Contacts of the helix formed by residues 844 - 858 (chain C) in PDB entry 4AY6
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 844 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C GLN* 4.8 1.3 - - - +
469C TRP* 3.6 8.0 - - - +
472C TYR* 3.6 22.8 + - + +
842C LYS 3.9 0.2 + - - -
843C ILE* 1.3 76.3 - - - +
845C PRO* 1.3 69.1 - - + +
846C SER* 3.9 11.6 + - - -
847C THR* 2.7 56.4 + - - -
848C LEU 3.0 9.4 + - - -
916C LEU* 4.1 28.4 - - + +
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Residues in contact with PRO 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C TRP* 3.5 48.9 - - + -
472C TYR* 3.9 31.6 - - + -
844C ASP* 1.3 90.0 - - + +
846C SER* 1.3 61.1 + - - +
848C LEU* 3.6 0.5 + - - +
849C GLN* 3.1 21.5 + - - +
883C MET* 3.8 13.5 - - + +
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Residues in contact with SER 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844C ASP* 3.0 13.3 + - - -
845C PRO* 1.3 75.6 - - - +
847C THR* 1.3 69.8 + - - +
849C GLN* 2.9 19.0 + - - +
850C MET* 3.0 19.1 + - - +
963C ARG* 3.5 33.5 + - - -
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Residues in contact with THR 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842C LYS 4.7 1.4 + - - -
843C ILE* 4.2 2.9 - - + -
844C ASP* 2.7 37.9 + - - -
846C SER* 1.3 73.7 - - - +
848C LEU* 1.3 63.9 + - - +
850C MET* 3.4 17.3 + - + +
851C TRP* 3.4 52.9 + - + +
914C THR* 4.1 7.9 - - + -
915C PRO* 3.3 32.9 - - + +
916C LEU 4.4 3.8 + - - -
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Residues in contact with LEU 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C TRP* 3.6 30.7 - - + -
843C ILE* 4.2 4.4 - - + +
844C ASP 3.0 10.2 + - - +
845C PRO 3.9 7.0 - - - +
847C THR* 1.3 75.9 - - - +
849C GLN* 1.3 65.7 + - - +
851C TRP* 3.0 29.4 + - + -
852C ALA* 2.9 23.3 + - + +
855C LEU* 6.5 0.2 - - + -
863C LEU* 4.9 6.3 - - + -
865C LEU* 5.9 0.7 - - + -
876C ILE* 4.1 28.3 - - + -
879C TYR* 4.1 15.5 - - + -
880C ALA* 4.5 9.4 - - + +
883C MET* 4.2 11.0 - - + -
885C LEU* 6.4 1.6 - - + -
890C ILE* 4.9 6.7 - - + -
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Residues in contact with GLN 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845C PRO 3.1 14.1 + - - +
846C SER* 2.9 14.4 + - - +
848C LEU* 1.3 75.6 - - - +
850C MET* 1.3 63.8 + - + +
852C ALA* 3.2 12.0 + - - +
853C ASN* 2.9 55.1 + - - +
856C LYS* 5.7 2.6 - - - +
883C MET* 3.9 31.6 + - + +
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Residues in contact with MET 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C SER* 3.0 11.0 + - - +
847C THR* 3.5 25.6 - - + +
849C GLN* 1.3 76.5 - - + +
851C TRP* 1.3 64.1 + - + +
853C ASN* 3.1 7.0 + - - +
854C ILE* 2.9 31.9 + - - +
915C PRO* 3.7 30.5 - - + -
936C MET* 5.1 4.5 - - + +
963C ARG* 3.8 38.1 - - + +
966C TYR* 3.8 30.5 - - + -
967C GLU* 3.4 26.4 - - + +
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Residues in contact with TRP 851 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836C ASN* 4.1 13.2 - - + -
843C ILE* 3.9 27.1 - - + -
847C THR* 3.6 36.8 + - + +
848C LEU* 3.0 21.8 + - + +
850C MET* 1.3 77.6 - - + +
852C ALA* 1.3 67.1 + - - +
854C ILE* 3.0 7.7 + - + +
855C LEU* 2.8 32.6 + - + +
863C LEU* 3.6 34.1 - - + -
