Contacts of the helix formed by residues 679 - 699 (chain D) in PDB entry 3A98
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 SER 679 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D TYR* 6.0 1.6 - - - -
663D CYS* 3.4 29.3 - - - +
666D THR* 4.9 8.6 - - - +
667D ASP* 2.5 35.0 + - - -
677D MSE 3.7 0.6 - - - -
678D MSE 1.3 85.3 - - - +
680D ASP* 1.3 62.1 + - - +
681D LEU* 3.3 2.4 + - - +
682D THR* 3.0 18.5 + - - -
683D ARG* 3.4 17.9 + - - +
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Residues in contact with ASP 680 (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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52A HIS* 2.8 44.4 + - - +
54A MSE 3.6 23.2 - - + +
55A LEU* 3.6 12.7 - - + +
659D LYS* 5.0 10.8 - - - +
663D CYS* 4.3 3.5 - - - -
679D SER* 1.3 73.7 - - - +
681D LEU* 1.3 55.2 + - - +
683D ARG* 3.0 35.1 + - - +
684D ASN* 2.7 34.7 + - - +
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Residues in contact with LEU 681 (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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54A MSE 3.8 15.0 - - + +
727B ASN* 3.7 24.7 - - - +
551D GLN* 5.7 0.4 - - - +
552D ARG* 3.6 13.9 - - - +
660D HIS* 3.9 25.8 - - + +
663D CYS* 3.7 19.5 - - + -
664D ILE* 3.4 34.3 - - + -
679D SER* 3.2 8.2 - - - +
680D ASP* 1.3 81.0 - - - +
682D THR* 1.3 56.6 + - - +
684D ASN* 3.2 6.1 + - + +
685D ASP* 2.7 47.8 + - - +
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Residues in contact with THR 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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545D LEU* 4.8 12.6 - - + -
548D ILE* 4.0 18.4 - - + +
552D ARG* 3.3 13.5 + - - +
667D ASP* 3.1 27.9 + - - -
677D MSE 3.7 28.4 - - + +
679D SER* 3.0 17.1 + - - +
680D ASP 3.2 0.2 - - - -
681D LEU* 1.3 73.8 - - - +
683D ARG* 1.3 67.4 + - - +
685D ASP* 4.0 2.4 - - - +
686D LEU* 2.9 27.3 + - + +
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Residues in contact with ARG 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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52A HIS* 5.8 3.4 + - - -
55A LEU* 4.1 21.4 - - + +
678D MSE 2.9 32.3 + - - +
679D SER 3.4 4.6 + - - +
680D ASP* 3.0 33.4 + - - +
682D THR* 1.3 81.5 - - - +
684D ASN* 1.3 59.1 + - - +
686D LEU* 3.7 10.4 - - + +
687D ASP* 3.1 23.6 + - - +
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Residues in contact with ASN 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.6 1.4 - - - +
54A MSE 3.2 27.6 + - - +
55A LEU* 3.9 9.3 - - + +
56A GLN* 3.6 27.5 + - - +
726B CYS* 6.0 2.9 - - - +
727B ASN* 5.0 5.0 - - - +
680D ASP 2.7 16.0 + - - +
681D LEU* 3.7 8.6 - - + +
683D ARG* 1.3 73.1 - - - +
685D ASP* 1.3 65.2 + - - +
687D ASP* 3.2 13.0 + - - +
688D THR* 2.8 42.8 + - - -
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Residues in contact with ASP 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 2.6 45.2 + - + +
548D ILE* 4.1 8.5 - - + -
551D GLN* 4.7 0.9 + - - -
552D ARG* 2.9 22.9 + - - +
681D LEU* 2.7 37.6 + - - +
682D THR 4.0 2.5 - - - +
684D ASN* 1.3 72.0 - - - +
686D LEU* 1.3 59.0 + - - +
688D THR* 3.0 6.2 + - - -
689D LEU* 2.7 38.8 + - - +
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Residues in contact with LEU 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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541D GLN* 4.0 33.9 - - + +
544D ILE* 3.8 22.4 - - + -
545D LEU* 3.9 24.9 - - + -
