Contacts of the helix formed by residues 722 - 728 (chain B) in PDB entry 1OFD
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 LEU 722 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B PRO* 5.7 1.3 - - + -
320B SER* 5.6 10.3 - - - -
325B PRO* 3.5 34.3 - - + -
327B ASP* 4.6 1.4 + - - +
346B ARG* 3.6 31.2 - - - +
515B VAL 4.3 0.4 - - - +
517B SER* 3.5 35.0 - - - +
715B LEU* 3.6 3.4 - - - -
720B ILE* 3.4 6.8 - - - +
721B SER* 1.3 80.4 - - - +
723B LEU* 1.3 64.7 + - - +
724B ALA* 4.0 14.6 - - + +
725B SER* 3.0 21.0 + - - +
726B TYR 3.2 8.5 + - - -
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Residues in contact with LEU 723 (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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517B SER 3.0 17.3 + - - +
518B LEU* 3.7 29.4 - - + +
519B ALA 4.5 0.2 - - - +
520B MET* 3.8 17.7 - - + -
544B PRO* 3.4 39.0 - - + -
657B VAL* 3.8 26.9 - - + -
711B LEU* 4.8 9.4 - - + -
715B LEU* 3.5 31.1 - - + +
722B LEU* 1.3 72.9 - - - +
724B ALA* 1.3 53.3 + - - +
726B TYR* 3.1 4.3 + - + +
727B HIS* 2.8 35.5 + - - +
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Residues in contact with ALA 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.7 0.3 + - - -
320B SER 5.0 10.5 - - - +
324B GLU* 3.3 28.4 - - + +
325B PRO* 5.0 0.2 - - + -
519B ALA 4.4 7.0 + - - +
520B MET* 3.7 16.3 - - - -
521B PHE* 5.6 6.5 - - + -
525B ARG* 4.7 4.8 + - - +
722B LEU* 3.1 14.3 - - + +
723B LEU* 1.3 79.8 - - - +
725B SER* 1.3 57.6 + - - +
727B HIS* 3.5 16.3 - - - +
728B GLY 4.5 1.9 + - - -
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Residues in contact with SER 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 3.7 27.3 - - - +
235B GLY* 5.2 2.6 - - - -
236B ASN* 5.4 0.5 - - - +
239B TRP* 5.4 0.5 + - - -
324B GLU* 3.9 9.7 - - - +
325B PRO* 2.7 46.0 + - - +
327B ASP* 4.4 3.2 + - - +
720B ILE* 4.0 6.1 - - - -
722B LEU* 3.0 13.1 + - - +
724B ALA* 1.3 75.2 - - - +
726B TYR* 1.3 65.6 + - - +
727B HIS 3.1 1.7 + - - -
728B GLY 4.0 3.8 + - - -
729B ALA* 3.5 14.6 - - - +
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Residues in contact with TYR 726 (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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497B GLN* 5.2 0.2 - - - +
654B ALA* 3.4 28.3 - - - +
657B VAL* 4.1 15.0 - - + -
658B GLY* 3.9 7.1 - - - -
714B ILE* 3.4 23.1 - - + +
715B LEU* 3.4 50.0 - - + -
718B MET* 6.0 0.4 - - + -
720B ILE* 4.0 23.8 - - + +
722B LEU 3.2 1.6 + - - +
723B LEU* 3.1 9.5 + - + +
725B SER* 1.3 77.6 - - - +
727B HIS* 1.3 66.1 + - - +
729B ALA* 3.0 22.6 + - - +
731B ILE* 3.8 25.8 + - + +
732B PHE* 3.0 31.3 - + - -
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Residues in contact with HIS 727 (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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239B TRP* 3.4 29.2 - + - -
520B MET* 3.6 19.7 - - + -
525B ARG* 4.2 11.2 - - - -
635B ARG* 3.9 4.8 + - - -
657B VAL* 2.7 34.9 + - + +
658B GLY 3.1 7.4 - - - +
660B GLY* 3.0 40.3 + - - -
661B ALA 3.4 15.6 + - - -
662B SER* 3.5 14.0 + - - -
723B LEU 2.8 17.2 + - - +
724B ALA* 3.5 9.9 - - - +
726B TYR* 1.3 75.3 - - - +
728B GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 728 (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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234B LEU* 3.8 5.7 - - - +
235B GLY* 3.6 13.2 - - - -
238B ASN* 4.6 3.7 + - - +
239B TRP* 3.2 37.3 - - - +
626B HIS* 4.6 11.9 + - - -
658B GLY 3.7 1.1 - - - +
724B ALA 4.5 0.2 + - - -
725B SER 4.0 3.8 + - - -
726B TYR 3.6 0.4 - - - -
727B HIS* 1.3 80.3 - - - +
729B ALA* 1.3 62.8 + - - +
730B GLN* 3.7 13.7 + - - +
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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