Contacts of the helix formed by residues 937 - 949 (chain M) in PDB entry 2O5J
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 937 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179K PHE 3.3 5.3 - - - +
180K GLN* 2.7 35.5 + - - +
181K VAL* 2.6 35.5 + - - +
182K GLU* 4.9 0.4 - - - -
183K ASP* 5.2 1.3 - - - -
936M VAL* 1.3 72.6 - - - +
938M LYS* 1.3 56.6 + - - +
939M ARG* 2.8 26.3 - - - +
940M GLU* 3.3 24.5 + - + +
941M VAL* 3.0 32.7 + - - +
975M TYR* 2.8 18.9 + - - +
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Residues in contact with LYS 938 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 2.9 49.4 - - - +
181K VAL* 2.5 25.7 + - - +
182K GLU 4.8 1.8 + - - -
183K ASP* 4.5 16.2 - - + +
192K LEU 3.9 6.6 + - - +
193K ASP* 2.6 48.3 + - - +
937M ASP* 1.3 73.9 + - - +
939M ARG* 1.3 69.5 - - - +
941M VAL* 3.5 4.5 + - - +
942M GLU* 2.5 48.8 + - + +
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Residues in contact with ARG 939 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 4.3 2.6 - - - +
31K GLY* 4.3 5.7 - - - -
34K VAL* 2.9 52.8 - - - +
179K PHE* 4.4 4.0 - - + -
181K VAL* 3.0 31.3 - - + +
193K ASP* 3.7 8.9 + - - -
42L ARG* 4.8 2.6 - - - +
937M ASP* 2.8 24.5 - - - +
938M LYS* 1.3 104.0 - - - +
940M GLU* 1.3 59.4 + - - +
942M GLU* 3.0 21.5 + - - +
943M VAL* 2.9 31.8 + - - +
975M TYR* 3.5 17.5 - - + -
980M GLY 4.1 8.1 - - - -
981M GLU* 5.1 2.6 + - - -
982M PRO* 3.3 30.0 - - + +
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Residues in contact with GLU 940 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K GLN* 2.9 22.9 - - - +
862M PRO* 3.5 15.1 - - + +
926M PHE* 4.8 2.1 - - - -
929M ARG* 3.4 16.1 + - - -
935M GLY 4.1 0.2 - - - +
936M VAL* 3.4 17.7 - - + +
937M ASP* 3.3 15.1 + - + +
939M ARG* 1.3 79.1 - - - +
941M VAL* 1.3 59.5 + - - +
943M VAL* 2.8 24.3 - - - +
944M LEU* 3.4 15.3 + - + +
963M LEU* 4.3 17.7 - - + +
973M VAL* 4.6 17.9 - - + -
975M TYR* 2.7 24.9 + - + +
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Residues in contact with VAL 941 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K ASP* 5.4 6.5 - - - +
936M VAL* 3.6 26.0 - - + -
937M ASP 3.0 19.7 + - - +
938M LYS* 4.0 4.7 - - - +
940M GLU* 1.3 76.2 - - - +
942M GLU* 1.3 67.9 + - - +
943M VAL 3.2 0.2 - - - -
944M LEU* 3.0 20.5 + - + +
945M ARG* 3.0 12.6 + - - +
959M PRO* 5.0 15.5 - - + -
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Residues in contact with GLU 942 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 3.5 17.5 + - - -
938M LYS* 2.5 46.5 + - + +
939M ARG* 3.0 20.8 + - - +
941M VAL* 1.3 77.7 - - + +
943M VAL* 1.3 61.0 + - - +
945M ARG* 3.1 24.3 + - - +
946M ARG* 3.4 11.2 + - - +
982M PRO* 5.0 5.9 - - + +
856N GLY* 5.9 2.8 - - - -
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Residues in contact with VAL 943 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939M ARG 2.9 8.7 + - - +
940M GLU 2.8 29.8 - - - +
942M GLU* 1.3 73.6 - - - +
944M LEU* 1.3 62.3 + - + +
946M ARG* 3.7 5.4 + - - +