548D ILE* 3.7 10.5 - - + +
682D THR* 2.9 21.4 + - + +
683D ARG* 3.7 9.4 - - + +
685D ASP* 1.3 77.4 - - - +
687D ASP* 1.3 54.4 + - - +
690D LEU* 2.8 51.1 + - + +
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Residues in contact with ASP 687 (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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23A GLY* 3.7 5.8 - - - -
24A ALA* 3.2 23.7 + - - +
26A GLN 4.3 6.6 - - - +
27A LEU* 5.7 2.1 - - - +
683D ARG 3.1 15.3 + - - +
684D ASN* 3.5 13.8 + - - +
685D ASP 3.2 0.2 - - - -
686D LEU* 1.3 79.6 - - - +
688D THR* 1.3 63.4 + - - +
690D LEU* 4.9 1.8 - - - -
691D SER* 2.7 51.3 + - - +
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Residues in contact with THR 688 (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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24A ALA* 3.7 16.7 - - - +
102C TRP* 3.5 20.1 - - + -
114C PHE* 4.3 11.4 - - + -
118C GLN* 3.5 29.9 + - - +
122C TYR* 4.6 2.9 + - - +
684D ASN* 2.8 30.5 + - - -
685D ASP* 3.5 7.4 - - - -
687D ASP* 1.3 79.9 - - - +
689D LEU* 1.3 64.2 + - + +
691D SER* 4.1 1.2 - - - -
692D MSE 3.3 20.4 + - - +
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Residues in contact with LEU 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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102C TRP* 3.7 31.2 - - + -
103C LYS* 4.9 7.4 - - + -
106C TYR* 3.5 44.6 - - + -
114C PHE* 4.3 14.8 - - + -
544D ILE* 3.7 30.4 - - + +
547D LEU* 4.4 14.1 - - + -
548D ILE* 4.1 5.8 - - + -
685D ASP* 2.7 23.2 + - - +
688D THR* 1.3 74.5 - - + +
690D LEU* 1.3 62.9 + - - +
692D MSE 3.3 4.0 + - - +
693D GLU* 3.1 22.7 + - - +
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Residues in contact with LEU 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LYS* 4.2 34.3 - - + +
540D ILE* 3.8 34.3 - - + -
541D GLN* 4.2 22.7 - - + +
544D ILE* 4.4 10.0 - - + +
686D LEU* 2.8 36.3 + - + +
687D ASP* 4.5 2.0 - - - +
689D LEU* 1.3 73.8 - - - +
691D SER* 1.3 56.5 + - - +
693D GLU* 3.1 4.8 + - + +
694D ILE* 2.9 43.8 + - + +
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Residues in contact with SER 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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22A SER 4.5 2.9 + - - -
23A GLY* 3.3 9.4 - - - -
24A ALA 3.2 27.5 + - - -
537D LYS* 6.2 0.2 - - - -
687D ASP* 2.7 38.6 + - - -
688D THR 4.1 1.8 - - - -
690D LEU* 1.3 77.1 - - - +
692D MSE 1.3 58.3 + - - +
694D ILE* 3.3 12.4 + - - +
695D LYS* 2.9 37.4 + - - +
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Residues in contact with MSE 692 (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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102C TRP* 3.4 37.9 - - + -
118C GLN* 5.2 1.1 - - - +
121C MSE 3.7 41.3 - - + +
122C TYR* 3.6 24.5 - - + -
125C MSE 3.2 25.4 - - + +
688D THR 3.3 9.0 + - - +
689D LEU 3.6 1.8 - - - +
690D LEU 3.1 0.4 - - - -
691D SER* 1.3 76.5 - - - +
693D GLU* 1.3 61.4 + - - +
695D LYS* 3.1 35.0 + - + +
696D LEU* 2.8 38.0 + - + +
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Residues in contact with GLU 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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96C TRP* 3.8 24.9 - - - -
103C LYS* 2.9 39.5 + - - -
540D ILE* 3.6 39.4 - - + +
543D GLU* 4.9 4.0 - - - +
544D ILE* 4.8 3.8 - - + +
689D LEU 3.1 11.2 + - - +
690D LEU* 3.3 12.1 - - - +
692D MSE 1.3 78.9 - - - +
