Contacts of the helix formed by residues 681 - 702 (chain D) in PDB entry 1IYH
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 THR 681 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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679D GLY 3.3 0.2 - - - -
680D ASN* 1.3 83.4 - - + +
682D GLU* 1.3 65.7 + - - +
683D MET* 3.7 8.2 + - - +
684D GLU* 2.7 39.5 + - - +
685D GLN* 2.9 30.6 + - - +
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Residues in contact with GLU 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B TYR* 3.7 33.5 + - + +
273B LYS* 4.4 23.7 + - + +
274B ASN* 2.6 32.9 + - - -
681D THR* 1.3 73.2 - - - +
683D MET* 1.3 62.7 + - + +
685D GLN* 3.2 16.9 + - - +
686D CYS* 3.0 17.5 + - - +
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Residues in contact with MET 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 4.4 16.2 - - + +
259B LEU* 4.0 35.2 - - + -
261B LEU* 3.8 32.5 - - + +
270B TYR* 3.4 34.1 - - + +
681D THR* 3.2 7.7 + - - +
682D GLU* 1.3 80.6 - - - +
684D GLU* 1.3 63.3 + - + +
686D CYS* 3.0 15.0 + - - +
687D HIS* 3.1 27.5 + - - +
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Residues in contact with GLU 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679D GLY* 4.2 2.2 - - - -
680D ASN* 3.5 25.3 + - - +
681D THR* 2.7 42.7 + - - +
683D MET* 1.3 77.9 - - + +
685D GLN* 1.3 65.5 + - - +
687D HIS* 3.1 15.9 + - + +
688D VAL* 3.0 26.9 + - - +
742D ILE* 3.7 16.2 - - + +
743D GLY* 3.5 25.4 - - - +
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Residues in contact with GLN 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LYS* 2.5 41.5 + - - +
678D ALA* 4.5 8.3 - - + +
679D GLY* 3.2 38.5 + - - +
680D ASN 4.5 1.2 - - - -
681D THR* 2.9 26.6 + - - +
682D GLU* 3.2 11.6 + - - +
684D GLU* 1.3 76.1 - - - +
686D CYS* 1.3 61.1 + - - +
688D VAL* 3.4 5.0 + - - +
689D ASP* 3.0 30.2 + - - +
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Residues in contact with CYS 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 3.8 31.2 - - + -
262B HIS 4.7 2.0 - - - -
266B ALA* 3.6 32.0 - - - +
267B ILE* 4.0 4.5 - - - -
270B TYR* 4.0 20.0 - - + -
273B LYS* 5.2 0.2 - - - +
682D GLU 3.0 11.7 + - - +
683D MET 3.0 11.6 + - - +
685D GLN* 1.3 78.2 - - - +
687D HIS* 1.3 58.0 + - - +
689D ASP* 3.3 7.8 + - - +
690D ALA* 2.8 31.6 + - - +
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Residues in contact with HIS 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 5.8 5.4 - - + +
260B THR 3.9 13.2 + - - -
261B LEU* 3.5 29.2 - - + +
262B HIS* 5.5 6.6 + - - -
683D MET* 3.1 26.5 + - + +
684D GLU* 3.1 21.5 + - + +
686D CYS* 1.3 73.9 - - - +
688D VAL* 1.3 60.8 + - - +
690D ALA* 3.3 5.5 + - - +
691D ILE* 2.9 34.8 + - - +
734D TYR* 3.8 21.5 + + - +
742D ILE* 3.8 13.9 - - + -
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Residues in contact with VAL 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D GLY 4.2 12.8 - - - +
684D GLU 3.0 19.3 + - - +
685D GLN* 3.6 7.9 - - - +
686D CYS 3.3 0.2 - - - -
687D HIS* 1.3 76.9 - - - +
689D ASP* 1.3 64.1 + - - +
691D ILE* 3.3 1.6 + - - +
692D VAL* 3.0 27.6 + - + +
742D ILE* 3.9 22.7 - - + -
