Contacts of the helix formed by residues 710 - 731 (chain B) in PDB entry 1XR2
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 ASN 710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PRO* 4.0 2.7 - - - -
708B THR 5.0 2.6 + - - +
709B ARG* 1.3 82.6 - - - +
711B TRP* 1.3 65.6 + - - +
712B ASP* 4.1 9.9 - - + +
713B GLU* 3.0 42.7 + - + +
714B VAL* 3.0 15.6 + - - +
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Residues in contact with TRP 711 (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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412B PHE* 3.6 39.3 - + + -
413B PRO* 3.7 44.7 + - + +
415B THR* 4.2 24.7 - - + +
446B ALA* 5.1 5.2 - - + -
449B LEU* 3.5 31.9 - - + -
463B PHE* 4.0 12.3 - + - -
710B ASN* 1.3 73.1 - - - +
712B ASP* 1.3 63.4 + - - +
714B VAL* 4.2 11.7 - - + -
715B ILE* 3.0 47.1 + - + +
718B LEU* 6.0 1.3 - - + -
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Residues in contact with ASP 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B ASN* 3.1 7.5 - - + +
711B TRP* 1.3 76.4 - - - +
713B GLU* 1.3 63.9 + - + +
715B ILE* 5.6 0.7 - - - -
716B PRO* 3.0 23.8 - - - +
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Residues in contact with GLU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B TRP* 4.8 2.9 - - + -
674B PRO* 3.6 36.9 - - - +
675B ALA 5.6 0.4 - - - +
676B VAL* 4.2 5.2 - - + +
709B ARG* 2.9 35.0 + - - -
710B ASN* 3.0 42.8 + - + +
712B ASP* 1.3 84.1 - - + +
714B VAL* 1.3 62.5 + - - +
716B PRO* 3.4 10.7 - - - +
717B SER* 2.8 25.6 + - - +
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Residues in contact with VAL 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B PHE* 5.0 0.4 - - + -
413B PRO* 3.6 23.1 - - + -
669B TRP* 3.8 14.0 - - + -
706B LEU* 3.6 22.0 - - + -
709B ARG* 3.8 17.5 - - + -
710B ASN 3.0 16.7 + - - +
711B TRP* 3.2 21.7 + - + +
713B GLU* 1.3 77.1 - - - +
715B ILE* 1.3 58.7 + - + +
717B SER* 3.3 3.1 + - - -
718B LEU* 2.9 50.6 + - + +
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Residues in contact with ILE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 4.0 35.7 - - + -
453B ILE* 4.3 7.2 - - + +
711B TRP* 3.0 30.2 + - + +
712B ASP* 5.6 0.7 - - - -
714B VAL* 1.3 75.8 - - + +
716B PRO* 1.3 67.5 - - + +
718B LEU* 3.2 9.0 + - + +
719B ARG* 3.0 58.4 + - - +
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Residues in contact with PRO 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B VAL* 4.0 20.4 - - + -
712B ASP* 3.0 29.2 - - - +
713B GLU 3.4 9.6 - - - +
715B ILE* 1.3 96.7 - - + +
717B SER* 1.3 58.0 + - - +
719B ARG* 3.5 10.6 + - + +
720B ASN* 2.9 31.3 + - - +
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Residues in contact with SER 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B TRP* 3.6 35.1 + - - +
675B ALA 4.3 1.0 + - - -
676B VAL* 3.7 15.4 - - - +
677B PRO* 3.4 22.6 - - - +
682B MET* 4.5 3.5 - - - +
713B GLU* 2.8 21.8 + - - +
714B VAL 3.3 0.9 + - - -
715B ILE 3.2 0.6 - - - -
716B PRO* 1.3 78.4 - - - +
718B LEU* 1.3 59.7 + - - +
720B ASN* 3.2 7.3 + - - +
721B MET* 2.9 27.4 + - - +
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Residues in contact with LEU 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B THR* 4.3 18.4 - - + -
412B PHE* 4.7 7.9 - - + -
449B LEU* 6.3 2.0 - - + -
450B GLN* 6.2 0.4 - - + -
453B ILE* 3.9 16.2 - - + -
455B LEU* 4.6 18.8 - - + +
669B TRP* 3.3 32.5 - - + -
702B PRO* 4.1 13.7 - - + -
706B LEU* 4.7 2.2 - - + -
711B TRP* 6.0 1.3 - - + -
714B VAL* 2.9 35.3 + - + +
715B ILE* 3.5 7.9 - - + +
717B SER* 1.3 75.2 - - - +
719B ARG* 1.3 64.7 + - - +
721B MET* 3.1 13.5 + - + +
722B VAL* 3.0 26.2 + - - +
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Residues in contact with ARG 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 5.2 3.4 - - - +
452B GLU* 2.8 35.7 + - - -
453B ILE* 3.7 36.3 + - + +
715B ILE* 3.0 36.1 + - - +
716B PRO* 3.7 10.1 - - - +
717B SER 3.3 0.2 - - - -
718B LEU* 1.3 75.4 - - - +
720B ASN* 1.3 60.2 - - - +
722B VAL* 3.3 4.8 + - - +
723B ALA* 2.9 27.8 + - - +
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Residues in contact with ASN 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B VAL* 3.3 16.6 - - - +
677B PRO 3.3 16.8 + - - +
678B SER* 5.1 1.2 - - - +
679B ILE* 4.0 20.2 - - + +
682B MET* 3.3 21.4 - - + +
716B PRO* 2.9 17.9 + - - +
717B SER* 3.2 5.5 + - - +
