Contacts of the helix formed by residues 717 - 725 (chain A) 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 TYR 717 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A GLU* 3.3 3.1 - - - -
506A GLU* 1.6 41.8 + - - -
715A VAL 3.5 1.0 + - - -
716A LEU* 1.3 75.4 - - + +
718A ALA* 1.3 56.8 + - - +
720A PHE* 2.9 7.8 + - + +
721A LYS* 2.8 24.6 + - - +
740A SER* 3.5 17.2 - - - +
741A LYS* 3.9 36.8 - - + -
744A SER* 2.9 38.0 + - - -
760A PHE* 3.1 5.5 - + - +
761A GLY 3.3 21.5 + - - -
762A HIS 4.8 0.9 - - - -
763A THR* 3.6 20.9 - - - +
764A MLY 3.6 2.7 - - - -
765A VAL* 3.4 25.7 - - + +
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Residues in contact with ALA 718 (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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149A GLN* 3.7 31.8 + - + +
150A GLU* 5.8 4.5 - - + -
716A LEU 3.5 0.6 - - - -
717A TYR* 1.3 71.3 - - - +
719A ASP* 1.4 56.0 + - - +
720A PHE 2.8 5.3 + - - -
721A LYS* 2.8 28.3 + - + +
722A GLN* 3.0 19.6 + - - +
740A SER* 4.3 14.2 + - - +
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Residues in contact with ASP 719 (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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89A GLU* 5.1 6.4 - - - +
93A MET* 4.5 14.6 - - + +
148A ARG 4.6 2.6 - - - +
149A GLN* 1.7 64.6 - - - +
715A VAL* 4.1 4.8 - - + +
716A LEU* 3.2 20.9 - - + +
718A ALA* 1.4 77.0 - - - +
720A PHE* 1.4 58.3 + - - +
722A GLN* 4.8 3.9 - - - +
723A ARG* 3.7 21.4 + - - +
724A TYR* 4.9 1.7 - - - -
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Residues in contact with PHE 720 (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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715A VAL* 3.3 32.1 - - + -
716A LEU 2.8 4.0 + - - +
717A TYR* 3.0 17.3 - + + +
718A ALA 2.8 0.4 - - - -
719A ASP* 1.4 80.0 - - - +
721A LYS* 1.3 67.4 + - - +
723A ARG 4.4 0.2 - - - -
724A TYR* 3.4 47.6 + + + +
736A GLN* 3.4 4.6 + - - -
744A SER* 3.3 26.7 - - - +
747A LEU* 4.8 10.1 - - + -
748A LEU* 3.6 35.4 - - + -
765A VAL* 5.5 3.4 - - + -
767A PHE* 3.5 26.2 - + - -
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Residues in contact with LYS 721 (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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717A TYR 2.8 7.7 + - - +
718A ALA* 2.8 13.6 + - - +
720A PHE* 1.3 73.6 - - - +
722A GLN* 1.3 62.3 + - - +
724A TYR 2.9 3.8 + - - -
725A ARG* 2.7 21.1 + - - +
733A PRO 3.9 0.4 - - - -
736A GLN* 0.8 216.9 + - + +
737A PHE* 2.1 28.0 + - + +
740A SER* 4.0 15.0 - - - +
743A ALA* 3.9 1.8 - - + -
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Residues in contact with GLN 722 (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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6A GLU* 4.2 19.8 + - - +
18A ARG* 6.0 3.2 - - - +
149A GLN 5.1 7.9 + - - -
150A GLU* 6.3 0.6 - - - +
718A ALA 3.0 11.5 + - - +
719A ASP* 5.2 2.9 - - - +
721A LYS* 1.3 81.2 - - - +
723A ARG* 1.3 70.7 + - + +
724A TYR 3.3 0.2 + - - -
725A ARG* 3.9 9.8 + - - +
726A VAL* 4.9 6.6 - - - +
736A GLN* 3.2 0.9 + - - -
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Residues in contact with ARG 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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24A ARG* 5.2 15.0 - - - +
28A GLN* 2.9 41.8 + - - +
84A MLY 3.4 32.3 - - - +
719A ASP 3.7 15.5 + - - +
720A PHE 4.1 0.6 + - - -
721A LYS 3.1 1.2 + - - -
722A GLN* 1.3 85.1 - - + +
724A TYR* 1.3 75.7 + - + +
726A VAL* 5.2 6.1 - - - +
727A LEU* 5.1 0.2 - - - +
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Residues in contact with TYR 724 (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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84A MLY 1.4 101.2 - - - -
715A VAL* 5.7 4.5 - - + -
719A ASP 5.0 2.5 - - - -
720A PHE* 3.5 52.0 - + + +
721A LYS 2.9 2.6 + - - -
723A ARG* 1.3 93.4 - - + +
725A ARG* 1.3 68.7 + - - +
726A VAL* 3.0 4.3 - - - -
727A LEU* 2.8 49.3 + - + +
736A GLN* 4.9 0.2 - - - +
747A LEU* 3.7 8.1 - - + +
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Residues in contact with ARG 725 (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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721A LYS 2.7 19.6 + - - +
722A GLN* 3.9 7.5 + - - +
723A ARG 3.9 0.4 - - - -
724A TYR* 1.3 70.2 - - - +
726A VAL* 1.3 55.7 + - + +
727A LEU 2.8 11.4 + - - -
729A ALA* 2.9 21.8 + - - +
732A ILE* 3.3 20.7 - - - +
733A PRO* 2.0 59.4 - - + +
734A GLU* 6.1 0.2 - - - +
736A GLN* 3.4 8.7 - - - +
737A PHE* 2.7 33.6 - - - -
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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