Contacts of the helix formed by residues 837 - 849 (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 GLU 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A GLY 4.4 2.6 - - - +
805A GLY* 3.7 22.5 - - - -
806A GLU* 4.0 2.9 + - - +
835A SER* 3.1 10.6 + - - +
836A LYS* 1.3 81.4 - - + +
838A LEU* 1.3 65.8 + - - +
839A TRP* 3.2 24.9 + - + -
840A ILE* 3.2 31.7 + - + +
841A LEU* 3.0 22.6 + - - +
871A ILE* 4.5 1.6 - - - -
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Residues in contact with LEU 838 (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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836A LYS 3.6 4.6 + - - -
837A GLU* 1.3 71.2 - - - +
839A TRP* 1.3 57.2 + - - +
841A LEU* 3.2 3.5 + - + +
842A ASN* 2.9 52.9 + - - +
871A ILE* 3.5 36.3 - - + +
875A LEU* 4.1 17.5 - - + +
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Residues in contact with TRP 839 (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 GLU* 3.5 35.2 - - + -
837A GLU* 3.2 29.8 + - + -
838A LEU* 1.3 79.1 - - - +
840A ILE* 1.3 79.4 + - + +
842A ASN* 3.4 7.1 + - - +
843A ARG* 3.0 62.3 + - + +
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Residues in contact with ILE 840 (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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805A GLY 4.9 0.9 - - - -
806A GLU* 4.4 17.5 - - + +
809A TRP* 3.4 44.5 - - + +
832A LEU 5.1 0.2 - - - +
835A SER* 3.5 21.5 - - - +
837A GLU* 3.2 33.1 + - + +
839A TRP* 1.3 112.3 - - + +
841A LEU* 1.3 59.6 + - + +
843A ARG* 3.3 10.3 + - - +
844A TYR* 2.9 27.7 + - - +
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Residues in contact with LEU 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LEU 4.2 2.5 - - - +
833A ALA* 3.6 33.7 - - - +
835A SER* 3.5 30.1 - - - +
837A GLU 3.0 13.3 + - - +
838A LEU* 3.8 7.2 - - + +
840A ILE* 1.3 76.8 - - - +
842A ASN* 1.3 56.4 + - - +
844A TYR* 3.3 6.2 + - + +
845A LEU* 2.9 28.9 + - - +
866A ILE* 4.4 14.3 - - + +
869A ASN* 3.7 13.0 - - + +
871A ILE* 3.9 17.0 - - + -
872A GLY* 3.7 25.4 - - - +
875A LEU* 3.7 16.1 - - + +
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Residues in contact with ASN 842 (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* 2.9 43.9 + - - +
839A TRP* 3.6 8.0 - - - +
841A LEU* 1.3 73.9 - - - +
843A ARG* 1.3 66.1 + - - +
845A LEU* 3.3 5.5 + - - +
846A SER* 3.1 20.6 + - - -
875A LEU* 3.3 33.4 - - - +
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Residues in contact with ARG 843 (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 GLU* 4.7 6.5 + - - +
809A TRP* 3.5 25.9 - - - -
810A ASP* 3.3 26.0 + - - -
839A TRP* 3.0 55.4 + - + +
840A ILE* 3.7 11.4 + - - +
842A ASN* 1.3 74.9 - - - +
844A TYR* 1.3 62.8 + - - +
846A SER* 2.7 26.2 + - - +
847A TYR* 3.2 40.6 + - + +
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Residues in contact with TYR 844 (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 TRP* 3.6 20.9 - + + -
813A TRP* 3.9 23.0 - + - -
829A ARG* 2.7 44.7 + - - +
832A LEU* 3.5 35.5 - - + +
833A ALA* 3.6 14.6 - - + -
840A ILE 2.9 17.9 + - - +
841A LEU* 3.6 8.1 - - + +
842A ASN 3.2 0.2 - - - -
843A ARG* 1.3 74.9 - - - +
845A LEU* 1.3 65.5 + - - +
847A TYR* 3.0 20.9 + + + -
848A THR* 3.2 11.8 + - - +
854A ILE* 3.9 10.1 - - + -
862A THR* 3.6 15.0 - - + -
866A ILE* 3.8 18.2 - - + -
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Residues in contact with LEU 845 (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 2.9 16.2 + - - +
842A ASN* 3.3 6.7 + - - +
844A TYR* 1.3 76.5 - - - +
846A SER* 1.3 61.7 + - - +
848A THR* 2.8 33.2 + - - +
849A LEU* 3.7 7.3 - - + +
863A ILE* 3.9 27.4 - - + -
866A ILE* 3.8 16.5 - - + +
875A LEU* 3.8 30.7 - - + +
876A VAL* 4.8 6.5 - - + -
879A PHE* 3.9 42.6 - - + -
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Residues in contact with SER 846 (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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842A ASN 3.1 12.4 + - - -
843A ARG* 2.7 21.8 + - - +
845A LEU* 1.3 75.7 - - - +
847A TYR* 1.3 71.8 + - - +
849A LEU* 3.4 22.9 + - - +
850A ASN* 3.8 7.4 + - - +
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Residues in contact with TYR 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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809A TRP* 4.0 16.3 - + - -
813A TRP* 3.5 48.8 + + + -
843A ARG* 3.3 46.5 + - + -
844A TYR* 3.0 20.6 + + + +
846A SER* 1.3 81.4 + - - +
848A THR* 1.3 65.0 + - - +
849A LEU 3.0 2.7 - - - -
850A ASN* 3.0 23.4 + - - +
853A LEU* 3.7 27.5 - - + +
854A ILE* 3.9 8.4 - - + +
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Residues in contact with THR 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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844A TYR* 3.2 15.3 + - + +
845A LEU* 2.8 18.3 + - - +
847A TYR* 1.3 75.0 - - - +
849A LEU* 1.3 63.5 + - - +
850A ASN 3.3 1.0 + - - -
854A ILE* 3.8 20.8 - - + +
859A ALA* 3.4 29.5 - - - +
862A THR* 3.5 33.7 - - + -
863A ILE* 3.5 26.2 - - + +
866A ILE* 4.2 13.2 - - + -
891A TYR* 4.6 0.5 + - - -
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Residues in contact with LEU 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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845A LEU* 3.7 13.2 - - + +
846A SER* 3.8 12.1 - - - +
847A TYR 3.0 1.0 - - - -
848A THR* 1.3 90.9 - - - +
850A ASN* 1.3 58.6 + - - +
851A PRO* 3.5 9.4 - - - +
863A ILE* 4.3 9.9 - - + -
879A PHE* 3.7 39.0 - - + -
886A LYS* 4.1 19.6 + - - +
887A LEU* 5.0 0.7 - - + -
891A TYR* 3.4 43.8 + - + +
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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