947M ALA* 2.9 28.6 + - + +
966M LEU* 6.5 0.2 - - + -
973M VAL* 3.3 43.5 - - + -
982M PRO* 5.0 5.1 - - + +
983M ILE 3.9 6.5 - - - +
984M GLU* 5.2 3.6 - - - +
985M GLY 3.4 39.5 + - - +
986M PRO* 4.0 4.7 - - + -
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Residues in contact with LEU 944 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936M VAL* 6.1 0.4 - - + -
940M GLU 3.5 12.3 - - - +
941M VAL* 3.0 18.3 + - + +
943M VAL* 1.3 81.4 - - + +
945M ARG* 1.3 55.0 + - - +
947M ALA* 2.9 5.7 + - - +
948M GLU* 2.7 45.9 + - - +
953M VAL* 4.1 7.9 - - + -
959M PRO* 4.1 25.4 - - + -
962M GLN* 3.4 28.9 - - + -
963M LEU* 3.5 31.0 - - + -
966M LEU* 3.5 22.4 - - + -
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Residues in contact with ARG 945 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941M VAL* 3.0 11.5 + - + +
942M GLU* 3.1 14.3 + - - +
944M LEU* 1.3 74.1 - - - +
946M ARG* 1.3 66.3 + - + +
948M GLU* 3.0 9.3 + - - +
949M LYS* 3.0 54.7 + - + +
827N ILE* 6.4 0.2 - - - +
856N GLY 4.9 10.8 + - - -
857N ILE 5.8 2.4 + - - -
859N ASP* 5.4 4.0 - - - -
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Residues in contact with ARG 946 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942M GLU 3.4 10.3 + - - +
943M VAL* 4.0 8.5 - - - +
945M ARG* 1.3 82.1 - - + +
947M ALA* 1.3 55.6 + - - +
948M GLU 3.4 0.2 - - - -
949M LYS* 3.7 10.4 + - - +
950M LEU* 3.1 46.5 + - - +
984M GLU* 3.4 47.3 + - - +
985M GLY 5.0 4.3 - - - +
791N TYR* 3.7 28.8 + - - -
796N ARG* 4.3 3.1 + - - +
859N ASP* 3.4 28.5 + - - +
861N GLN* 2.7 39.6 + - - +
1017N PHE* 5.4 1.8 - - - -
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Residues in contact with ALA 947 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943M VAL* 2.9 20.2 + - + +
944M LEU* 2.9 12.4 + - - +
946M ARG* 1.3 76.7 - - - +
948M GLU* 1.3 57.2 + - - +
950M LEU* 3.3 13.0 + - - +
951M GLY 3.1 20.8 + - - -
952M LEU* 3.2 12.9 + - + +
953M VAL* 3.7 16.8 - - + +
966M LEU* 4.4 10.3 - - + -
986M PRO* 4.5 15.0 - - + -
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Residues in contact with GLU 948 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944M LEU* 2.7 27.0 + - + +
945M ARG* 3.7 7.9 - - - +
947M ALA* 1.3 69.7 - - - +
949M LYS* 1.3 64.1 + - + +
950M LEU 3.0 5.6 + - - -
951M GLY* 3.5 11.0 + - - +
953M VAL* 3.7 24.7 - - + +
955M PRO* 3.0 39.5 - - + +
956M GLY 3.9 2.9 + - - -
957M LYS 4.5 4.2 - - - +
962M GLN* 2.7 31.4 + - - +
798N GLU* 4.2 4.2 - - - +
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Residues in contact with LYS 949 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945M ARG* 3.0 52.5 + - + +
946M ARG* 3.9 2.5 - - - +
947M ALA 3.3 0.2 - - - -
948M GLU* 1.3 77.5 - - + +
950M LEU* 1.3 57.3 + - - +
796N ARG* 2.9 51.2 + - - +
798N GLU* 3.1 22.4 - - - +
827N ILE* 5.1 15.0 - - - +
828N LYS* 4.9 3.5 + - - +
859N ASP* 2.9 29.7 + - - +
862N ASP* 3.5 14.7 + - - -
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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