747D THR* 3.8 24.0 - - + +
748D TRP* 3.4 41.1 - - + +
749D ALA* 3.8 14.8 - - + +
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Residues in contact with ASP 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ALA* 3.8 15.5 - - + +
269B ARG* 3.2 31.5 + - - +
273B LYS* 5.0 4.9 + - - -
669D ARG* 2.9 35.1 + - - +
685D GLN* 3.0 21.5 + - - +
686D CYS* 3.6 6.8 - - - +
688D VAL* 1.3 78.6 - - - +
690D ALA* 1.3 55.9 + - - +
692D VAL* 3.4 7.3 + - - +
693D ASP* 3.0 33.6 + - - +
748D TRP* 3.7 11.8 + - - -
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Residues in contact with ALA 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B HIS* 3.4 49.6 - - + +
263B GLN* 3.4 11.1 - - + +
266B ALA* 3.7 3.8 - - + +
686D CYS* 2.8 22.0 + - - +
687D HIS* 3.7 5.8 - - - +
689D ASP* 1.3 72.0 - - - +
691D ILE* 1.3 65.6 + - - +
693D ASP 3.3 0.7 + - - -
694D THR* 2.9 27.4 + - - -
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Residues in contact with ILE 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 3.6 31.0 - - + -
262B HIS* 4.6 4.9 - - + +
687D HIS 2.9 20.3 + - - +
688D VAL 3.7 3.4 - - - +
690D ALA* 1.3 76.1 - - - +
692D VAL* 1.3 64.9 + - - +
694D THR* 3.3 4.7 + - - -
695D LEU* 3.1 37.7 + - + +
731D LEU* 4.9 7.9 - - + -
734D TYR* 3.6 37.9 - - + +
741D LEU* 4.1 24.2 - - + -
742D ILE* 4.0 7.6 - - + -
749D ALA* 4.2 11.4 - - + -
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Residues in contact with VAL 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665D LEU* 3.6 39.5 - - + -
669D ARG* 5.5 0.9 - - - +
688D VAL 3.0 20.2 + - - +
689D ASP 3.7 5.6 - - - +
691D ILE* 1.3 77.0 - - + +
693D ASP* 1.3 58.4 + - - +
695D LEU* 3.2 4.4 + - - +
696D ASP* 2.8 26.9 + - - +
748D TRP* 3.8 31.4 - - + -
749D ALA* 4.0 23.3 - - + -
752D TYR* 3.8 19.8 - - + -
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Residues in contact with ASP 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLN* 3.5 26.8 - - + +
265B LEU* 4.1 25.8 - - - +
266B ALA* 4.5 6.1 + - - +
269B ARG* 5.4 3.2 + - - -
293B ASP* 5.2 5.8 - - - +
1902B MG 4.6 8.5 - - - -
665D LEU* 3.8 19.4 - - - +
669D ARG* 4.8 7.6 + - - -
689D ASP* 3.0 20.2 + - - +
690D ALA 3.8 0.7 - - - +
692D VAL* 1.3 75.1 - - - +
694D THR* 1.3 59.8 + - - +
696D ASP* 3.8 4.5 - - - +
697D ASP* 2.8 38.0 + - - +
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Residues in contact with THR 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 3.9 31.7 - - + +
262B HIS* 3.4 17.5 + - - -
263B GLN* 3.1 19.9 + - - +
690D ALA 2.9 17.7 + - - -
691D ILE* 3.3 8.5 + - - +
693D ASP* 1.3 76.4 - - - +
695D LEU* 1.3 62.2 + - - +
697D ASP* 3.5 4.6 + - - +
698D PHE* 3.4 20.1 + - - +
727D LEU* 3.9 19.0 - - + +
731D LEU* 5.1 3.6 - - + -
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Residues in contact with LEU 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691D ILE* 3.1 32.7 + - + +
692D VAL* 3.5 5.4 - - - +
694D THR* 1.3 75.0 - - - +
696D ASP* 1.3 64.5 + - - +
698D PHE* 3.2 7.4 + - + +
699D MET* 3.0 28.2 + - - +
727D LEU* 4.6 9.9 - - + -
728D MET* 5.8 0.4 - - + -
731D LEU* 4.0 31.9 - - + -
749D ALA 4.6 0.2 - - - +