694D ILE* 1.3 62.6 + - - +
696D LEU* 3.3 11.5 + - - +
697D ARG* 2.9 33.2 + - + +
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Residues in contact with ILE 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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533D ILE* 3.9 18.4 - - + +
536D LEU* 4.7 17.0 - - + -
537D LYS* 3.4 44.6 - - + +
540D ILE* 5.6 1.3 - - + -
690D LEU* 2.9 29.6 + - + +
691D SER* 3.6 12.6 - - - +
692D MSE 3.2 0.2 - - - -
693D GLU* 1.3 76.6 - - + +
695D LYS* 1.3 65.3 + - + +
697D ARG* 3.1 9.3 + - - +
698D LEU* 2.9 42.9 + - + +
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Residues in contact with LYS 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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22A SER* 4.5 22.4 + - - -
23A GLY 4.7 0.6 + - - -
24A ALA 3.5 24.8 + - - -
25A PRO* 4.1 13.3 - - - +
26A GLN* 6.1 0.2 - - - +
122C TYR* 4.5 3.1 - - + -
125C MSE 3.4 25.8 - - + -
691D SER* 2.9 19.7 + - - +
692D MSE 3.1 24.9 - - + +
694D ILE* 1.3 76.5 - - + +
696D LEU* 1.3 64.2 + - - +
698D LEU* 3.1 18.0 + - + +
699D LEU* 3.2 16.1 + - - +
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Residues in contact with LEU 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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95C LEU* 3.7 33.7 - - + +
96C TRP* 3.6 40.6 + - + +
99C GLY* 4.6 9.0 - - - -
103C LYS* 6.1 1.3 - - - -
121C MSE 3.9 20.4 - - + -
125C MSE 3.4 19.3 - - + -
692D MSE 2.8 21.6 + - + +
693D GLU* 3.5 19.3 - - - +
695D LYS* 1.3 75.3 - - - +
697D ARG* 1.3 63.9 + - - +
698D LEU 3.0 1.4 + - - -
699D LEU* 3.1 29.5 + - + +
700D ASP 5.0 0.2 + - - -
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Residues in contact with ARG 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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30C GLN* 3.3 40.6 - - - +
31C ILE 4.6 3.2 + - - +
32C GLY* 3.5 28.6 - - - +
33C ASP* 3.4 16.0 + - - -
96C TRP* 3.7 24.9 - - + -
536D LEU* 3.7 29.1 - - + +
540D ILE* 4.0 22.8 - - + +
543D GLU* 5.9 0.6 + - - -
693D GLU* 2.9 35.4 + - + +
694D ILE 3.1 6.0 + - - +
696D LEU* 1.3 74.2 - - - +
698D LEU* 1.3 59.2 + - - +
699D LEU 3.5 0.4 + - - -
700D ASP 4.8 1.2 + - - -
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Residues in contact with LEU 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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31C ILE* 4.1 26.2 - - + +
533D ILE* 4.8 13.2 - - + -
536D LEU* 4.9 3.8 - - + -
694D ILE* 2.9 36.7 + - + +
695D LYS* 3.1 9.2 + - + +
696D LEU 3.0 0.4 - - - -
697D ARG* 1.3 80.9 - - + +
699D LEU* 1.3 65.2 + - - +
700D ASP 3.3 3.1 - - - -
701D LEU* 3.0 44.7 + - + +
702D GLU* 4.2 4.3 + - - +
706D ILE* 5.3 2.2 - - + -
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Residues in contact with LEU 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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92C THR* 4.0 29.6 - - + +
95C LEU* 3.9 33.2 - - + -
96C TRP* 4.3 4.9 - - - +
125C MSE 4.5 14.8 - - + +
128C ARG* 3.0 47.4 + - - +
695D LYS 3.2 11.3 + - - +
696D LEU* 3.1 33.2 + - + +
697D ARG 3.5 0.2 - - - -
698D LEU* 1.3 76.9 - - - +
700D ASP* 1.3 59.0 + - - +
701D LEU 3.1 4.2 + - - -
702D GLU* 3.5 10.3 + - - +
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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
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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