865C LEU* 4.4 6.7 - - + -
912C LEU* 3.5 46.7 - - + +
914C THR* 3.8 21.1 - - + -
966C TYR* 3.1 32.9 + + - -
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Residues in contact with ALA 852 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848C LEU* 2.9 14.1 + - + +
849C GLN* 3.3 21.8 - - - +
851C TRP* 1.3 74.8 - - - +
853C ASN* 1.3 63.7 + - - +
855C LEU* 3.3 3.0 + - - +
856C LYS* 3.0 32.8 + - - +
880C ALA* 6.3 0.2 - - - -
883C MET* 4.2 20.4 - - + -
885C LEU* 3.9 27.2 - - + +
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Residues in contact with ASN 853 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849C GLN* 2.9 41.8 + - - +
850C MET* 3.1 7.7 + - - +
852C ALA* 1.3 73.0 - - - +
854C ILE* 1.3 65.5 + - - +
856C LYS* 2.9 25.6 + - - +
857C ARG* 3.0 22.8 + - - +
967C GLU* 2.9 37.8 + - + +
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Residues in contact with ILE 854 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834C TYR* 4.0 28.3 - - + +
850C MET 2.9 19.4 + - - +
851C TRP* 3.4 13.5 - - + +
853C ASN* 1.3 77.1 - - - +
855C LEU* 1.3 65.7 + - + +
857C ARG* 3.0 15.1 + - - +
858C VAL* 3.1 12.9 + - - +
912C LEU* 4.7 4.7 - - + -
966C TYR* 3.7 34.5 - - + -
967C GLU* 3.6 24.7 - - + +
970C ALA* 3.7 27.8 - - + -
971C VAL* 4.2 12.8 - - + -
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Residues in contact with LEU 855 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C TYR* 4.5 8.1 - - + -
848C LEU* 6.5 0.2 - - + -
851C TRP* 2.8 30.5 + - + +
852C ALA 3.6 4.9 - - - +
854C ILE* 1.3 75.4 - - + +
856C LYS* 1.3 59.4 + - - +
858C VAL 3.1 10.6 - - - +
859C PRO* 4.7 0.5 - - - +
861C SER* 3.2 26.7 - - - +
862C VAL* 3.8 30.7 - - - +
863C LEU* 3.8 26.7 - - + +
885C LEU* 3.9 22.9 - - + -
889C ARG* 2.5 36.5 + - + +
890C ILE* 5.0 5.6 - - + -
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Residues in contact with LYS 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849C GLN* 5.7 2.0 - - - +
852C ALA* 3.0 27.0 + - - +
853C ASN* 2.9 16.1 + - - +
855C LEU* 1.3 76.5 - - - +
857C ARG* 1.3 63.7 + - + +
858C VAL 3.5 1.9 + - - -
859C PRO* 4.9 3.6 - - - +
883C MET* 3.0 28.4 + - - -
884C GLY* 3.4 21.6 + - - -
885C LEU* 4.0 11.7 - - + +
889C ARG* 4.8 4.3 - - - +
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Residues in contact with ARG 857 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853C ASN* 3.4 20.6 - - - +
854C ILE* 3.0 9.0 + - - +
856C LYS* 1.3 78.3 - - + +
858C VAL* 1.3 62.1 + - - +
859C PRO* 3.8 8.4 - - - +
964C GLN* 4.4 5.7 - - - +
967C GLU* 4.0 18.1 + - - +
968C ASP* 2.9 29.1 + - - +
971C VAL* 3.8 44.3 - - + +
975C THR* 4.6 4.0 - - - +
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Residues in contact with VAL 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832C ILE* 4.4 7.2 - - + -
834C TYR* 3.8 20.4 - - + +
854C ILE 3.1 13.2 + - - +
855C LEU 3.1 6.4 - - - +
856C LYS 3.3 0.6 - - - -
857C ARG* 1.3 83.4 - - - +
859C PRO* 1.3 69.2 - - + +
860C ASN* 4.4 4.0 - - + +
861C SER* 2.6 44.4 + - - +
889C ARG* 3.5 0.2 + - - -
971C VAL* 3.8 27.4 - - + +
974C GLY* 3.5 23.1 - - - +
975C THR* 3.9 9.6 - - + -
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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