Contacts of the helix formed by residues 730 - 739 (chain D) in PDB entry 1O1F
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 SER 730 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728D ASN* 2.7 11.0 + - - -
729D ALA* 1.3 71.8 - - - +
731D ALA* 1.3 59.6 + - - +
733D PRO* 3.0 16.0 - - - +
734D GLU* 2.7 41.8 - - - +
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Residues in contact with ALA 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D ASN* 2.6 25.3 + - + +
730D SER* 1.3 77.3 - - - +
732D ILE* 1.3 62.3 + - + +
733D PRO* 3.3 0.2 - - - -
734D GLU* 4.1 12.0 - - - +
735D GLY* 3.5 15.4 + - - -
746D LYS* 4.4 12.0 - - + +
747D LEU* 4.3 8.1 + - - +
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Residues in contact with ILE 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724D TYR 3.7 0.9 - - - +
725D ARG* 3.3 12.1 - - - +
727D LEU* 3.5 14.6 - - + -
728D ASN* 3.1 37.8 + - + +
731D ALA* 1.3 73.1 - - + +
733D PRO* 1.4 70.2 - - - +
735D GLY* 3.4 0.9 + - - -
736D GLN* 3.0 47.5 + - - +
747D LEU* 0.6 137.3 - - + +
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Residues in contact with PRO 733 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725D ARG* 2.0 57.4 - - + +
729D ALA* 1.3 55.6 - - - +
730D SER* 3.0 14.8 - - - +
732D ILE* 1.4 96.2 - - + +
734D GLU* 1.3 52.6 + - + +
736D GLN* 3.3 1.3 + - + -
737D PHE* 1.7 46.1 + - + -
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Residues in contact with GLU 734 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725D ARG* 6.1 0.2 - - - +
730D SER* 2.7 32.7 + - - +
731D ALA* 4.2 9.3 - - - +
733D PRO* 1.3 81.4 - - + +
735D GLY* 1.3 51.9 + - - +
737D PHE* 4.1 2.5 - - - -
738D MET* 2.3 54.4 + - + +
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Residues in contact with GLY 735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731D ALA 3.5 5.4 + - - -
732D ILE 3.4 4.2 + - - -
733D PRO 3.2 0.8 - - - -
734D GLU* 1.3 80.7 - - - +
736D GLN* 1.3 47.5 - - - +
738D MET* 4.1 2.6 - - - +
739D ASP 3.0 18.0 + - - +
742D LYS 3.7 0.6 - - - -
743D ALA* 1.9 50.8 + - - +
746D LYS* 3.9 16.2 - - - -
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Residues in contact with GLN 736 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720D PHE* 3.4 9.1 + - - -
721D LYS* 0.8 195.4 + - + +
722D GLN* 3.2 0.7 + - - -
725D ARG* 3.4 15.2 - - - +
732D ILE* 3.0 42.6 + - + +
733D PRO 3.7 3.1 - - - +
735D GLY* 1.3 68.4 - - - +
737D PHE* 1.3 53.7 - - + +
740D SER* 3.4 14.6 - - - -
743D ALA* 2.0 27.3 - - + +
744D SER* 4.2 7.6 - - - +
747D LEU* 3.6 1.4 - - - +
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Residues in contact with PHE 737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721D LYS* 2.2 16.9 + - - +
725D ARG* 2.7 60.1 - - + -
733D PRO* 1.7 42.9 + - + +
734D GLU* 3.6 4.3 - - - +
736D GLN* 1.3 79.7 - - + +
738D MET* 1.3 72.1 + - + +
739D ASP* 3.6 0.9 + - - -
740D SER 4.8 1.6 + - - -
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Residues in contact with MET 738 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734D GLU* 2.3 42.9 + - + +
735D GLY* 4.1 3.6 - - - +
737D PHE* 1.3 85.8 - - - +
739D ASP* 1.3 60.6 + - - +
742D LYS* 5.7 3.8 - - + +
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Residues in contact with ASP 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735D GLY 3.0 8.4 + - - +
736D GLN 3.7 0.9 - - - -
737D PHE 4.4 0.2 - - - -
738D MET* 1.3 80.3 - - - +
740D SER* 1.3 77.7 + - - +
741D LYS* 2.6 22.0 + - - +
742D LYS* 2.7 45.8 + - + +
743D ALA 2.5 30.7 + - - -
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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