6 1.6 + - - -
875A LEU* 4.4 3.5 + - - +
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Residues in contact with GLY 872 (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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841A LEU* 3.7 13.1 - - - +
866A ILE* 3.3 22.9 - - - -
867A THR* 4.1 1.6 - - - -
869A ASN 2.7 12.1 + - - -
871A ILE* 1.3 80.5 - - - +
873A GLN* 1.3 56.0 + - - +
874A GLY 3.5 0.4 - - - -
875A LEU* 3.5 6.8 + - - +
876A VAL* 2.9 35.9 + - - +
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Residues in contact with GLN 873 (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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711A ARG* 4.0 19.3 - - - +
867A THR* 3.6 15.5 + - - +
869A ASN 3.2 4.4 + - - -
870A VAL 3.5 14.8 - - - +
871A ILE 3.4 1.0 - - - -
872A GLY* 1.3 77.0 - - - +
874A GLY* 1.3 60.5 + - - +
876A VAL* 4.0 0.2 - - - -
877A TRP* 3.0 36.8 + - + +
904A ALA 4.7 3.8 - - - +
905A VAL 2.9 26.9 + - - +
908A ARG* 3.2 48.0 + - - +
909A PHE* 3.5 21.8 - - - -
914A GLU* 4.8 1.0 + - - -
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Residues in contact with GLY 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A VAL 4.8 1.0 + - - -
871A ILE 4.6 2.6 + - - -
873A GLN* 1.3 80.6 - - - +
875A LEU* 1.3 57.2 + - - +
877A TRP* 4.8 4.5 - - - -
878A ASP* 2.9 45.8 + - - -
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Residues in contact with LEU 875 (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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838A LEU* 4.1 15.6 - - + +
841A LEU* 3.7 44.0 - - + +
842A ASN* 3.3 32.8 - - - +
845A LEU* 3.8 21.5 - - + -
866A ILE* 3.9 15.9 - - + -
871A ILE 4.6 1.8 + - - -
872A GLY* 3.5 10.3 - - - +
874A GLY* 1.3 76.5 - - - +
876A VAL* 1.3 57.6 + - - +
878A ASP* 4.0 3.9 - - - +
879A PHE* 3.1 27.6 + - + +
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Residues in contact with VAL 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LEU* 4.8 6.3 - - + -
863A ILE* 3.6 31.0 - - + +
866A ILE* 3.6 26.2 - - + -
867A THR* 3.6 26.9 - - - +
872A GLY 2.9 23.0 + - - +
875A LEU* 1.3 76.5 - - + +
877A TRP* 1.3 61.0 + - - +
879A PHE* 3.1 8.5 + - + +
880A VAL* 2.8 35.1 + - + +
901A LEU* 5.1 1.6 - - + -
905A VAL* 4.0 10.8 - - + -
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Residues in contact with TRP 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A GLN* 3.0 25.9 + - + +
874A GLY* 4.1 3.8 - - - +
876A VAL* 1.3 77.4 - - - +
878A ASP* 1.3 66.7 + - - +
880A VAL* 3.2 17.1 + - + -
881A GLN* 3.0 63.2 + - + +
905A VAL* 3.5 32.3 - - + +
906A THR* 4.7 0.9 - - + -
909A PHE* 3.4 33.2 - + - -
914A GLU* 5.6 1.3 - - + -
917A GLN* 2.9 43.0 + - + +
918A LEU* 3.9 23.3 - - + -
921A PHE* 3.8 25.4 - + + -
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Residues in contact with ASP 878 (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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874A GLY* 2.9 27.0 + - - +
875A LEU* 4.0 4.4 - - - +
877A TRP* 1.3 80.6 - - - +
879A PHE* 1.3 62.0 + - - +
881A GLN* 3.3 19.0 + - - +
882A SER* 2.9 32.2 + - - +
917A GLN* 4.6 6.1 + - - -
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Residues in contact with PHE 879 (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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845A LEU* 3.9 31.6 - - + -
849A LEU* 3.7 38.8 - - + -
863A ILE* 4.6 12.8 - - + -
875A LEU* 3.1 18.8 + - + +
876A VAL* 3.1 10.5 + - + +
878A ASP* 1.3 77.6 - - - +
880A VAL* 1.3 65.9 + - + +
882A SER* 3.2 1.1 + - - -
883A ASN* 2.9 76.3 + - + +
886A LYS* 4.8 3.6 - - - -
887A LEU* 3.9 28.7 - - + -
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Residues in contact with VAL 880 (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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863A ILE* 5.5 0.4 - - + -
876A VAL* 2.8 37.3 + - + +
877A TRP* 3.7 19.3 - - + +
879A PHE* 1.3 75.4 - - + +
881A GLN* 1.3 63.1 + - - +
882A SER 3.3 0.3 + - - -
884A TRP* 3.4 52.6 + - + +
887A LEU* 4.0 19.5 - - + -
901A LEU* 4.7 14.8 - - + -
902A ILE* 6.3 1.1 - - + -
905A VAL* 4.4 13.9 - - + -
921A PHE* 4.1 10.0 - - + -
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Residues in contact with GLN 881 (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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877A TRP* 3.0 72.5 + - + +
878A ASP* 3.3 20.0 + - - +
880A VAL* 1.3 77.4 - - - +
882A SER* 1.3 60.6 + - - +
883A ASN 3.7 0.2 + - - -
884A TRP* 4.4 6.6 + - - +
917A GLN* 4.0 25.9 + - - +
921A PHE* 4.2 18.1 - - + +
925A ASN* 5.1 3.5 + - - -
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Residues in contact with SER 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ASP* 2.9 20.8 + - - +
879A PHE* 3.2 0.6 + - - -
880A VAL 3.2 0.2 - - - -
881A GLN* 1.3 78.3 - - - +
883A ASN* 1.3 74.6 + - - +
884A TRP 3.8 0.9 - - - -
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Residues in contact with ASN 883 (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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879A PHE* 2.9 63.2 + - + +
880A VAL 3.8 2.2 - - - -
881A GLN 3.4 0.2 - - - -
882A SER* 1.3 93.5 - - - +
884A TRP* 1.3 64.3 + - - +
885A LYS 3.4 2.7 - - - -
886A LYS* 3.3 24.3 + - + +
887A LEU* 3.0 23.2 + - + +
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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