Contacts of the helix formed by residues 750 - 754 (chain B) in PDB entry 1B0P
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 ASN 750 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698B VAL* 3.8 20.4 - - + +
700B PRO* 4.1 5.9 - - + +
748B CYS* 3.4 23.1 - - - -
749B GLY* 1.3 75.0 - - - +
751B CYS* 1.3 56.9 + - - +
753B ASP* 3.3 2.3 + - - +
754B ILE* 2.9 33.1 + - - +
814B GLY* 3.8 8.3 - - - +
1080B MET 3.1 15.4 + - - +
1081B GLY 3.2 17.9 + - - -
1083B SER* 3.3 12.3 + - - +
1084B GLN* 3.2 36.5 - - + +
1234B SF4 4.1 2.0 - - - -
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Residues in contact with CYS 751 (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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682B PRO* 3.7 26.7 - - - -
695B CYS* 3.9 10.0 - - + +
698B VAL* 3.9 8.0 - - - +
704B ILE* 3.6 14.8 - - + -
749B GLY 3.1 0.6 - - - -
750B ASN* 1.3 77.0 - - - +
752B ALA* 1.3 69.9 - - - +
754B ILE* 3.1 4.4 + - - +
755B CYS* 2.9 29.1 + - - +
762B LEU* 3.6 20.9 - - + +
764B MET* 4.2 1.6 - - - -
1234B SF4 2.3 42.6 - - - -
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Residues in contact with ALA 752 (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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1222A GLN* 3.7 12.8 - - + +
749B GLY 3.2 0.8 + - - -
751B CYS* 1.3 81.0 - - - +
753B ASP* 1.3 61.6 + - - +
754B ILE 3.4 0.5 + - - -
755B CYS* 3.6 1.3 + - - -
760B LYS* 3.3 28.2 + - - +
762B LEU* 3.6 32.5 - - + +
764B MET* 3.5 31.6 - - + +
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Residues in contact with ASP 753 (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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1219A THR* 4.6 2.4 + - - +
1221A GLU* 5.2 1.9 - - - +
1222A GLN* 3.5 11.9 + - - +
749B GLY 2.9 16.7 + - - +
750B ASN 3.5 3.6 - - - +
752B ALA* 1.3 78.0 - - - +
754B ILE* 1.3 68.9 + - + +
760B LYS* 3.5 12.2 + - - +
1081B GLY 3.5 21.3 - - - +
1082B LYS* 2.8 38.5 + - - +
1085B ASP* 4.1 10.2 + - - +
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Residues in contact with ILE 754 (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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694B GLN* 3.9 42.7 - - + +
695B CYS 4.4 0.7 - - - +
698B VAL* 4.3 12.3 - - + -
750B ASN* 2.9 14.2 + - - +
751B CYS 3.1 5.8 + - - +
753B ASP* 1.3 96.7 - - - +
755B CYS* 1.3 69.6 + - - +
756B PRO* 2.8 11.3 - - - +
760B LYS* 4.1 0.6 + - - -
1046B LYS* 4.8 7.0 - - - +
1084B GLN* 3.3 37.9 - - + +
1085B ASP* 4.4 6.5 - - + +
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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