Contacts of the helix formed by residues 717 - 723 (chain A) in PDB entry 1IK2
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 ASP 717 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713A ILE* 6.2 2.5 - - + -
714A LEU* 3.2 35.8 + - + +
716A GLY* 1.3 77.3 - - - +
718A PHE* 1.3 66.4 + - - +
719A ARG 3.0 2.5 - - - -
720A GLN* 3.0 19.7 + - + +
721A ARG* 3.4 12.1 + - + +
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Residues in contact with PHE 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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713A ILE* 4.1 21.1 - - + -
714A LEU 3.1 9.9 + - - +
715A TYR* 3.1 19.1 - - - +
717A ASP* 1.3 77.0 - - - +
719A ARG* 1.3 63.6 + - - +
720A GLN 3.4 0.2 + - - -
721A ARG* 3.8 9.4 + - - +
722A TYR* 3.8 36.8 + + - -
742A ALA* 4.2 20.9 - - + -
745A LEU* 3.0 30.2 - - + +
746A LEU* 3.8 33.7 - - + -
764A PHE 4.6 1.8 - - - -
765A PHE* 3.8 21.3 - + - -
770A LEU* 4.0 18.4 - - + -
773A LEU* 4.9 3.8 - - + -
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Residues in contact with ARG 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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715A TYR 4.2 0.2 + - - -
716A GLY 3.4 18.9 + - - +
718A PHE* 1.3 79.0 - - - +
720A GLN* 1.3 65.5 + - - +
723A ARG* 3.2 52.0 + - + +
736A ILE* 4.3 19.3 - - - +
737A ASP 4.2 19.4 + - - -
738A SER* 4.8 11.6 - - - +
741A GLY* 4.0 20.5 + - - +
744A LYS* 5.0 17.0 - - + +
745A LEU* 3.6 7.4 - - - +
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Residues in contact with GLN 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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717A ASP* 3.0 12.3 + - - +
719A ARG* 1.3 78.0 - - + +
721A ARG* 1.3 75.7 + - - +
722A TYR 2.9 2.3 + - - -
723A ARG* 3.2 22.4 + - - +
783A ARG* 4.8 1.4 + - - -
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Residues in contact with ARG 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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27A GLN* 5.9 3.2 - - - +
28A THR* 5.4 11.9 - - - +
83A LYS* 3.7 31.5 + - - +
713A ILE* 5.5 10.1 - - - -
717A ASP* 3.4 12.4 + - + +
718A PHE* 3.8 2.2 + - - +
719A ARG 3.6 0.4 - - - -
720A GLN* 1.3 86.8 + - - +
722A TYR* 1.3 97.2 + - + +
774A GLU* 3.7 16.0 + - - -
777A ARG* 3.0 27.4 + - - +
783A ARG* 2.9 20.3 + - - -
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Residues in contact with TYR 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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83A LYS* 4.3 1.9 + - - -
713A ILE* 5.5 1.4 - - + +
718A PHE* 3.8 49.3 + + - -
720A GLN 3.6 0.2 - - - -
721A ARG* 1.3 110.2 + - + +
723A ARG* 1.3 55.5 + - - +
724A ILE 2.7 18.7 + - - -
725A LEU* 3.1 23.3 + - + +
745A LEU* 3.8 15.9 - - + -
770A LEU* 3.7 20.7 - - + +
773A LEU* 5.2 8.1 - - + -
774A GLU* 3.6 30.2 + - + +
777A ARG* 3.8 35.9 - - + -
783A ARG* 2.7 18.9 + - - +
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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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719A ARG* 3.2 42.9 + - + +
720A GLN* 3.4 18.2 - - - +
722A TYR* 1.3 71.9 - - - +
724A ILE* 1.3 67.8 + - + +
725A LEU 3.2 5.4 + - - -
727A PRO* 3.6 10.9 - - - +
729A ALA* 5.7 0.7 - - - +
744A LYS* 6.3 3.0 - - - +
745A LEU* 3.2 21.5 - - - +
783A ARG* 5.1 0.9 - - - +
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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