Contacts of the helix formed by residues 722 - 728 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A PRO* 5.6 1.1 - - + -
300A TYR* 6.6 0.2 - - + -
320A SER* 5.5 8.5 - - - +
325A PRO* 3.6 31.6 - - + -
327A ASP* 4.6 1.6 + - - -
346A ARG* 3.6 32.1 - - - +
516A MET 4.3 0.4 - - - -
517A SER* 3.5 35.2 - - - +
715A LEU* 3.6 2.9 - - - -
720A ILE* 3.5 6.8 - - - +
721A SER* 1.3 80.6 - - - +
723A LEU* 1.3 65.4 + - - +
724A ALA* 4.0 14.6 - - + +
725A SER* 3.0 24.9 + - - +
726A TYR 3.2 8.3 + - - -
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Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A SER 3.0 17.0 + - - +
518A LEU* 3.7 29.4 - - + +
520A MET* 3.8 18.8 - - + -
544A PRO* 3.5 37.9 - - + -
657A VAL* 3.8 26.0 - - + -
711A LEU* 4.7 9.6 - - + -
715A LEU* 3.4 30.2 - - + +
722A LEU* 1.3 72.0 - - - +
724A ALA* 1.3 56.2 + - - +
726A TYR* 3.2 6.0 + - + +
727A HIS* 2.8 32.2 + - - +
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Residues in contact with ALA 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 4.6 1.4 + - - -
320A SER 5.1 9.6 - - - +
324A GLU* 3.4 28.0 - - + +
519A ALA 4.3 11.2 + - - +
520A MET* 3.8 11.7 - - - -
521A PHE* 5.6 6.3 - - + -
525A ARG* 5.1 1.9 + - - -
722A LEU* 3.1 15.3 - - + +
723A LEU* 1.3 77.7 - - - +
725A SER* 1.3 58.9 + - - +
727A HIS* 3.5 17.5 - - - +
728A GLY 4.3 2.4 + - - -
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Residues in contact with SER 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.7 28.8 - - - +
235A GLY* 5.2 1.9 - - - -
236A ASN* 5.2 0.5 - - - +
239A TRP* 5.3 0.2 + - - -
324A GLU* 3.8 10.1 - - - +
325A PRO* 2.8 45.6 + - - +
327A ASP* 4.5 3.6 - - - +
720A ILE* 4.2 4.9 - - - -
722A LEU* 3.0 13.1 + - - +
724A ALA* 1.3 75.3 - - - +
726A TYR* 1.3 65.8 + - - +
727A HIS 3.2 0.7 - - - -
728A GLY* 3.9 5.0 + - - -
729A ALA* 3.6 14.9 - - - +
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Residues in contact with TYR 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLN* 5.3 0.2 - - - +
654A ALA* 3.3 29.3 - - - +
657A VAL* 4.1 6.5 - - + -
658A GLY* 3.9 7.9 - - - -
714A ILE* 3.4 27.7 - - + +
715A LEU* 3.3 39.0 - - + -
718A MET* 6.1 0.4 - - + -
720A ILE* 4.0 23.4 - - + +
722A LEU 3.2 7.6 + - - +
723A LEU* 3.2 18.8 + - + +
725A SER* 1.3 76.5 - - - +
727A HIS* 1.3 65.3 + - - +
729A ALA* 3.0 23.6 + - - +
731A ILE* 3.9 24.5 + - + -
732A PHE* 3.1 31.2 - + - -
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Residues in contact with HIS 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TRP* 3.3 29.9 - + - -
520A MET* 3.8 18.6 - - + -
525A ARG* 3.9 12.3 + - - -
626A HIS* 5.5 0.2 - - - -
635A ARG* 4.0 4.6 + - - -
657A VAL* 2.8 29.3 + - - +
658A GLY 3.3 6.4 - - - +
660A GLY* 3.0 39.3 + - - -
661A ALA 3.2 21.0 + - - -
662A SER* 3.6 14.5 + - - -
723A LEU 2.8 17.8 + - - +
724A ALA* 3.5 10.3 - - - +
725A SER 3.2 0.2 - - - -
726A TYR* 1.3 72.8 - - - +
728A GLY* 1.3 63.1 + - - +
729A ALA 3.1 0.9 + - - -
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Residues in contact with GLY 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 3.6 15.4 - - - +
235A GLY* 3.6 7.0 - - - -
238A ASN* 4.7 3.6 + - - +
239A TRP* 3.0 42.4 - - - +
626A HIS* 4.6 11.1 + - - -
658A GLY 3.9 3.6 - - - +
724A ALA 4.3 0.4 + - - -
725A SER 3.9 4.4 + - - -
726A TYR 3.5 0.4 - - - -
727A HIS* 1.3 76.6 - - - +
729A ALA* 1.3 61.8 + - - +
730A GLN* 4.0 5.9 + - - +
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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