Contacts of the helix formed by residues 738 - 746 (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 GLY 738 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737B LEU* 1.3 75.4 - - - +
739B ALA* 1.3 66.5 + - - -
740B GLU* 3.2 5.5 + - - -
741B LEU* 3.3 4.5 + - - +
742B VAL* 3.1 20.1 + - - +
754B GLY* 4.3 2.0 - - - -
755B GLY 3.3 21.0 - - - +
756B LEU 2.8 23.2 + - - -
757B THR* 5.6 0.7 - - - -
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Residues in contact with ALA 739 (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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737B LEU 4.8 0.2 - - - -
738B GLY* 1.3 72.7 - - - -
740B GLU* 1.3 71.3 + - - +
742B VAL* 3.3 7.7 + - - +
743B GLU* 2.9 31.5 + - - +
751B SER* 6.3 0.7 - - - -
754B GLY* 5.2 2.6 - - - -
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Residues in contact with GLU 740 (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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738B GLY* 3.2 1.4 - - - -
739B ALA* 1.3 92.4 + - - +
741B LEU* 1.3 63.2 + - - +
743B GLU* 3.4 5.6 + - - +
744B TYR* 3.1 23.4 + - - +
757B THR* 6.2 4.3 - - + -
758B ILE* 5.5 6.2 - - + +
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Residues in contact with LEU 741 (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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491B LEU* 4.8 4.3 - - + -
620B LEU* 3.6 31.6 - - + -
737B LEU* 4.0 28.7 - - + -
738B GLY 3.3 8.3 + - - +
740B GLU* 1.3 79.3 - - - +
742B VAL* 1.3 62.8 + - - +
744B TYR* 3.2 7.4 + - + +
745B ALA 3.2 18.4 + - - -
746B PHE* 3.9 12.8 - - + -
756B LEU* 3.8 21.3 + - + +
757B THR* 4.4 1.5 - - - +
758B ILE* 3.9 29.9 - - + +
761B VAL* 3.7 28.7 - - + -
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Residues in contact with VAL 742 (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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734B ALA* 5.0 3.1 - - + -
737B LEU* 3.8 30.3 - - + +
738B GLY 3.1 17.5 + - - +
739B ALA* 3.7 7.2 - - - +
741B LEU* 1.3 75.3 - - - +
743B GLU* 1.3 58.8 + - - +
746B PHE* 2.7 48.9 + - + +
747B ALA* 2.8 12.3 + - - +
748B GLY 4.8 1.3 - - - +
749B THR* 3.6 26.5 - - - +
751B SER* 3.8 16.4 - - - -
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Residues in contact with GLU 743 (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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631B ARG* 2.6 58.2 + - - +
739B ALA 2.9 17.8 + - - +
740B GLU* 3.8 5.8 - - - +
742B VAL* 1.3 77.4 - - - +
744B TYR* 1.3 57.5 + - - +
747B ALA* 3.7 14.7 - - - +
748B GLY 5.6 0.3 + - - -
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Residues in contact with TYR 744 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577B GLU* 5.6 5.6 - - + -
580B LEU* 3.4 32.8 + - + -
581B THR* 3.4 35.6 + - - +
584B VAL* 4.2 6.3 - - + +
620B LEU* 5.2 1.3 - - + -
624B ALA* 3.7 17.7 - - + -
627B HIS* 4.1 6.4 - - - +
628B HIS* 3.3 52.1 + + - -
631B ARG* 4.3 1.0 + - - +
740B GLU 3.1 17.0 + - - +
741B LEU* 3.2 8.9 + - + +
743B GLU* 1.3 80.6 - - - +
745B ALA* 1.3 61.8 + - + +
758B ILE* 4.8 17.0 - - + -
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Residues in contact with ALA 745 (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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620B LEU* 3.5 31.9 - - + +
623B GLY* 3.1 25.6 - - - +
624B ALA* 3.5 24.5 - - + +
627B HIS* 3.3 10.9 - - - -
659B TYR* 4.3 0.7 - - - -
741B LEU 3.2 4.3 + - - +
744B TYR* 1.3 79.1 - - + +
746B PHE* 1.3 77.8 + - + +
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Residues in contact with PHE 746 (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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491B LEU* 4.2 8.5 - - + -
495B PHE* 3.7 27.4 - + + -
619B LEU* 3.6 37.2 - - + -
620B LEU* 3.9 24.2 - - + -
627B HIS* 4.0 3.4 - - - -
659B TYR* 3.7 30.3 - + + -
730B GLN* 4.2 0.7 - - - -
737B LEU* 4.4 9.9 - - + -
741B LEU* 3.9 24.7 - - + -
742B VAL* 2.7 26.7 + - + +
745B ALA* 1.3 100.2 - - + +
747B ALA* 1.3 65.6 + - - +
748B GLY 3.3 0.2 + - - -
749B THR* 2.9 28.0 + - - +
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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