Contacts of the helix formed by residues 905 - 915 (chain A) in PDB entry 4FUL
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 905 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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903A LYS* 3.8 1.6 - - + +
904A ASP* 1.3 77.0 - - + +
906A VAL* 1.4 52.7 + - + +
907A LEU 3.4 0.7 - - - -
908A ASN* 3.2 4.8 + - - +
909A HIS* 2.7 64.7 + - + +
993A PHE* 3.5 45.8 - - + -
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Residues in contact with VAL 906 (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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891A ILE* 3.8 14.6 - - + +
892A GLN* 3.4 50.0 - - + +
895A THR* 3.9 25.1 - - - -
903A LYS* 3.4 23.3 - - + +
904A ASP 3.3 0.4 - - - -
905A GLU* 1.4 76.2 - - + +
907A LEU* 1.4 59.3 + - - +
909A HIS* 3.3 17.7 - - + +
910A TRP* 2.9 29.5 + - - +
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Residues in contact with LEU 907 (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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888A ILE* 3.9 12.6 - - + -
891A ILE* 3.8 33.2 - - + -
904A ASP 4.3 1.6 + - - -
905A GLU 3.4 0.8 - - - -
906A VAL* 1.4 75.7 - - + +
908A ASN* 1.3 55.6 + - - +
910A TRP* 3.1 9.4 + - + +
911A LEU* 2.8 36.7 + - + +
928A PHE* 3.8 21.8 - - + -
954A ILE* 3.9 19.1 - - + -
990A ASP* 4.2 18.1 - - + +
991A PHE* 3.8 29.8 - - + -
994A VAL* 3.9 16.2 - - + -
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Residues in contact with ASN 908 (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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904A ASP 4.9 0.4 + - - -
905A GLU 3.2 9.5 + - - +
907A LEU* 1.3 77.0 - - - +
909A HIS* 1.4 62.7 + - - +
911A LEU* 3.3 4.6 + - - +
912A LYS* 3.1 30.7 + - - +
921A PHE* 3.5 27.1 - - - -
925A VAL* 4.8 0.8 - - - +
993A PHE* 3.3 36.6 + - + +
994A VAL* 3.6 36.5 + - + +
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Residues in contact with HIS 909 (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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905A GLU* 2.7 59.1 + - + +
906A VAL* 3.3 21.8 - - + +
908A ASN* 1.4 73.5 - - + +
910A TRP* 1.4 53.1 + - - +
912A LYS* 3.8 4.2 - - - +
913A GLU* 2.8 39.6 + - - +
993A PHE* 5.8 0.4 - + - -
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Residues in contact with TRP 910 (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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884A ASP 5.2 0.2 - - - -
885A ALA 5.4 0.7 - - - -
886A THR* 3.3 30.8 - - + +
891A ILE* 3.6 37.1 - - + +
894A SER* 6.1 3.6 - - - -
906A VAL 2.9 14.8 + - - +
907A LEU* 3.3 9.9 - - + +
909A HIS* 1.4 74.4 - - - +
911A LEU* 1.4 71.5 + - + +
913A GLU* 3.4 18.4 + - - +
914A LYS* 2.7 66.3 + - + +
954A ILE* 3.9 12.1 - - + -
955A THR 3.7 20.0 - - - -
956A GLU* 3.6 34.5 - - + -
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Residues in contact with LEU 911 (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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907A LEU* 2.8 29.4 + - + +
908A ASN* 3.3 2.7 + - - +
910A TRP* 1.4 94.5 - - + +
912A LYS* 1.3 60.6 + - - +
914A LYS* 3.2 3.4 + - - +
915A SER* 2.9 32.4 + - - -
921A PHE* 3.7 18.6 - - + -
924A ALA* 4.9 8.5 - - + +
925A VAL* 5.2 2.2 - - + -
928A PHE* 4.8 5.2 - - + -
954A ILE* 4.1 11.9 - - + -
955A THR 4.1 0.9 - - - +
956A GLU 4.6 5.4 - - - +
958A GLY* 3.9 30.7 - - - +
994A VAL* 3.9 32.8 - - + -
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Residues in contact with LYS 912 (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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908A ASN* 3.1 24.6 + - - +
909A HIS* 3.8 4.3 - - - +
911A LEU* 1.3 73.5 - - - +
913A GLU* 1.3 62.8 + - - +
915A SER* 3.2 20.1 + - - +
918A GLU* 3.3 26.5 - - - +
921A PHE* 3.3 35.4 - - + -
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Residues in contact with GLU 913 (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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909A HIS* 2.8 19.1 + - - +
910A TRP* 3.6 21.3 + - - +
912A LYS* 1.3 75.8 - - - +
914A LYS* 1.4 84.1 + - - +
915A SER 4.3 3.5 - - - +
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Residues in contact with LYS 914 (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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910A TRP* 2.7 59.7 + - + +
911A LEU* 3.2 5.4 + - - +
913A GLU* 1.4 91.9 - - - +
915A SER* 1.4 58.2 + - - +
916A PRO* 3.9 5.2 - - - +
956A GLU* 3.3 57.6 + - + +
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Residues in contact with SER 915 (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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911A LEU 2.9 20.3 + - - -
912A LYS 3.2 13.9 + - - +
913A GLU 4.3 3.1 - - - +
914A LYS* 1.4 76.5 - - - +
916A PRO* 1.4 71.4 - - - +
917A THR 3.7 7.9 + - - -
920A LYS 4.1 2.6 + - - -
921A PHE* 3.3 39.2 + - - +
924A ALA* 4.5 5.4 - - - +
956A GLU 4.7 5.2 + - - -
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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