Contacts of the helix formed by residues 679 - 698 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B TYR* 5.9 1.8 - - - -
663B CYS* 3.2 30.7 - - - +
666B THR* 4.3 5.4 - - - -
667B ASP* 2.4 36.5 + - - -
677B MSE 3.7 0.6 - - - -
678B MSE 1.3 82.2 - - - +
680B ASP* 1.3 64.2 + - - +
681B LEU* 3.1 10.6 + - - +
682B THR* 3.1 14.8 + - - -
683B ARG* 3.3 11.3 + - - +
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Residues in contact with ASP 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LYS* 4.8 12.4 + - - -
663B CYS* 4.2 7.8 - - - -
678B MSE 4.9 1.9 - - - +
679B SER* 1.3 74.7 - - - +
681B LEU* 1.3 57.6 + - - +
683B ARG* 3.4 10.9 + - - +
684B ASN* 3.0 27.9 + - - +
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Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B GLN* 5.6 1.1 - - - +
552B ARG* 3.3 27.1 - - - +
660B HIS* 3.8 44.2 - - + +
663B CYS* 3.6 19.3 - - + -
664B ILE* 3.9 13.7 - - + -
679B SER* 3.0 10.5 + - - +
680B ASP* 1.3 78.9 - - - +
682B THR* 1.3 60.8 + - - +
684B ASN* 4.5 8.1 - - + +
685B ASP* 2.8 48.7 + - - +
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Residues in contact with THR 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LEU* 4.3 23.6 - - + -
548B ILE* 4.0 12.1 - - + +
552B ARG* 3.4 11.5 + - - +
667B ASP* 2.7 29.4 + - - -
677B MSE 3.6 29.0 - - + +
679B SER* 3.1 13.1 + - - -
681B LEU* 1.3 74.9 - - - +
683B ARG* 1.3 60.1 + - - +
685B ASP* 3.9 2.7 - - - +
686B LEU* 2.8 34.2 + - + +
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Residues in contact with ARG 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B SER 3.3 8.7 + - - +
680B ASP* 3.6 14.8 - - - +
682B THR* 1.3 81.9 - - - +
684B ASN* 1.3 67.0 + - - +
686B LEU* 3.5 9.2 + - + +
687B ASP* 3.1 41.8 + - - +
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Residues in contact with ASN 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B ASP 3.0 17.6 + - - +
681B LEU* 4.0 10.7 - - + +
683B ARG* 1.3 86.1 - - - +
685B ASP* 1.3 63.3 + - - +
687B ASP* 3.2 11.4 + - - +
688B THR* 2.8 42.5 + - - -
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Residues in contact with ASP 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 2.8 40.5 + - + +
548B ILE* 3.9 9.4 - - + -
551B GLN* 4.5 1.4 + - - -
552B ARG* 2.9 24.3 + - - +
681B LEU* 2.8 37.9 + - - +
682B THR 3.9 2.5 - - - +
684B ASN* 1.3 75.1 - - - +
686B LEU* 1.3 63.7 + - - +
688B THR* 3.3 6.5 + - - -
689B LEU* 2.9 30.2 + - - +
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B GLN* 3.5 40.4 - - + +
544B ILE* 3.5 30.3 - - + -
545B LEU* 4.1 22.2 - - + -
548B ILE* 3.7 7.4 - - + +
682B THR* 2.8 20.2 + - + +
683B ARG* 3.6 9.0 - - + +
685B ASP* 1.3 78.1 - - - +
687B ASP* 1.3 54.2 + - - +
690B LEU* 2.8 47.9 + - + +
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Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LYS* 5.7 2.6 + - - -
683B ARG* 3.1 33.5 + - - +
684B ASN* 3.6 12.5 + - - +
686B LEU* 1.3 76.4 - - - +
688B THR* 1.3 56.9 + - - +
690B LEU* 4.7 2.5 - - - -
691B SER* 2.8 51.1 + - - +
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Residues in contact with THR 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 3.8 16.7 - - + -
114A PHE* 4.5 9.9 - - + -
118A GLN* 3.4 29.8 + - - +
122A TYR* 4.2 8.5 + - - +
684B ASN* 2.8 30.7 + - - -
685B ASP* 3.7 9.0 + - - -
686B LEU 3.3 0.2 - - - -
687B ASP* 1.3 77.2 - - - +
689B LEU* 1.3 64.5 + - + +
691B SER* 4.0 2.1 - - - -
692B MSE 3.2 22.7 + - - +
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Residues in contact with LEU 689 (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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102A TRP* 3.7 32.3 - - + -
103A LYS* 4.5 12.1 - - + +
106A TYR* 3.7 52.3 - - + -
114A PHE* 4.2 8.3 - - + -
544B ILE* 3.8 32.0 - - + +
547B LEU* 4.9 7.4 - - + -
548B ILE* 4.1 5.8 - - + -
685B ASP 2.9 23.1 + - - +
688B THR* 1.3 73.5 - - + +
