Contacts of the helix formed by residues 774 - 791 (chain B) in PDB entry 5IXC
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 774 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ALA* 4.8 2.9 - - - +
772B THR 4.2 1.6 + - - -
773B TYR* 1.3 71.0 - - - +
775B GLU* 1.3 66.9 + - - +
776B GLU* 3.1 24.2 + - + +
777B ASP* 2.8 39.9 + - - +
778B PHE 3.0 10.6 + - - -
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Residues in contact with GLU 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG* 3.1 34.4 + - - +
390B GLU* 4.3 16.3 - - - +
393B ALA* 3.7 23.6 - - + +
773B TYR 3.4 2.1 + - - -
774B LYS* 1.3 70.2 - - - +
776B GLU* 1.3 63.2 + - - +
778B PHE* 3.3 10.5 + - - +
779B GLU* 3.0 29.0 + - + +
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Residues in contact with GLU 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B GLN* 5.1 3.3 - - - +
774B LYS* 4.1 24.3 + - + -
775B GLU* 1.3 79.0 - - - +
777B ASP* 1.3 62.7 + - - +
779B GLU* 3.3 7.4 + - - +
780B ARG* 3.3 56.6 + - - +
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Residues in contact with ASP 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ASP* 5.7 2.3 - - - +
765B PRO* 3.7 34.7 - - + +
766B TYR* 2.4 39.9 + - + +
773B TYR* 5.0 3.8 - - + -
774B LYS* 2.8 47.1 + - - +
776B GLU* 1.3 76.5 - - - +
778B PHE* 1.3 64.9 + - - +
779B GLU 3.4 0.2 + - - -
780B ARG* 3.6 15.1 + - - +
781B LEU 3.5 4.7 + - - -
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Residues in contact with PHE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR* 3.6 37.5 + - + -
339B TYR* 5.2 2.0 - + - -
385B ILE* 3.6 41.5 - - + -
388B ALA* 4.2 11.4 - - + -
389B ARG* 3.6 40.4 - - + +
392B LEU* 4.0 13.0 - - + -
773B TYR* 4.2 15.3 - - + +
774B LYS 3.0 9.5 + - - +
775B GLU* 3.4 10.3 - - - +
777B ASP* 1.3 78.2 - - - +
779B GLU* 1.3 69.2 + - - +
781B LEU* 3.4 3.8 + - - +
782B LEU* 2.9 39.8 + - + +
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Residues in contact with GLU 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 5.3 1.1 - - - +
389B ARG* 2.8 41.2 + - - +
775B GLU* 3.0 16.4 + - + +
776B GLU* 3.6 10.8 - - - +
777B ASP 3.2 0.2 - - - -
778B PHE* 1.3 83.3 - - - +
780B ARG* 1.3 66.5 + - + +
782B LEU* 4.3 11.7 - - - +
783B ARG* 2.9 72.5 + - - +
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Residues in contact with ARG 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B PHE* 4.4 1.6 - - - -
753B GLN* 2.7 56.8 + - - +
754B GLY* 3.7 14.8 - - - +
756B GLN* 3.6 23.0 + - - +
757B VAL* 4.2 18.9 - - + +
758B ASP 5.5 1.1 - - - +
766B TYR* 3.8 11.0 - - - +
776B GLU* 3.3 48.1 + - - +
777B ASP* 3.9 15.6 + - - +
778B PHE 3.4 0.2 - - - -
779B GLU* 1.3 77.0 - - + +
781B LEU* 1.3 59.0 + - - +
783B ARG* 3.8 3.5 - - - +
784B LEU* 2.8 33.2 + - - +
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Residues in contact with LEU 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ARG* 3.9 24.0 - - + +
336B THR* 3.3 20.6 - - - +
337B SER* 4.1 7.4 - - - -
732B LEU* 3.8 32.1 - - + -
757B VAL* 4.3 3.6 - - - +
759B LEU* 4.8 12.1 - - + -
766B TYR* 3.6 43.2 + - + +
773B TYR* 4.3 1.8 - - + -
777B ASP 3.5 1.6 + - - -
778B PHE* 3.4 6.8 + - - +
779B GLU 3.3 0.4 - - - -
780B ARG* 1.3 75.7 - - - +
782B LEU* 1.3 65.0 + - - +
784B LEU* 3.4 8.3 + - + +
785B SER* 2.9 31.5 + - - +
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Residues in contact with LEU 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR* 3.5 16.5 + - - +
339B TYR* 3.7 12.1 - - + -
340B GLY* 3.2 33.2 - - - +
343B LEU* 4.7 11.4 - - + -
382B GLU* 4.6 10.5 - - - +
385B ILE* 3.7 32.3 - - + -
778B PHE* 2.9 28.9 + - + +
779B GLU* 3.8 19.1 - - - +
781B LEU* 1.3 76.3 - - - +
783B ARG* 1.3 61.3 + - + +
785B SER* 3.1 5.5 + - - -
786B ASP* 2.9 27.3 + - + +
