Contacts of the helix formed by residues 895 - 910 (chain C) in PDB entry 3H2U
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 895 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C ILE* 1.3 72.1 - - - +
896C GLN* 1.3 57.5 + - - +
897C PRO* 3.2 15.7 - - - +
898C MET* 2.9 50.7 - - + +
899C MET* 3.1 21.8 + - - +
934C SER* 2.9 24.1 + - - +
937C VAL* 3.8 18.1 - - + +
938C ARG* 3.9 3.9 - - + +
1020C THR* 4.2 10.9 - - - +
1024C VAL* 3.5 23.0 - - - +
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Residues in contact with GLN 896 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C GLU 5.6 1.2 - - - +
894C ILE* 3.7 30.2 + - + +
895C ASN* 1.3 68.3 - - - +
897C PRO* 1.3 70.4 - - + +
898C MET 3.1 2.0 - - - -
899C MET* 3.4 5.0 + - - +
900C MET* 2.8 30.3 + - - +
938C ARG* 5.2 1.7 + - - -
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Residues in contact with PRO 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ASN* 3.2 16.4 - - - +
896C GLN* 1.3 97.8 - - + +
898C MET* 1.3 55.4 + - - +
900C MET* 3.2 8.0 - - + +
901C ALA* 2.9 27.4 + - - +
1024C VAL* 3.7 13.2 - - + -
1028C GLN* 3.6 27.1 + - - +
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Residues in contact with MET 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ASN* 2.9 39.2 - - + +
897C PRO* 1.3 73.8 - - - +
899C MET* 1.3 60.7 + - - +
900C MET 3.0 1.3 - - - -
901C ALA* 3.2 7.1 + - - +
902C ALA* 2.9 28.5 + - - +
930C MET* 3.7 20.9 - - - +
933C MET* 3.5 38.1 - - + +
934C SER* 3.9 18.2 - - - -
937C VAL* 4.3 9.4 - - + -
1023C LEU* 3.9 19.7 - - + +
1024C VAL* 4.1 18.8 - - + +
1027C ALA* 3.7 16.6 - - + -
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Residues in contact with MET 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C PHE* 3.7 17.4 - - - -
892C GLU* 5.3 0.4 - - - +
894C ILE* 3.8 29.2 - - + -
895C ASN 3.1 15.9 + - - +
896C GLN* 3.4 3.8 + - - +
898C MET* 1.3 80.7 - - - +
900C MET* 1.3 56.1 + - - +
902C ALA* 3.5 4.6 - - - +
903C ARG* 2.8 47.0 + - - +
931C ALA* 3.7 37.2 - - + +
934C SER* 3.4 23.9 - - - +
935C ARG* 4.2 8.7 - - - +
92D TYR* 3.9 24.2 - - + +
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Residues in contact with MET 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896C GLN 2.8 18.5 + - - +
897C PRO* 3.2 11.2 - - + +
899C MET* 1.3 76.4 - - - +
901C ALA* 1.3 60.5 + - - +
902C ALA 3.1 0.2 - - - -
903C ARG* 3.2 26.9 + - + +
904C GLN* 2.8 77.1 + - - +
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Residues in contact with ALA 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897C PRO 2.9 16.8 + - - +
898C MET* 3.6 7.2 - - - +
900C MET* 1.3 75.1 - - - +
902C ALA* 1.3 62.6 - - - +
904C GLN* 3.3 13.9 + - - +
905C LEU 3.2 17.0 + - - -
930C MET* 5.4 0.4 - - + -
1027C ALA* 4.1 9.0 - - + +
1028C GLN* 4.3 16.8 - - + +
1031C MET* 3.3 32.3 - - + +
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Residues in contact with ALA 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C PHE* 4.7 4.5 - - + -
898C MET 2.9 16.9 + - - +
899C MET* 3.5 10.5 - - - +
901C ALA* 1.3 75.3 - - - +
903C ARG* 1.3 65.2 + - - +
905C LEU* 3.1 4.3 + - - +
906C HIS* 2.9 24.5 + - - +
927C ALA* 3.7 23.8 - - - +
930C MET* 3.9 10.1 - - + -
931C ALA* 4.1 11.0 - - + +
1031C MET* 3.9 12.1 - - - +
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Residues in contact with ARG 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C GLU* 5.8 0.2 - - - -