690B LEU* 1.3 64.8 + - - +
692B MSE 3.4 3.6 + - - +
693B GLU* 3.2 23.7 + - - +
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LYS* 3.7 48.9 - - + +
540B ILE* 4.0 33.7 - - + -
541B GLN* 3.8 24.0 - - + +
544B ILE* 4.3 9.8 - - + +
686B LEU* 2.8 37.2 + - + +
687B ASP* 4.5 2.7 - - - +
689B LEU* 1.3 71.0 - - - +
691B SER* 1.3 65.8 + - - +
693B GLU* 3.3 3.9 + - + +
694B ILE* 3.0 33.1 + - + +
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Residues in contact with SER 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LYS* 5.8 4.1 + - - +
687B ASP* 2.8 40.5 + - - -
688B THR* 4.0 2.7 - - - -
690B LEU* 1.3 76.0 - - - +
692B MSE 1.3 63.0 + - - +
694B ILE* 3.3 7.1 + - - +
695B LYS* 3.0 44.6 + - - +
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Residues in contact with MSE 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 5.9 0.2 - - - -
102A TRP* 3.5 43.1 - - + -
118A GLN 4.1 2.2 - - - +
121A MSE 3.3 45.1 - - + +
122A TYR* 3.4 32.1 - - + -
125A MSE 3.8 28.5 - - - +
688B THR 3.2 9.8 + - - +
689B LEU 3.7 2.0 - - - +
690B LEU 3.2 0.6 - - - -
691B SER* 1.3 79.3 - - - +
693B GLU* 1.3 57.6 + - - +
695B LYS* 3.2 5.6 + - - +
696B LEU* 2.9 50.4 + - + +
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Residues in contact with GLU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.9 23.9 - - - -
103A LYS* 2.9 36.4 + - - +
540B ILE* 3.9 34.1 - - + -
543B GLU* 4.7 6.1 - - - +
544B ILE* 4.5 6.6 - - + +
689B LEU 3.2 11.1 + - - +
690B LEU* 3.6 11.4 - - - +
692B MSE 1.3 77.5 - - - +
694B ILE* 1.3 57.8 + - - +
696B LEU* 3.4 14.1 + - - +
697B ARG* 2.9 39.8 + - - +
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Residues in contact with ILE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ILE* 4.1 15.5 - - + +
536B LEU* 3.9 28.0 - - + -
537B LYS* 3.7 34.3 - - + +
540B ILE* 4.3 10.3 - - + -
690B LEU* 3.0 19.2 + - + +
691B SER* 3.5 9.9 - - - +
693B GLU* 1.3 75.7 - - - +
695B LYS* 1.3 60.5 + - + +
697B ARG* 2.9 8.6 + - - +
698B LEU* 2.8 54.7 + - + +
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Residues in contact with LYS 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 5.5 11.7 - - + -
125A MSE 3.1 37.7 - - + -
691B SER* 3.0 33.9 + - - +
692B MSE 3.6 6.3 - - - +
694B ILE* 1.3 78.0 - - + +
696B LEU* 1.3 62.7 + - - +
698B LEU* 3.3 8.0 + - - +
699B LEU* 3.2 28.8 + - - +
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Residues in contact with LEU 696 (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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51A LYS* 5.2 0.2 + - - -
95A LEU* 3.6 48.9 - - + +
96A TRP* 3.5 35.5 + - + +
99A GLY* 4.6 12.1 - - - -
121A MSE 5.9 1.1 - - - -
125A MSE 5.2 6.5 - - - -
692B MSE 2.9 42.5 + - + +
693B GLU* 3.5 19.5 - - - +
695B LYS* 1.3 76.3 - - + +
697B ARG* 1.3 61.3 + - - +
699B LEU* 3.4 28.6 + - + +
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Residues in contact with ARG 697 (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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30A GLN* 3.1 40.2 + - - +
31A ILE 4.7 4.1 + - - +
32A GLY* 3.5 27.5 - - - +
33A ASP* 4.3 9.4 + - - -
96A TRP* 3.7 25.3 - - - -
536B LEU* 3.9 28.3 - - + +
540B ILE* 3.9 28.7 - - + +
543B GLU* 5.8 1.0 + - - -
693B GLU* 2.9 34.9 + - + +
694B ILE* 2.9 8.6 + - - +
696B LEU* 1.3 77.7 - - - +
698B LEU* 1.3 60.0 + - + +
699B LEU 3.4 0.9 + - - -
700B ASP 4.9 0.7 + - - -
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 4.2 28.9 - - + +
32A GLY* 4.8 0.2 - - - -
533B ILE* 3.8 24.0 - - + -
536B LEU* 4.8 1.3 - - + -
694B ILE* 2.8 38.2 + - + +
695B LYS* 3.3 6.9 + - - +
696B LEU 3.3 0.4 - - - -
697B ARG* 1.3 83.4 - - + +
699B LEU* 1.3 64.6 + - - +
700B ASP 3.2 2.9 - - - -
701B LEU* 2.8 44.1 + - + +
702B GLU* 3.9 2.4 + - - +
706B ILE* 5.1 5.6 - - + -
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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