Contacts of the helix formed by residues 925 - 937 (chain C) in PDB entry 1U6G
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 LEU 925 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888C LEU* 4.1 10.5 - - + -
892C LEU* 4.1 26.0 - - + -
916C ILE* 4.2 13.0 - - + -
917C ILE* 3.8 33.7 - - + +
920C ALA* 4.6 4.3 - - + -
921C SER 4.1 19.3 - - - +
922C VAL* 4.0 5.5 - - - +
923C VAL 3.0 1.2 - - - +
924C GLY* 1.3 78.0 - - - +
926C LYS* 1.3 68.8 + - - +
927C PRO* 2.8 5.0 - - - -
928C TYR* 2.9 16.5 + - + -
929C VAL* 3.0 17.5 + - + -
932C ILE* 5.1 6.7 - - + -
958C LEU* 5.0 1.6 - - + -
961C ILE* 3.7 25.6 - - + -
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Residues in contact with LYS 926 (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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922C VAL 3.7 13.7 + - - +
923C VAL* 3.7 6.4 + - - +
925C LEU* 1.3 73.1 - - - +
927C PRO* 1.3 76.4 - - + +
929C VAL* 3.0 35.6 + - + +
930C GLU* 4.1 9.3 + - - +
961C ILE* 4.8 16.5 + - + +
962C ASP* 3.6 30.8 + - + +
966C LEU* 6.1 1.2 - - - +
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Residues in contact with PRO 927 (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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923C VAL 3.1 19.5 - - - +
924C GLY* 3.8 7.6 - - - +
925C LEU 3.1 4.7 - - - -
926C LYS* 1.3 96.9 - - + +
928C TYR* 1.3 78.1 + - + +
929C VAL 3.1 0.2 + - - -
930C GLU* 3.8 13.0 + - - +
931C ASN* 4.6 1.9 + - - +
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Residues in contact with TYR 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C LEU* 4.3 7.6 - - + -
889C PRO* 3.0 34.6 - - + +
892C LEU* 3.4 38.1 - - + -
893C PRO* 4.1 24.7 - - + -
896C LEU* 5.7 1.8 - - + -
924C GLY 3.4 25.4 - - - -
925C LEU* 2.9 8.5 + - + +
927C PRO* 1.3 87.2 - - + +
929C VAL* 1.3 55.4 + - - +
930C GLU 3.3 0.7 - - - -
931C ASN* 2.7 37.7 + - + +
932C ILE* 2.7 23.1 + - + +
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Residues in contact with VAL 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925C LEU* 3.0 18.9 + - + +
926C LYS* 3.0 35.7 + - + +
928C TYR* 1.3 74.9 - - - +
930C GLU* 1.3 77.5 + - + +
931C ASN 2.9 1.9 + - - -
932C ILE* 3.7 7.3 - - - +
933C TRP* 3.0 29.7 + - + +
958C LEU* 3.9 26.1 - - + +
961C ILE* 4.2 22.9 - - + +
966C LEU* 5.2 15.0 - - + -
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Residues in contact with GLU 930 (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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926C LYS* 5.4 7.8 + - - +
927C PRO 3.8 9.4 + - - +
928C TYR 3.3 0.6 - - - -
929C VAL* 1.3 87.4 - - + +
931C ASN* 1.3 63.5 + - - +
933C TRP* 4.1 5.0 - - - +
934C ALA* 3.5 18.5 + - - +
966C LEU* 6.1 0.5 - - - +
969C ARG* 3.8 31.8 + - - -
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Residues in contact with ASN 931 (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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896C LEU* 4.3 19.5 - - + +
927C PRO 4.6 1.9 + - - +
928C TYR* 2.7 23.9 + - + +
930C GLU* 1.3 79.8 - - - +
932C ILE* 1.3 69.9 + - - +
934C ALA* 2.9 15.2 + - - +
935C LEU* 3.1 10.7 + - - +
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Residues in contact with ILE 932 (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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892C LEU* 3.6 21.8 - - + -
896C LEU* 3.6 27.6 - - + -
913C LEU* 3.7 35.9 - - + -
916C ILE* 6.2 0.4 - - + -
917C ILE* 3.8 15.9 - - + -
925C LEU* 5.1 7.6 - - + -
928C TYR* 2.7 38.0 + - + +
929C VAL* 3.7 7.2 - - - +
931C ASN* 1.3 69.7 - - - +
933C TRP* 1.3 56.6 + - - +
935C LEU* 2.7 28.5 + - - +
936C LEU* 3.0 14.7 + - + -
958C LEU* 3.7 12.1 - - + -
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Residues in contact with TRP 933 (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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929C VAL* 3.0 18.0 + - + +
930C GLU* 4.1 7.9 - - - +
932C ILE* 1.3 79.4 - - - +
934C ALA* 1.3 57.9 + - - +
936C LEU* 3.3 5.5 + - - +
937C LEU* 3.0 75.7 + - + +
955C LEU* 3.6 33.4 - - + -
958C LEU* 3.6 31.5 - - + +
959C THR* 3.7 16.8 - - - -
966C LEU* 3.3 35.7 - - + -
969C ARG* 3.4 36.0 - - + +
970C LEU* 3.8 31.2 - - + -
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Residues in contact with ALA 934 (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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930C GLU 3.5 12.8 + - - +
931C ASN* 2.9 12.6 + - - +
933C TRP* 1.3 80.2 - - - +
935C LEU* 1.3 62.5 + - - +
937C LEU* 3.6 15.7 + - - +
938C LYS* 3.2 23.2 + - - +
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Residues in contact with LEU 935 (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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896C LEU* 4.2 25.6 - - + +
899C ILE* 3.4 27.8 - - + -
900C THR* 3.6 26.5 - - + +
910C LEU* 4.9 4.0 - - + -
913C LEU* 4.8 4.5 - - + -
931C ASN 3.1 8.7 + - - +
932C ILE* 2.7 18.6 + - - +
934C ALA* 1.3 74.0 - - - +
936C LEU* 1.3 58.4 + - + +
938C LYS* 3.4 17.6 + - - +
939C HIS* 3.1 66.9 + - + +
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Residues in contact with LEU 936 (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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910C LEU* 4.0 20.9 - - + -
913C LEU* 4.8 5.6 - - + -
932C ILE* 3.0 20.6 + - + +
933C TRP 3.8 4.3 - - - +
935C LEU* 1.3 77.2 - - + +
937C LEU* 1.3 58.5 + - - +
938C LYS 3.2 5.1 + - - -
939C HIS* 3.8 5.7 + - + +
940C CYS* 4.0 8.1 - - - -
951C VAL* 3.3 40.9 - - + +
954C CYS* 3.3 45.3 - - + -
955C LEU* 3.6 20.9 - - + +
958C LEU* 4.0 22.7 - - + -
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Residues in contact with LEU 937 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933C TRP* 3.0 58.6 + - + +
934C ALA* 3.6 8.5 + - - +
935C LEU 3.3 0.4 - - - -
936C LEU* 1.3 76.5 - - - +
938C LYS* 1.3 58.3 + - - +
940C CYS* 4.2 14.8 - - - +
955C LEU* 4.4 14.8 - - + -
969C ARG* 5.1 0.9 - - - +
970C LEU* 5.3 2.7 - - + -
973C TYR* 3.0 50.2 - - + +
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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