885C PHE* 3.3 35.3 + - + -
886C PRO 3.2 27.9 + - - -
887C GLU* 3.2 24.9 - - - +
888C GLN 4.5 4.4 - - - +
894C ILE* 6.1 0.4 - - - +
899C MET* 2.8 36.6 + - - +
900C MET* 3.2 29.2 + - + +
902C ALA* 1.3 75.4 - - - +
904C GLN* 1.3 62.5 + - - +
906C HIS* 3.2 6.9 + - - +
907C ASP* 2.8 48.5 + - - +
92D TYR* 5.2 2.0 + - - -
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Residues in contact with GLN 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900C MET* 2.8 64.1 + - - +
901C ALA* 3.3 13.7 - - - +
902C ALA 3.2 0.2 - - - -
903C ARG* 1.3 78.0 - - - +
905C LEU* 1.3 63.6 + - - +
907C ASP* 3.4 6.3 + - - +
908C GLU 3.2 17.2 + - - -
1031C MET* 5.6 2.5 - - + +
1032C GLN* 5.2 7.0 - - - +
1035C LYS* 3.7 30.3 + - + +
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Residues in contact with LEU 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C ALA 3.2 2.9 + - - +
902C ALA 3.1 8.1 + - - +
904C GLN* 1.3 78.7 - - - +
906C HIS* 1.3 64.7 + - - +
908C GLU* 3.1 5.5 + - + -
909C ALA* 3.1 23.6 + - + +
923C ALA* 4.0 27.4 - - + +
926C MET* 4.3 4.3 - - + -
927C ALA* 4.2 3.6 - - + -
1031C MET* 3.7 40.8 + - + +
1034C VAL* 3.3 36.1 - - + -
1035C LYS* 3.8 31.2 - - + +
1038C VAL* 5.1 2.0 - - + -
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Residues in contact with HIS 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883C GLU* 4.2 22.9 + - + -
884C GLU* 3.6 10.1 - - - -
885C PHE* 2.8 59.1 - + + +
902C ALA 2.9 15.0 + - - +
903C ARG 3.6 3.4 - - - +
905C LEU* 1.3 76.9 - - - +
907C ASP* 1.3 57.4 + - - +
909C ALA* 4.2 2.9 - - - +
910C ARG* 2.8 67.9 + - + +
924C LYS* 5.2 13.4 - - + +
927C ALA* 3.7 16.9 - - + +
928C LEU* 4.7 7.2 - - + +
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Residues in contact with ASP 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C GLU* 4.1 4.3 - - - +
885C PHE* 4.5 0.7 - - - +
903C ARG* 2.8 42.8 + - - +
904C GLN* 3.9 6.7 + - - +
906C HIS* 1.3 74.5 + - - +
908C GLU* 1.3 67.0 + - - +
910C ARG* 2.9 43.1 + - - +
911C LYS* 3.5 16.0 - - - +
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Residues in contact with GLU 908 (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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904C GLN 3.2 6.5 + - - +
905C LEU* 3.1 7.2 + - + +
907C ASP* 1.3 77.2 - - - +
909C ALA* 1.3 59.3 + - - +
911C LYS* 2.9 63.8 + - - +
912C TRP* 3.8 10.0 + - - -
1035C LYS* 3.6 36.8 + - + +
1038C VAL* 3.7 24.4 - - + +
1039C ARG* 3.0 39.1 - - + +
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Residues in contact with ALA 909 (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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905C LEU* 3.1 15.2 + - + +
906C HIS* 4.2 2.0 - - - +
908C GLU* 1.3 82.2 - - + +
910C ARG* 1.3 56.0 + - - +
911C LYS 3.2 1.3 - - - -
912C TRP* 3.0 16.4 + - - +
920C ILE* 3.5 27.8 - - + +
923C ALA* 4.3 18.6 - - + -
924C LYS* 3.3 35.7 - - + +
1038C VAL* 5.3 1.1 - - + -
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Residues in contact with ARG 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883C GLU 3.1 31.7 + - - +
884C GLU* 3.4 34.5 + - - +
906C HIS* 2.8 42.7 + - + +
907C ASP* 2.9 39.6 + - - +
908C GLU 3.1 1.2 - - - -
909C ALA* 1.3 74.2 - - - +
911C LYS* 1.3 63.2 + - + +
912C TRP 3.1 5.2 + - - +
924C LYS* 4.5 9.1 + - + +
1061C LYS* 4.1 14.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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