Contacts of the helix formed by residues 926 - 937 (chain B) in PDB entry 4YZ9
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 PRO 926 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836B GLU* 3.5 37.5 - - + +
839B LEU* 3.2 26.0 - - + +
925B LEU* 1.3 102.2 - - + +
927B ASP* 1.3 70.2 + - - +
928B ASP 3.4 1.1 - - - -
929B PHE* 3.2 2.5 + - + +
930B VAL* 2.8 33.2 + - - +
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Residues in contact with ASP 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B LEU* 3.4 34.1 - - + +
836B GLU* 3.9 5.0 + - - +
924B SER* 5.4 2.5 - - - +
925B LEU 3.1 4.1 - - - +
926B PRO* 1.3 93.3 - - - +
928B ASP* 1.3 64.5 + - - +
930B VAL* 3.2 11.6 - - - +
931B CYS* 3.0 32.5 + - - +
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Residues in contact with ASP 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921B THR 5.1 3.2 - - - +
922B LEU* 4.0 9.2 - - - +
923B GLY 4.8 0.8 + - - +
924B SER* 3.0 40.4 + - - +
925B LEU 4.1 2.0 - - - +
926B PRO 3.4 0.2 - - - -
927B ASP* 1.3 80.2 - - - +
929B PHE* 1.3 60.5 + - - +
931B CYS* 3.7 7.3 - - - +
932B TYR* 2.9 30.1 + - - +
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Residues in contact with PHE 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839B LEU* 3.4 33.7 - - + -
904B MET* 3.3 28.9 - - + -
907B LYS* 4.2 8.3 - - + -
908B LYS* 3.6 24.7 - - + -
911B TYR* 4.4 11.7 - + - -
922B LEU* 3.5 52.4 + - + +
925B LEU* 4.3 11.8 - - + +
926B PRO* 3.2 13.1 + - + +
928B ASP* 1.3 78.7 - - - +
930B VAL* 1.3 61.9 + - - +
932B TYR* 3.3 8.2 + - - +
933B PHE* 3.2 44.8 - + - -
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Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B LEU* 3.6 35.2 - - + +
838B GLN* 4.2 11.4 - - + +
839B LEU* 3.7 37.5 - - + +
842B PHE* 4.4 15.5 - - + -
904B MET* 5.7 1.1 - - + -
926B PRO 2.8 18.1 + - - +
927B ASP 3.2 14.1 - - - +
929B PHE* 1.3 77.1 - - - +
931B CYS* 1.3 64.3 + - - +
933B PHE* 3.3 6.5 + - - +
934B THR* 2.8 30.8 + - + +
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Residues in contact with CYS 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B GLU* 5.5 7.0 - - - -
835B LEU* 3.9 28.5 - - - -
927B ASP 3.0 22.6 + - - +
928B ASP* 3.7 9.2 - - - +
929B PHE 3.3 0.2 - - - -
930B VAL* 1.3 75.6 - - - +
932B TYR* 1.3 66.5 + - - +
934B THR* 3.2 8.5 + - - -
935B SER* 3.1 27.9 + - - -
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Residues in contact with TYR 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B ILE* 3.3 25.7 - - + +
879B THR* 3.0 43.2 + - + +
882B LEU* 3.7 14.5 - - + +
921B THR* 4.1 15.3 - - - +
922B LEU* 3.1 33.4 - - + -
928B ASP 2.9 11.6 + - - +
929B PHE 3.5 10.1 - - - +
930B VAL 3.2 0.2 - - - -
931B CYS* 1.3 78.0 - - - +
933B PHE* 1.3 77.2 + + - +
935B SER* 3.2 6.2 + - - -
936B ARG* 2.7 65.8 + - - +
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Residues in contact with PHE 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874B TRP* 6.3 1.1 - + - -
878B ILE* 4.9 4.0 - - + -
882B LEU* 4.6 15.0 - - + -
900B LEU* 4.4 15.0 - - + -
903B ALA* 5.3 2.2 - - + -
904B MET* 3.4 55.9 - - + -
907B LYS* 5.3 4.5 - - + -
922B LEU* 4.6 4.5 - - + -
929B PHE* 3.2 54.7 - + - -
930B VAL* 3.3 4.2 + - - +
931B CYS 3.3 0.4 - - - -
932B TYR* 1.3 101.6 - + - +
934B THR* 1.3 62.3 + - + +
936B ARG* 3.3 1.9 + - - +
937B PHE* 3.0 43.2 + + + +
940B LEU* 4.8 6.4 - - + +
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Residues in contact with THR 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B HIS* 3.5 45.9 + - + +
801B GLU* 5.3 2.1 + - - -
835B LEU* 6.0 0.9 - - - +
838B GLN* 4.4 5.6 - - - +
842B PHE* 4.2 26.5 - - + -
930B VAL* 2.8 24.7 + - + +
931B CYS* 3.2 15.9 + - - -
933B PHE* 1.3 75.9 - - - +
935B SER* 1.3 60.6 + - - +
937B PHE 4.0 6.1 - - - +
938B PRO* 3.2 27.0 - - - +
940B LEU* 5.7 1.8 - - + -
941B LEU 5.6 0.4 - - - +
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Residues in contact with SER 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B GLU 4.6 6.8 - - - +
800B HIS* 5.1 4.7 - - - +
871B LYS* 5.4 0.7 + - - -
931B CYS 3.1 19.7 + - - -
932B TYR* 4.2 0.2 - - - -
934B THR* 1.3 79.2 + - - +
936B ARG* 1.3 84.5 + - - +
938B PRO* 4.0 6.8 - - - +
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Residues in contact with ARG 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B LYS* 3.2 29.8 + - - +
877B ASN* 4.0 30.4 + - + +
878B ILE* 4.2 8.9 - - - +
879B THR* 4.5 8.3 - - - +
932B TYR* 2.7 79.9 + - - +
933B PHE* 3.3 4.1 + - - +
935B SER* 1.3 98.4 + - - +
937B PHE* 1.3 79.4 + - + +
938B PRO* 3.5 0.6 - - - +
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Residues in contact with PHE 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B HIS* 4.9 0.7 - - - -
869B VAL 3.7 17.7 - - - +
870B VAL* 3.2 31.2 - - - -
871B LYS* 4.5 5.4 - - + +
874B TRP* 3.4 35.4 - - + -
877B ASN* 4.0 19.1 - - + -
878B ILE* 5.0 7.0 - - + -
900B LEU* 4.2 22.2 - - + -
933B PHE* 3.0 24.8 + + + +
934B THR* 3.3 8.8 - - - +
936B ARG* 1.3 94.7 - - + +
938B PRO* 1.3 67.5 - - - +
939B HIS 3.1 2.7 - - - -
940B LEU* 3.0 32.9 + - + +
941B LEU 4.7 0.2 + - - -
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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