718B LEU 3.2 0.6 - - - -
719B ARG* 1.3 77.0 - - - +
721B MET* 1.3 64.6 + - - +
723B ALA* 3.3 6.9 + - - +
724B LEU* 2.9 25.1 + - - +
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Residues in contact with MET 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B THR* 4.3 4.7 - - + -
407B THR 3.1 28.3 - - - +
455B LEU* 3.9 23.3 - - + -
668B VAL* 4.2 8.3 - - + -
669B TRP* 5.0 4.3 - - + -
682B MET* 3.7 12.7 - - - +
700B ILE* 3.6 28.7 - - + +
701B ASN* 3.5 27.6 - - - +
702B PRO* 3.7 14.6 - - + -
717B SER 2.9 12.8 + - - +
718B LEU* 3.1 18.8 + - + +
720B ASN* 1.3 78.6 - - - +
722B VAL* 1.3 61.3 + - - +
724B LEU* 3.4 4.7 + - - +
725B ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B THR* 4.4 7.9 - - + +
453B ILE* 3.7 34.3 - - + +
454B GLY* 3.9 20.0 - - - +
455B LEU* 4.0 17.0 - - + -
718B LEU 3.0 13.6 + - - +
719B ARG* 3.6 8.3 - - - +
720B ASN 3.2 0.2 - - - -
721B MET* 1.3 75.6 - - + +
723B ALA* 1.3 66.4 + - - +
725B ALA* 3.1 8.1 + - - +
726B LYS* 2.9 25.1 + - + +
729B ARG* 5.4 6.1 + - - +
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Residues in contact with ALA 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ILE* 3.7 23.1 - - + -
719B ARG 2.9 16.7 + - - +
720B ASN* 3.6 7.6 - - - +
722B VAL* 1.3 76.6 - - - +
724B LEU* 1.3 63.6 + - - +
726B LYS* 3.2 9.1 + - - +
727B GLU* 3.0 27.3 + - - +
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Residues in contact with LEU 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ILE* 3.9 20.8 - - + +
682B MET* 4.1 20.6 - - + -
683B ARG* 3.8 38.6 - - + +
686B VAL* 3.7 17.0 - - + -
700B ILE* 3.5 28.9 - - + -
720B ASN 2.9 18.1 + - - +
721B MET* 3.6 6.7 - - - +
723B ALA* 1.3 74.0 - - - +
725B ALA* 1.3 69.1 + - - +
727B GLU* 2.8 7.3 + - + +
728B MET* 2.8 32.9 + - + +
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Residues in contact with ALA 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 3.9 15.3 - - - +
406B THR* 3.5 31.0 - - + -
700B ILE* 3.9 17.7 - - + -
721B MET 3.1 6.1 + - - +
722B VAL* 3.1 8.0 + - - +
724B LEU* 1.3 79.7 - - - +
726B LYS* 1.3 63.6 + - - +
728B MET* 3.2 3.1 + - - +
729B ARG* 3.0 36.0 + - - +
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Residues in contact with LYS 726 (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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722B VAL* 2.9 15.8 + - + +
723B ALA* 3.4 12.1 - - - +
725B ALA* 1.3 77.0 - - - +
727B GLU* 1.3 63.3 + - + +
729B ARG* 3.2 21.8 + - - +
730B GLU* 3.2 19.2 + - - +
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Residues in contact with GLU 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ILE* 3.6 31.9 - - - +
683B ARG* 2.5 44.0 + - - +
723B ALA* 3.0 14.9 + - - +
724B LEU* 2.8 10.8 + - + +
726B LYS* 1.3 75.7 - - + +
728B MET* 1.3 57.3 + - - +
730B GLU* 2.9 10.4 + - - +
731B LYS* 2.9 27.4 + - - +
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Residues in contact with MET 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 5.4 0.5 - - - +
404B PHE* 3.5 29.4 - - + -
683B ARG* 4.3 15.0 - - - -
686B VAL* 3.4 32.8 - - + -
687B GLU* 4.1 16.8 - - + -
690B LEU* 3.8 17.9 - - + -
700B ILE* 4.8 0.9 - - + -
724B LEU* 2.8 47.7 + - + +
725B ALA* 3.6 6.1 - - - +
727B GLU* 1.3 72.9 - - - +
729B ARG* 1.3 63.5 + - - +
731B LYS* 3.1 28.9 + - + +
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Residues in contact with ARG 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PRO* 3.5 25.1 - - - +
403B LEU* 2.8 67.3 + - + +
404B PHE* 3.0 29.3 + - + -
406B THR* 5.5 1.2 + - - +
456B ASP* 3.5 16.2 + - - -
722B VAL* 5.4 6.1 + - - +
725B ALA* 3.0 28.1 + - - +
726B LYS* 3.5 22.4 - - - +
727B GLU 3.2 0.2 - - - -
728B MET* 1.3 75.6 - - - +
730B GLU* 1.3 62.1 + - - +
731B LYS 4.5 1.7 - - - -
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Residues in contact with GLU 730 (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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726B LYS 3.2 9.8 + - - +
727B GLU* 2.9 12.8 + - - +
729B ARG* 1.3 76.5 - - - +
731B LYS* 1.3 67.7 + - - +
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Residues in contact with LYS 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B GLU 2.9 12.5 + - - +
728B MET* 3.1 29.5 + - + +
729B ARG 4.5 2.0 - - - -
730B GLU* 1.3 81.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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