Contacts of the helix formed by residues 768 - 782 (chain C) in PDB entry 1IW1
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 LYS 768 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C ILE* 4.6 0.9 - - - -
767C ALA* 1.3 83.3 - - + +
769C LEU* 1.3 60.7 + - - +
770C LYS 3.3 1.6 - - - +
771C VAL* 3.3 46.3 - - + +
772C TYR* 2.8 29.7 + - - +
775C GLU* 4.7 3.0 + - - -
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Residues in contact with LEU 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737C LEU* 3.8 47.8 - - + +
741C GLN* 4.9 10.5 - - + +
763C PHE* 5.4 5.4 - - + -
766C ILE* 4.3 17.0 - - + +
767C ALA 3.2 9.1 + - - +
768C LYS* 1.3 70.5 - - - +
770C LYS* 1.3 60.1 + - - +
772C TYR* 3.2 4.2 + - + +
773C LYS* 2.9 46.2 + - - +
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Residues in contact with LYS 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LYS 3.3 0.4 - - - -
769C LEU* 1.3 75.9 - - - +
771C VAL* 1.3 62.8 + - + +
773C LYS* 3.4 17.8 + - - +
774C ASP* 2.9 47.5 + - - +
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Residues in contact with VAL 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LYS* 3.3 54.2 + - + +
770C LYS* 1.3 79.2 - - + +
772C TYR* 1.3 62.5 + - - +
774C ASP* 3.4 8.6 + - + +
775C GLU* 3.1 45.9 + - + +
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Residues in contact with TYR 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672C LEU 5.0 0.9 + - - -
674C ASP* 2.6 44.0 + - - +
677C LEU* 3.6 19.3 - - + +
737C LEU* 3.9 30.1 - - + -
766C ILE* 3.7 36.3 - - + -
768C LYS 2.8 18.1 + - - +
769C LEU* 3.4 4.7 - - + +
771C VAL* 1.3 77.4 - - - +
773C LYS* 1.3 58.0 + - - +
775C GLU* 3.4 8.9 + - + +
776C TYR* 2.9 35.0 + + + +
779C LYS* 5.0 13.3 + - - -
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Residues in contact with LYS 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734C LEU* 4.2 7.7 - - + +
737C LEU* 3.7 44.0 + - + +
738C SER* 3.8 26.1 + - - +
769C LEU* 2.9 37.6 + - + +
770C LYS* 3.9 19.1 - - - +
772C TYR* 1.3 74.6 - - - +
774C ASP* 1.3 67.7 + - - +
776C TYR* 3.2 8.3 + - - +
777C ARG* 3.1 42.4 + - - +
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Residues in contact with ASP 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C LYS* 2.9 42.7 + - - +
771C VAL* 3.6 9.6 - - + +
773C LYS* 1.3 78.0 - - - +
775C GLU* 1.3 64.0 + - + +
777C ARG* 3.3 15.6 + - - +
778C GLU* 3.1 23.7 + - - +
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Residues in contact with GLU 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LYS* 4.7 3.3 + - - -
771C VAL* 3.1 37.8 + - + +
772C TYR* 3.7 7.0 - - + +
774C ASP* 1.3 78.7 - - + +
776C TYR* 1.3 60.0 + - - +
778C GLU* 3.2 9.0 + - - +
779C LYS* 2.8 49.0 + - - +
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Residues in contact with TYR 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C LEU* 3.4 31.4 - - + +
677C LEU* 4.7 4.0 - - + -
729C HIS* 2.8 40.7 + + - +
730C TYR* 3.2 23.8 + + - +
733C TYR* 5.3 2.5 - - + -
734C LEU* 4.0 37.2 - - + -
737C LEU* 5.4 2.7 - - + -
772C TYR* 2.9 34.9 + + + +
773C LYS* 3.5 10.1 - - - +
774C ASP 3.1 0.6 - - - -
775C GLU* 1.3 74.9 - - - +
777C ARG* 1.3 66.3 + - - +
779C LYS* 3.1 14.5 + - + +
780C LEU* 3.0 42.2 + - + +
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Residues in contact with ARG 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ALA* 3.5 21.9 - - + +
613C LYS* 5.5 3.4 - - - +
734C LEU* 4.2 20.7 - - + +
738C SER* 4.4 12.1 + - - -
773C LYS* 3.1 33.9 + - - +
774C ASP* 3.6 15.9 + - - +
776C TYR* 1.3 75.6 - - - +
778C GLU* 1.3 58.3 + - - +
780C LEU* 3.3 9.6 + - + +
781C ASN* 3.0 33.9 + - - +
903C HEM 2.8 44.3 + - - +
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Residues in contact with GLU 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774C ASP 3.1 14.5 + - - +
775C GLU* 3.6 12.6 - - - +
776C TYR 3.1 0.2 - - - -
777C ARG* 1.3 75.3 - - - +
779C LYS* 1.3 60.9 + - + +
781C ASN* 3.1 22.9 + - - +
782C ASN* 2.8 70.1 + - - +
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Residues in contact with LYS 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671C SER* 3.0 49.5 + - - +
672C LEU* 3.6 27.0 + - + +
674C ASP* 5.4 1.6 - - - +
772C TYR* 5.0 17.6 + - - -
775C GLU* 2.8 33.6 + - + +
776C TYR* 3.1 14.1 + - + +
778C GLU* 1.3 76.0 - - - +
780C LEU* 1.3 62.3 + - - +
782C ASN* 3.2 7.2 + - - +
783C LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C LEU* 3.3 32.6 - - + +
609C ALA* 4.1 19.7 - - + +
612C LEU* 3.9 26.2 - - + -
672C LEU* 3.8 13.9 - - + -
726C VAL* 3.7 30.3 - - + -
730C TYR* 3.9 12.8 - - + -
776C TYR* 3.0 41.2 + - + +
777C ARG* 3.4 9.4 - - + +
779C LYS* 1.3 77.9 - - - +
781C ASN* 1.3 61.0 + - - +
783C LEU* 3.4 15.6 + - + +
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Residues in contact with ASN 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607C GLY* 3.4 11.7 - - - -
608C LEU* 3.1 15.1 + - - +
609C ALA* 3.0 30.7 + - - +
610C VAL* 4.5 2.7 + - - +
777C ARG* 3.0 21.9 + - - +
778C GLU* 3.1 29.2 + - - +
780C LEU* 1.3 80.2 - - - +
782C ASN* 1.3 61.9 + - - +
783C LEU 3.3 4.4 + - - +
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Residues in contact with ASN 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778C GLU* 2.8 47.3 + - - +
779C LYS* 3.2 7.2 + - - +
781C ASN* 1.3 78.8 - - - +
783C LEU* 1.3 62.6 + - - +
784C GLU* 3.3 9.8 + - - +
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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