Contacts of the helix formed by residues 849 - 860 (chain A) in PDB entry 4KXA
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 ASP 849 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A ARG* 4.1 7.3 + - - -
807A TYR* 5.0 4.8 + - - +
817A GLU* 4.8 8.1 - - - +
820A LEU* 4.6 20.9 - - + +
845A ILE* 4.1 11.7 - - + -
846A LYS* 2.9 23.6 + - - +
848A GLN* 1.3 109.4 + - - +
850A VAL* 1.3 66.6 + - - +
851A PHE 3.3 2.7 - - - -
852A THR* 3.3 12.0 + - - -
853A VAL* 3.0 23.6 + - - +
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Residues in contact with VAL 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A LEU* 3.8 29.7 - - + +
845A ILE* 4.1 8.1 - - + -
846A LYS 3.4 12.3 + - - +
847A THR 3.7 0.2 + - - -
848A GLN 3.6 1.6 - - - -
849A ASP* 1.3 75.6 - - - +
851A PHE* 1.3 61.6 + - + +
853A VAL* 3.2 4.5 + - - +
854A ILE* 3.0 44.5 + - + +
870A TRP* 5.3 0.2 - - + -
878A LEU* 4.6 9.9 - - + -
881A ARG* 3.9 22.4 - - - +
882A TYR* 3.2 34.8 - - + +
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Residues in contact with PHE 851 (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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847A THR 5.3 1.3 - - - -
848A GLN 5.0 3.2 + - - +
849A ASP 3.3 0.8 - - - -
850A VAL* 1.3 72.5 - - + +
852A THR* 1.3 66.5 + - - +
854A ILE* 3.5 14.3 + - + -
855A ARG* 3.1 27.0 + - - +
878A LEU* 4.6 8.5 - - + -
882A TYR* 3.7 49.1 - + - -
886A ASN* 4.2 0.7 - - - -
888A ASN* 3.7 29.6 - - + +
889A LEU* 3.5 47.6 - - + -
892A ILE* 3.7 37.7 - - + +
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Residues in contact with THR 852 (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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368A ARG* 4.5 7.8 + - - -
817A GLU* 4.0 18.9 + - + +
820A LEU* 5.8 2.5 - - + -
848A GLN 4.4 9.6 + - - -
849A ASP* 3.3 16.2 + - + +
851A PHE* 1.3 76.8 - - - +
853A VAL* 1.3 59.2 + - + +
855A ARG* 3.2 10.0 + - - +
856A TYR* 3.0 62.0 + - + +
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Residues in contact with VAL 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LEU* 4.0 26.5 - - + -
835A TYR* 3.5 43.3 - - + +
839A LEU* 3.8 17.0 - - + -
845A ILE* 4.5 11.0 - - + -
849A ASP 3.0 21.0 + - - +
850A VAL 3.2 6.5 + - - +
852A THR* 1.3 73.5 - - - +
854A ILE* 1.3 66.4 + - - +
856A TYR* 3.1 9.2 + - + +
857A ILE* 2.9 33.4 + - + +
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Residues in contact with ILE 854 (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 LEU* 5.0 1.6 - - + -
839A LEU* 3.6 17.0 - - + -
850A VAL* 3.0 29.3 + - + +
851A PHE* 3.8 21.3 - - + +
853A VAL* 1.3 76.7 - - - +
855A ARG* 1.3 57.4 + - - +
857A ILE* 3.3 6.7 + - - +
858A SER* 2.9 24.1 + - - -
867A ALA* 3.5 20.7 - - + +
870A TRP* 3.7 28.9 - - + -
871A ILE* 3.9 22.7 - - + -
878A LEU* 4.8 1.1 - - + -
892A ILE* 3.8 15.9 - - + -
895A ILE* 4.3 4.5 - - + -
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Residues in contact with ARG 855 (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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851A PHE* 3.1 17.9 + - - +
852A THR* 3.4 7.9 - - - +
854A ILE* 1.3 78.4 - - - +
856A TYR* 1.3 63.0 + - + +
858A SER* 2.7 23.7 + - - -
859A TYR* 3.3 40.3 + - + +
888A ASN 5.2 0.8 + - - -
891A ARG* 3.2 37.2 + - - +
892A ILE* 3.7 14.6 - - + +
894A THR* 2.9 22.8 + - - -
895A ILE* 4.0 23.5 - - + +
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Residues in contact with TYR 856 (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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817A GLU* 3.7 33.1 + - + +
820A LEU* 4.0 9.4 - - + -
821A TYR* 3.6 65.0 - + + -
824A ALA* 3.6 22.3 - - + +
852A THR* 3.0 40.8 + - + +
853A VAL* 3.5 8.3 - - - +
855A ARG* 1.3 77.3 - - + +
857A ILE* 1.3 61.5 + - - +
859A TYR* 3.0 35.1 + + - +
860A ASN 3.7 2.9 + - - -
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Residues in contact with ILE 857 (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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824A ALA* 4.1 11.7 - - + -
832A LEU* 4.6 13.7 - - + +
835A TYR* 3.6 38.4 - - + -
836A LEU* 3.6 36.6 - - + +
853A VAL* 2.9 29.6 + - + +
854A ILE 3.7 4.5 - - - +
856A TYR* 1.3 74.6 - - - +
858A SER* 1.3 63.9 + - - +
860A ASN* 3.0 15.2 + - - +
863A GLY* 3.1 32.7 - - - +
866A MET* 4.8 3.1 - - + -
867A ALA* 4.1 12.6 - - + +
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Residues in contact with SER 858 (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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854A ILE 2.9 13.4 + - - -
855A ARG 2.7 18.1 + - - -
856A TYR 3.2 0.4 - - - -
857A ILE* 1.3 76.4 - - - +
859A TYR* 1.3 69.2 + - - +
860A ASN 3.3 0.2 - - - -
863A GLY 3.4 11.7 - - - -
864A LYS* 3.1 30.1 - - - +
867A ALA* 3.9 8.7 - - - +
895A ILE* 3.6 36.9 + - - +
898A PRO* 5.9 1.4 - - - +
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Residues in contact with TYR 859 (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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788A ARG* 6.0 1.1 - - - +
821A TYR* 3.3 31.6 - + + +
855A ARG* 3.5 43.5 + - + +
856A TYR* 3.0 30.6 + + - +
858A SER* 1.3 85.0 - - - +
860A ASN* 1.3 62.0 + - - +
861A SER* 3.7 2.3 + - - -
864A LYS* 5.5 0.2 - - - -
895A ILE* 6.4 0.7 - - - -
898A PRO* 6.3 3.1 - - + -
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Residues in contact with ASN 860 (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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824A ALA 2.9 27.2 + - - +
825A SER* 3.5 10.8 + - - +
826A VAL 2.8 28.7 + - - +
827A LYS* 5.0 3.7 - - - +
832A LEU* 3.6 12.7 - - + +
856A TYR 3.7 1.6 + - - -
857A ILE 3.0 13.8 + - - +
859A TYR* 1.3 78.3 - - - +
861A SER* 1.3 62.0 + - - +
862A TYR* 2.8 34.8 + - - +
863A GLY* 3.0 4.4 + - - +
864A LYS* 2.7 33.5 + - - +
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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