Contacts of the helix formed by residues 906 - 918 (chain S) in PDB entry 1KFX
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 ASN 906 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692L ILE* 4.7 31.0 - - + +
904S HIS* 5.2 1.5 - - + +
905S LEU* 1.3 75.7 - - - +
907S GLU* 1.3 72.9 + - - +
908S HIS* 2.7 38.5 + - - +
909S LEU* 3.8 18.4 + - + +
910S TYR* 2.8 32.0 + - - +
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Residues in contact with GLU 907 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906S ASN* 1.3 75.2 + - - +
908S HIS* 1.3 83.5 + - + +
910S TYR* 3.1 22.5 - - - +
911S ASN* 3.2 20.3 + - - +
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Residues in contact with HIS 908 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692L ILE* 6.2 1.3 - - + -
696L CYS* 4.4 12.6 - - - -
906S ASN* 2.7 29.8 + - - +
907S GLU* 1.3 94.6 + - + +
909S LEU* 1.3 65.8 + - - +
911S ASN* 3.4 14.6 + - - +
912S MET* 3.4 20.9 + - - +
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Residues in contact with LEU 909 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692L ILE* 5.9 4.5 - - + -
695L LEU* 3.7 46.7 - - + +
696L CYS* 4.0 15.5 - - - -
699L VAL* 4.2 11.9 - - + -
903S PHE* 6.4 2.0 - - + -
904S HIS* 6.2 2.0 - - + -
905S LEU* 5.1 7.6 - - + +
906S ASN* 3.5 26.5 + - + +
908S HIS* 1.3 77.1 - - - +
910S TYR* 1.3 72.8 + - - +
912S MET* 2.9 21.1 + - - +
913S ILE* 3.1 18.3 + - + +
936S LEU* 4.4 17.5 - - + -
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Residues in contact with TYR 910 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891S SER 3.5 9.0 + - - -
894S LEU* 3.1 38.5 - - + +
895S PRO* 3.6 26.2 - - + +
898S PHE* 5.4 12.1 - + + -
905S LEU* 6.0 2.2 - - + -
906S ASN 2.8 14.8 + - - +
907S GLU* 3.1 13.7 - - - +
909S LEU* 1.3 73.5 - - - +
911S ASN* 1.3 69.7 + - - +
913S ILE* 2.4 46.5 + - + +
914S ILE* 3.0 29.3 + - + +
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Residues in contact with ASN 911 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907S GLU* 3.2 26.8 + - - +
908S HIS* 3.5 15.3 + - - +
910S TYR* 1.3 83.3 - - - +
912S MET* 1.3 56.8 + - + +
914S ILE* 2.6 14.2 + - - +
915S ARG* 2.5 46.6 + - - +
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Residues in contact with MET 912 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582L ASP* 4.8 11.2 - - - +
696L CYS* 4.1 23.6 - - + +
697L PHE* 5.8 0.7 - - - -
699L VAL* 3.7 37.2 - - + +
700L LEU* 4.8 3.8 - - - +
908S HIS 3.4 15.3 - - - +
909S LEU* 2.9 19.1 + - - +
910S TYR 2.8 2.6 + - - -
911S ASN* 1.3 74.2 - - + +
913S ILE* 1.3 58.6 + - - +
915S ARG* 2.5 51.5 - - + +
916S ARG* 3.3 5.4 - - + +
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Residues in contact with ILE 913 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699L VAL* 4.5 8.3 - - + -
898S PHE* 3.4 35.9 - - + -
909S LEU* 3.6 26.7 - - + +
910S TYR* 2.4 29.4 + - + +
912S MET* 1.3 73.5 - - - +
914S ILE* 1.3 67.3 + - + +
915S ARG 3.2 0.2 + - - -
917S TYR* 3.0 35.1 + - + -
924S MET* 3.5 19.8 - - + +
932S CYS* 3.5 26.9 - - - -
936S LEU* 4.6 12.3 - - + -
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Residues in contact with ILE 914 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578L LYS* 4.6 1.4 + - - -
894S LEU* 3.3 21.5 - - + -
898S PHE* 5.6 0.7 - - + -
910S TYR* 3.3 59.9 - - + +
911S ASN* 2.6 16.1 + - - +
913S ILE* 1.3 79.6 - - + +
915S ARG* 1.3 54.9 + - - +
916S ARG 3.3 4.5 + - - -
918S SER* 2.4 40.3 + - - +
922S GLY* 5.4 6.3 - - - +
924S MET* 4.6 5.6 - - + -
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Residues in contact with ARG 915 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578L LYS* 4.1 12.1 - - + +
581L VAL* 4.4 7.9 - - - +
582L ASP* 2.9 32.1 + - - +
585L ASP* 3.0 37.4 + - - +
588L GLY* 4.3 9.1 + - - -
589L SER 4.1 12.1 + - - -
590L GLY* 4.5 5.6 - - - -
911S ASN* 2.5 33.7 + - - +
912S MET* 2.5 40.4 - - + +
914S ILE* 1.3 70.4 - - - +
916S ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 916 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575L GLU* 3.6 27.8 + - - +
578L LYS* 3.2 38.3 - - - +
582L ASP* 5.1 2.2 - - - -
664L ARG* 2.8 31.3 - - - +
699L VAL* 4.1 10.1 - - + +
700L LEU* 3.1 41.5 - - - +
842S ASP* 4.6 4.2 + - - -
912S MET* 3.3 11.2 - - + +
914S ILE 3.3 0.4 + - - -
915S ARG* 1.3 78.8 - - - +
917S TYR* 1.3 89.8 + - + +
928S ASN* 4.0 6.9 + - - +
935S ARG* 4.4 8.7 - - - +
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Residues in contact with TYR 917 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578L LYS* 4.7 0.4 - - - +
699L VAL* 3.9 21.4 - - + +
913S ILE* 3.0 31.9 + - + -
916S ARG* 1.3 106.3 - - + +
918S SER* 1.3 61.1 + - - +
919S ASP* 4.3 3.3 - - - +
924S MET* 3.2 30.8 - - + +
925S ASP 4.7 0.3 + - - -
928S ASN* 3.3 52.9 + - + +
931S SER* 4.1 8.1 - - - -
932S CYS* 3.2 54.4 + - + -
935S ARG* 4.1 19.8 + - - +
936S LEU* 5.0 1.0 + - - +
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Residues in contact with SER 918 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551L PHE* 3.8 8.5 - - - -
574L ILE* 5.3 0.7 - - - +
578L LYS* 3.6 16.0 + - - +
894S LEU* 5.4 0.7 - - - -
914S ILE* 2.4 41.7 + - - +
917S TYR* 1.3 79.1 - - - +
919S ASP* 1.3 66.3 + - - +
922S GLY* 3.7 26.3 - - - -
923S ASN 3.3 9.9 - - - -
924S MET* 4.1 8.2 - - - +
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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