Contacts of the helix formed by residues 931 - 941 (chain C) in PDB entry 5C0V
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 931 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898C GLN* 2.5 26.8 + - + +
902C VAL* 5.0 8.2 - - + +
929C ASP 3.8 1.0 + - - -
930C ILE* 1.3 71.9 - - - +
932C PRO* 1.3 68.8 - - - +
933C LYS* 2.8 41.4 + - - +
934C LEU* 3.0 17.7 + - + +
935C GLN* 2.9 24.1 + - - +
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Residues in contact with PRO 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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929C ASP* 5.8 0.9 - - - +
930C ILE 3.2 7.6 - - - +
931C ASP* 1.3 91.8 - - - +
933C LYS* 1.3 61.3 + - - +
935C GLN* 3.3 11.5 + - + +
936C GLU* 3.2 26.9 + - - +
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Residues in contact with LYS 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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902C VAL* 3.8 15.5 - - + +
906C GLU* 2.7 33.8 + - - +
931C ASP* 2.8 20.2 + - - +
932C PRO* 1.3 74.6 - - - +
934C LEU* 1.3 60.9 + - - +
936C GLU* 3.2 13.6 + - + +
937C TYR* 3.0 49.6 + - + +
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Residues in contact with LEU 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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898C GLN* 3.7 34.5 - - + +
901C THR* 3.7 24.7 - - + -
902C VAL* 4.2 12.7 - - + +
913C LEU* 3.7 15.9 - - + -
916C PHE* 3.6 40.6 - - + -
930C ILE* 4.2 2.5 - - + -
931C ASP* 3.0 17.6 + - + +
933C LYS* 1.3 76.8 - - - +
935C GLN* 1.3 66.1 + - - +
937C TYR* 3.1 9.9 + - + -
938C LEU* 2.9 33.4 + - + +
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Residues in contact with GLN 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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928C LEU 5.7 0.8 + - - -
930C ILE* 3.6 45.6 + - + +
931C ASP 2.9 18.2 + - - +
932C PRO* 3.3 13.2 + - + +
934C LEU* 1.3 75.7 - - - +
936C GLU* 1.3 63.8 + - + +
938C LEU* 3.5 10.7 + - - +
939C GLY* 3.1 18.2 + - - -
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Residues in contact with GLU 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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932C PRO* 3.2 17.0 - - - +
933C LYS* 3.3 11.4 - - - +
934C LEU 3.1 0.6 - - - -
935C GLN* 1.3 75.2 - - + +
937C TYR* 1.3 65.1 + - + +
939C GLY* 2.7 27.4 + - - -
940C LYS* 3.3 5.7 + - - +
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Residues in contact with TYR 937 (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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902C VAL* 4.4 9.4 - - + -
905C TYR* 3.3 52.2 - + + -
906C GLU* 2.9 33.5 + - + +
913C LEU* 3.7 25.4 - - + +
933C LYS* 3.0 42.9 + - + +
934C LEU* 3.5 18.4 - - + +
936C GLU* 1.3 81.6 - - + +
938C LEU* 1.3 61.5 + - - +
940C LYS* 3.3 14.4 + - - +
941C PHE 3.6 6.4 + - - -
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Residues in contact with LEU 938 (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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913C LEU* 3.7 24.7 - - + +
916C PHE* 3.8 17.0 - - + -
917C TRP* 4.0 42.8 - - + +
920C LEU* 3.8 25.4 - - + -
930C ILE* 4.8 2.5 - - + -
934C LEU* 2.9 25.8 + - + +
935C GLN* 3.6 15.7 - - - +
937C TYR* 1.3 74.6 - - - +
939C GLY* 1.3 64.4 + - - +
941C PHE* 3.2 24.0 + - + +
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Residues in contact with GLY 939 (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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935C GLN 3.1 9.9 + - - -
936C GLU* 2.7 17.8 + - - -
938C LEU* 1.3 73.1 - - - +
940C LYS* 1.3 57.4 + - - -
941C PHE 3.5 3.5 + - - +
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Residues in contact with LYS 940 (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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823A GLU* 5.7 1.6 + - - -
833A GLN* 3.7 43.9 - - + +
834A GLU* 5.4 9.9 - - - +
837A THR* 5.3 4.9 + - - -
905C TYR* 4.2 9.2 - - - +
936C GLU 3.3 7.1 + - - +
937C TYR* 3.3 9.4 + - - +
938C LEU 3.2 0.8 - - - -
939C GLY* 1.3 75.7 - - - +
941C PHE* 1.3 63.4 + - - +
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Residues in contact with PHE 941 (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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833A GLN* 5.9 0.9 - - - -
840A ARG* 4.6 21.5 - - - -
872A TYR* 4.3 15.7 - + - -
910C LEU* 4.3 22.2 - - + -
913C LEU* 3.9 28.3 - - + -
914C GLU* 3.7 48.2 - - + -
917C TRP* 4.0 43.6 + + + -
937C TYR 3.6 1.6 + - - +
938C LEU* 3.2 20.0 + - + +
939C GLY 4.3 3.3 - - - +
940C LYS* 1.3 82.0 - - - +
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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