Contacts of the helix formed by residues 717 - 725 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715J VAL 3.5 1.2 + - - -
716J LEU* 1.3 75.6 - - + +
718J ALA* 1.3 56.9 + - - +
720J PHE* 2.9 7.6 + - + +
721J LYS* 2.8 24.6 + - - +
740J SER* 3.5 18.5 - - - +
741J LYS* 3.9 42.0 - - + +
744J SER* 2.9 37.3 + - - -
745J GLU* 5.7 0.2 - - + -
760J PHE* 3.1 37.5 - + - +
761J GLY 3.3 24.7 + - - -
762J HIS 4.8 1.1 - - - -
763J THR* 3.6 20.4 - - - +
764J MLY 3.6 5.8 - - - -
765J VAL* 3.4 25.7 - - + +
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Residues in contact with ALA 718 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716J LEU* 3.5 7.5 - - + +
717J TYR* 1.3 70.9 - - - +
719J ASP* 1.4 60.2 - - - +
720J PHE 2.8 5.9 + - - -
721J LYS* 2.8 27.5 + - - +
722J GLN* 3.0 20.1 + - - +
740J SER* 4.3 15.2 + - - +
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Residues in contact with ASP 719 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLN* 4.2 15.9 + - - +
84J MLY 0.9 187.4 + - - +
85J TYR* 5.0 1.0 - - - -
88J ILE* 5.4 4.2 - - - +
716J LEU* 4.0 19.9 - - + +
718J ALA* 1.4 78.4 - - - +
720J PHE* 1.4 52.9 + - - +
722J GLN* 4.8 3.9 - - - +
723J ARG* 3.7 18.2 + - - +
724J TYR* 4.9 0.7 - - - -
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Residues in contact with PHE 720 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J MLY 2.6 3.5 - - - -
715J VAL* 3.3 31.0 - - + -
716J LEU 2.8 2.9 + - - +
717J TYR* 3.0 18.2 - + + +
718J ALA 2.8 0.4 - - - -
719J ASP* 1.4 79.5 - - - +
721J LYS* 1.3 66.3 + - - +
723J ARG 4.4 0.2 - - - -
724J TYR* 3.4 48.1 + + + +
736J GLN* 3.4 5.0 + - - -
744J SER* 3.3 26.0 - - - +
747J LEU* 4.8 10.5 - - + -
748J LEU* 3.6 35.2 - - + -
765J VAL* 5.5 3.4 - - + -
767J PHE* 3.5 26.5 - + - -
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Residues in contact with LYS 721 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717J TYR 2.8 7.3 + - - +
718J ALA* 2.8 13.3 + - - +
720J PHE* 1.3 73.9 - - - +
722J GLN* 1.3 61.7 + - - +
724J TYR 2.9 3.3 + - - -
725J ARG* 2.7 21.1 + - - +
733J PRO 3.9 0.7 - - - -
736J GLN* 0.8 217.2 + - + +
737J PHE* 2.1 27.9 + - + +
740J SER* 4.0 13.9 - - - +
743J ALA* 3.9 1.6 - - + -
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Residues in contact with GLN 722 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLN* 5.8 2.2 + - - -
29J ASN* 3.4 28.8 + - - +
718J ALA 3.0 10.6 + - - +
719J ASP* 5.2 2.5 - - - +
721J LYS* 1.3 80.8 - - - +
723J ARG* 1.3 70.3 + - + +
724J TYR 3.3 0.5 + - - -
725J ARG* 3.9 9.9 + - - +
726J VAL* 4.9 6.4 - - - +
736J GLN* 3.2 1.1 + - - -
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Residues in contact with ARG 723 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLN 5.2 7.1 + - - -
32J PHE* 5.9 4.9 - - - +
82J PRO* 5.4 14.9 - - - +
83J PRO* 6.2 1.8 - - - +
84J MLY 5.1 20.7 + - + +
719J ASP 3.7 15.9 + - - +
720J PHE 4.1 0.4 + - - -
721J LYS 3.1 1.2 + - - -
722J GLN* 1.3 85.0 - - + +
724J TYR* 1.3 95.1 + - + +
726J VAL* 5.2 6.3 - - - +
727J LEU* 5.2 0.3 - - - +
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Residues in contact with TYR 724 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J MLY 5.6 2.7 - - + -
715J VAL* 5.7 3.6 - - + -
719J ASP 5.0 2.9 - - - -
720J PHE* 3.5 52.7 - + + +
721J LYS 2.9 2.6 + - - -
723J ARG* 1.3 109.9 - - + +
725J ARG* 1.3 67.8 + - - +
726J VAL* 3.0 4.7 - - - -
727J LEU* 2.8 48.9 + - + +
732J ILE* 5.5 0.2 - - + -
736J GLN* 4.9 0.2 - - - +
747J LEU* 3.7 8.5 - - + +
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Residues in contact with ARG 725 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721J LYS 2.7 19.3 + - - +
722J GLN* 4.3 7.2 - - - +
723J ARG 3.9 0.6 - - - -
724J TYR* 1.3 70.0 - - - +
726J VAL* 1.3 56.3 + - + +
727J LEU 2.8 11.8 + - - -
729J ALA* 2.9 21.9 + - - -
732J ILE* 3.3 20.7 - - - +
733J PRO* 2.0 61.4 - - + +
734J GLU* 6.1 0.2 - - - +
736J GLN* 3.4 8.2 - - - +
737J PHE* 2.7 33.4 - - - -
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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