Contacts of the helix formed by residues 970 - 976 (chain B) in PDB entry 5IYB
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 HIS 970 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A GLN* 3.6 38.4 - - - +
540A ASP* 3.1 26.9 - - - -
543A THR* 2.9 21.5 + - - -
685A HIS* 3.4 23.3 - + - -
769A MET* 3.4 19.2 - - + +
774A ALA* 3.7 21.1 - - + -
775A LYS* 4.0 16.5 - - + +
968B ASN* 2.9 22.7 + - - +
969B PRO* 1.3 74.3 - - - +
971B ALA* 1.3 64.6 + - - +
972B ILE 3.1 0.4 - - - -
973B PRO* 3.3 13.1 - - - +
974B SER* 4.4 5.5 + - - -
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Residues in contact with ALA 971 (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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792B ASP* 4.9 12.6 - - - +
941B GLN* 3.7 23.3 + - + +
967B ILE* 4.6 14.8 - - + -
968B ASN* 3.0 19.0 + - + +
970B HIS* 1.3 79.9 - - - +
972B ILE* 1.3 60.1 + - + +
975B ARG* 3.0 43.7 - - - +
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Residues in contact with ILE 972 (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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687A ILE* 3.8 26.7 - - + -
766A PHE* 5.4 2.2 - - + -
782B ILE* 5.1 6.5 - - + -
941B GLN* 4.3 7.2 - - + +
967B ILE* 6.2 2.9 - - + -
968B ASN 5.2 0.9 - - - +
969B PRO* 2.9 18.9 + - + +
971B ALA* 1.3 82.9 - - + +
973B PRO* 1.4 57.4 - - + +
975B ARG* 5.0 0.2 - - - -
976B MET* 2.6 34.7 + - - -
977B THR* 3.7 31.6 - - - +
978B ILE* 4.9 9.0 - - + -
980B HIS* 4.3 17.0 - - + +
981B LEU* 4.2 28.9 - - + -
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Residues in contact with PRO 973 (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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687A ILE* 4.3 0.2 - - + -
766A PHE* 4.2 29.0 - - + -
769A MET* 3.8 31.2 - - + -
770A VAL* 5.9 0.9 - - + -
775A LYS* 4.1 20.0 - - + +
776A GLY* 4.5 3.1 - - - -
780A ASN* 3.5 13.9 - - - +
969B PRO 3.2 14.1 - - - +
970B HIS 3.3 11.9 - - - +
972B ILE* 1.4 92.7 - - + +
974B SER* 1.3 64.9 + - - +
976B MET* 3.3 17.0 - - + +
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Residues in contact with SER 974 (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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775A LYS* 3.1 36.5 + - - -
776A GLY* 3.9 14.1 - - - -
780A ASN* 3.7 21.9 + - - +
718B GLN* 5.0 1.4 - - - +
721B ARG* 5.5 0.3 + - - -
970B HIS 4.4 2.6 + - - -
972B ILE 3.7 0.2 - - - -
973B PRO* 1.3 83.0 - - - +
975B ARG* 1.3 72.5 + - - +
976B MET* 3.7 6.2 + - - +
279U ARG* 5.0 21.3 + - - +
284U PRO* 6.0 1.3 - - - -
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Residues in contact with ARG 975 (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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497A ASP* 5.2 3.6 + - - +
718B GLN* 3.1 21.3 - - - +
721B ARG* 3.6 39.4 + - - +
792B ASP* 2.8 40.8 + - - -
940B GLY 5.6 1.3 - - - -
941B GLN* 3.0 25.5 + - - +
942B LYS 5.6 2.8 + - - -
970B HIS 5.4 0.2 - - - +
971B ALA* 3.0 29.7 + - - +
972B ILE 3.5 0.6 + - - +
974B SER* 1.3 87.5 + - - +
976B MET* 1.3 68.5 + - - +
977B THR* 3.2 7.0 + - + +
279U ARG* 3.3 42.7 - - + +
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Residues in contact with MET 976 (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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780A ASN* 2.9 40.4 - - - +
783A GLN* 3.7 18.8 - - - +
784A VAL* 4.0 10.8 - - + -
827A TYR* 3.8 21.0 - - + -
716B HIS 3.8 1.6 - - - +
718B GLN* 3.2 50.8 + - + +
972B ILE 2.6 19.7 + - - -
973B PRO* 3.3 18.4 - - + +
974B SER 3.9 7.4 - - - +
975B ARG* 1.3 72.6 - - - +
977B THR* 1.3 59.5 + - - +
978B ILE* 3.3 20.0 + - + +
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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