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Residues in contact with ARG 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B PHE* 3.6 16.9 - - + -
741B SER 5.9 2.5 - - - -
779B GLU* 2.9 58.5 + - - +
780B ARG* 3.9 3.1 - - - +
782B LEU* 1.3 76.5 - - + +
784B LEU* 1.3 61.0 + - - +
786B ASP* 3.5 12.7 + - - +
787B TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B LEU* 4.6 11.4 - - + -
733B VAL 3.5 26.0 - - - +
734B ASN* 3.9 6.7 - - - +
737B PHE* 3.5 44.5 - - + -
757B VAL* 4.0 26.7 - - + -
759B LEU* 4.2 15.7 - - + -
780B ARG 2.8 17.7 + - - +
781B LEU* 3.6 7.4 - - + +
783B ARG* 1.3 76.6 - - - +
785B SER* 1.3 59.4 + - - +
787B TYR* 3.4 1.6 + - - +
788B ASN* 3.0 43.8 + - - +
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Residues in contact with SER 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 2.6 49.4 + - - -
340B GLY* 4.1 1.6 - - - -
341B HIS* 3.3 23.8 - - - -
732B LEU* 4.5 3.9 - - - +
781B LEU* 2.9 18.1 + - - +
782B LEU 3.5 7.2 - - - -
784B LEU* 1.3 74.7 - - - +
786B ASP* 1.3 65.7 + - - +
788B ASN* 3.2 16.2 + - - +
789B VAL* 3.3 10.0 + - - +
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Residues in contact with ASP 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLY* 3.2 17.8 + - - +
343B LEU* 4.1 21.5 - - + +
344B ALA* 3.3 20.0 + - - +
347B LYS* 4.2 8.0 + - - -
782B LEU* 2.9 16.2 + - + +
783B ARG* 3.6 13.0 - - - +
785B SER* 1.3 76.2 - - - +
787B TYR* 1.3 57.2 + - - +
790B GLN* 2.9 55.2 + - - +
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Residues in contact with TYR 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B GLU* 4.1 1.6 - - - -
736B SER* 2.6 35.8 + - - -
737B PHE* 3.3 38.6 - + + -
740B HIS* 3.5 23.0 - - + +
741B SER 5.7 0.2 - - - +
742B ALA* 3.6 29.4 - - - -
743B PRO* 3.7 21.0 - - + +
744B GLY 5.1 0.3 + - - -
783B ARG 2.9 18.6 + - - +
784B LEU 3.5 1.8 - - - +
785B SER 3.2 0.2 - - - -
786B ASP* 1.3 78.9 - - - +
788B ASN* 1.3 72.2 + - - +
790B GLN* 4.5 6.7 - - - +
791B THR* 2.8 50.8 + - + +
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Residues in contact with ASN 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B HIS* 5.0 6.9 + - - +
712B GLU* 3.2 34.7 - - + +
730B PHE* 4.3 6.0 - - + -
731B PRO 4.4 12.5 + - - +
732B LEU* 5.3 3.6 - - - +
733B VAL* 3.1 25.1 + - - +
734B ASN 4.4 0.7 - - - +
784B LEU* 3.0 36.3 + - - +
785B SER* 3.2 8.5 + - - +
787B TYR* 1.3 85.7 - - - +
789B VAL* 1.3 56.7 + - + +
791B THR* 3.4 9.6 - - - +
792B SER* 2.7 28.6 + - - -
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Residues in contact with VAL 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B HIS* 3.3 34.5 - - + +
344B ALA* 3.4 26.0 - - + -
345B LEU* 3.9 28.3 - - + +
348B LEU* 4.3 3.5 - - + +
672B PHE* 3.8 19.3 - - + -
730B PHE* 4.1 13.7 - - + -
785B SER 3.3 2.0 + - - -
786B ASP 4.0 0.4 - - - +
788B ASN* 1.3 77.2 - - + +
790B GLN* 1.3 66.1 + - - +
792B SER* 3.0 17.5 + - - -
793B GLN 3.6 3.3 + - - -
796B ILE* 4.1 13.1 - - + +
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Residues in contact with GLN 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ALA* 3.7 17.0 - - + +
347B LYS* 3.4 42.0 - - - +
348B LEU* 4.1 19.2 - - + +
743B PRO* 3.8 31.6 - - + +
786B ASP* 2.9 40.0 + - - +
787B TYR* 4.0 2.2 + - - +
789B VAL* 1.3 77.5 - - - +
791B THR* 1.3 57.8 + - - +
792B SER 3.1 4.7 + - - -
793B GLN* 3.2 21.0 + - - +
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Residues in contact with THR 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B GLU* 3.9 23.8 - - + -
736B SER* 5.1 0.6 + - - +
743B PRO* 4.0 15.7 - - - +
744B GLY 4.9 2.4 + - - -
787B TYR* 2.8 48.5 + - + +
788B ASN 3.4 13.7 - - - +
790B GLN* 1.3 76.1 - - - +
792B SER* 1.3 57.1 + - - +
793B GLN* 3.4 2.1 + - - -
794B GLY 5.2 0.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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