752D TYR* 3.9 21.8 - - + +
753D TRP* 3.8 44.4 - - + +
756D CYS* 4.1 11.4 - - + -
760D LEU* 6.4 1.6 - - + -
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Residues in contact with ASP 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ASP* 5.3 2.3 - - - +
1902B MG 3.9 12.6 - - - -
614D ARG* 2.8 29.2 + - - -
665D LEU* 3.7 24.0 - - + +
692D VAL 2.8 16.8 + - - +
693D ASP* 3.4 5.8 + - - +
695D LEU* 1.3 74.9 - - - +
697D ASP* 1.3 61.3 + - - +
699D MET* 3.3 4.6 + - - +
700D SER* 2.8 40.8 + - - -
752D TYR* 2.6 30.5 + - - +
1800D GSH 5.2 3.3 + - - +
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Residues in contact with ASP 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLN* 3.1 17.2 + - - +
296B ASP* 5.3 1.4 - - - +
300B SER* 5.7 0.7 + - - -
1400B GSH 2.9 32.8 + - - +
1902B MG 4.0 16.3 - - - -
693D ASP* 2.8 25.8 + - - +
694D THR* 3.7 6.1 - - - +
696D ASP* 1.3 73.7 - - - +
698D PHE* 1.3 62.0 + - - +
700D SER* 3.4 6.7 + - - -
701D CYS* 3.3 25.8 + - - -
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Residues in contact with PHE 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694D THR 3.4 4.8 + - - +
695D LEU* 3.2 8.1 + - + +
697D ASP* 1.3 77.4 - - - +
699D MET* 1.3 70.7 + - - +
701D CYS* 2.9 26.5 + - + +
702D PHE* 3.4 40.6 - + - -
719D LEU* 3.7 13.0 - - + -
723D ASN* 3.5 30.7 - - + -
724D ALA* 3.7 28.0 - - + -
727D LEU* 3.7 32.1 - - + -
728D MET* 5.3 0.2 - - + -
760D LEU* 3.9 27.6 - - + -
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Residues in contact with MET 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D ARG* 4.9 6.1 - - - +
695D LEU 3.0 19.8 + - - +
696D ASP* 3.9 7.0 - - - +
698D PHE* 1.3 81.7 - - - +
700D SER* 1.3 61.6 + - - +
701D CYS 3.3 1.2 + - - -
702D PHE* 3.3 12.3 + - + -
704D TRP* 3.0 48.1 + - + +
752D TYR* 5.4 1.3 - - - +
756D CYS* 3.7 44.6 - - + +
759D THR* 4.1 17.7 - - + -
760D LEU* 3.9 33.4 - - + -
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Residues in contact with SER 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ASP* 5.5 2.5 + - - -
614D ARG* 2.6 30.0 + - - +
696D ASP* 2.8 26.3 + - - -
697D ASP* 3.7 8.3 - - - -
698D PHE 3.1 0.2 - - - -
699D MET* 1.3 72.9 - - - +
701D CYS* 1.3 63.1 + - - +
702D PHE 3.3 6.7 + - - +
704D TRP* 4.9 3.1 - - - +
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Residues in contact with CYS 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D ASP* 3.3 22.5 + - - -
698D PHE* 2.9 20.2 + - + +
700D SER* 1.3 77.1 - - - +
702D PHE* 1.3 62.9 + - - +
703D PRO* 3.5 7.3 - - - +
715D MET* 4.3 7.3 - - - +
719D LEU* 3.7 28.8 - - + +
723D ASN* 5.8 2.0 - - - -
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Residues in contact with PHE 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D PHE* 3.4 57.0 - + - -
699D MET* 3.4 10.5 - - - -
700D SER 3.3 7.1 - - - +
701D CYS* 1.3 76.9 - - - +
703D PRO* 1.3 66.0 - - + +
704D TRP* 2.9 49.6 + + + -
716D PHE* 3.7 33.7 - + + -
719D LEU* 3.8 26.7 - - + -
720D LEU* 3.9 28.7 - - + -
760D LEU* 4.0 11.2 - - + -
763D PHE* 6.3 0.7 - + + -
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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