Contacts of the helix formed by residues 787 - 798 (chain B) in PDB entry 1S2S
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 GLY 787 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784B PHE 2.7 22.0 + - - -
785B GLY 3.2 2.7 + - - -
786B ASP* 1.4 71.1 - - - +
788B GLU* 1.4 53.9 + - - +
789B MET 3.3 2.9 - - - -
790B GLU* 3.2 13.1 + - - +
791B GLU* 2.6 37.7 + - - +
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Residues in contact with GLU 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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464A ILE* 6.1 1.3 - - + -
467A LYS* 2.4 44.0 + - + +
783B LEU* 2.9 36.1 + - + +
786B ASP* 3.4 9.6 + - + +
787B GLY* 1.4 74.3 - - - +
789B MET* 1.4 52.8 + - - +
791B GLU* 4.5 5.4 - - - -
792B LEU* 2.6 41.1 + - + +
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Residues in contact with MET 789 (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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460A PHE* 3.7 22.9 - - + -
464A ILE* 5.2 10.5 - - + +
529A PHE* 3.5 22.0 - - - +
530A ILE* 4.7 5.6 - - + -
531A GLU 5.3 2.0 - - - +
780B ILE* 5.9 2.9 - - + -
783B LEU* 2.7 20.6 + - - +
784B PHE* 3.4 42.4 - - + +
788B GLU* 1.4 70.8 - - - +
790B GLU* 1.3 100.0 + - - +
792B LEU* 4.6 3.8 - - - -
793B GLU* 2.6 65.4 + - - +
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Residues in contact with GLU 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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784B PHE* 3.2 33.7 - - - +
787B GLY* 3.2 12.7 + - - +
789B MET* 1.3 103.3 - - - +
791B GLU* 1.3 53.5 + - - +
793B GLU* 4.4 3.4 - - - -
794B ALA* 2.6 39.6 + - - +
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Residues in contact with GLU 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B GLY 2.6 21.3 + - - +
788B GLU* 3.9 4.5 - - - +
790B GLU* 1.3 72.8 - - - +
792B LEU* 1.3 54.4 + - - +
794B ALA* 4.5 4.3 - - - -
795B LEU* 2.6 64.9 + - + +
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Residues in contact with LEU 792 (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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460A PHE* 3.8 20.6 - - + -
463A ASP* 3.9 15.5 - - + +
464A ILE* 3.6 36.6 - - + +
467A LYS* 5.1 7.9 - - + -
788B GLU* 2.6 24.3 + - + +
789B MET* 3.8 1.6 - - - +
791B GLU* 1.3 73.2 - - - +
793B GLU* 1.3 52.0 + - - +
795B LEU* 3.4 7.3 + - + -
796B TRP* 2.7 76.2 + - + +
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Residues in contact with GLU 793 (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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460A PHE* 3.9 25.9 - - + -
529A PHE 4.5 1.0 - - - +
530A ILE* 3.0 36.4 - - + +
737B ASN* 5.0 1.9 + - - -
789B MET* 2.6 58.1 + - - +
790B GLU* 3.8 3.6 - - - +
792B LEU* 1.3 72.8 - - - +
794B ALA* 1.3 51.7 + - - +
796B TRP* 2.9 4.7 + - - -
797B LEU* 2.6 54.5 + - + +
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Residues in contact with ALA 794 (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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790B GLU 2.6 24.8 + - - +
791B GLU* 3.8 4.0 - - - +
793B GLU* 1.3 71.2 - - - +
795B LEU* 1.4 55.2 + - + +
797B LEU* 2.9 7.3 + - - +
798B THR* 2.6 39.3 + - - +
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Residues in contact with LEU 795 (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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791B GLU* 2.6 53.7 + - + +
792B LEU* 3.7 7.0 - - + +
794B ALA* 1.4 73.4 - - + +
796B TRP* 1.3 70.3 + - + +
798B THR* 3.5 21.4 + - + +
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Residues in contact with TRP 796 (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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448A GLU* 3.7 22.4 - - + -
457A CYS 5.4 0.2 - - - -
458A LYS* 3.4 65.8 - - + +
459A GLY 3.5 1.8 - - - +
460A PHE* 3.4 40.8 - - + -
462A ILE* 4.8 0.2 - - + -
463A ASP* 3.2 45.7 + - + -
738B TYR* 3.7 20.2 + - - +
792B LEU* 2.7 47.3 + - + +
793B GLU* 3.6 5.8 - - - +
795B LEU* 1.3 82.1 - - + +
797B LEU* 1.4 60.2 + - - +
798B THR 5.0 0.7 - - - +
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Residues in contact with LEU 797 (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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460A PHE* 6.4 0.2 - - + -
737B ASN* 3.7 26.0 - - + +
738B TYR* 3.3 67.9 - - + +
741B GLY* 5.3 3.7 - - - -
793B GLU* 2.6 43.5 + - + +
794B ALA* 2.9 9.3 + - - +
796B TRP* 1.4 74.2 - - - +
798B THR* 1.4 66.8 + - - +
799B GLY* 2.7 8.4 + - - +
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Residues in contact with THR 798 (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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794B ALA* 2.6 24.1 + - - +
795B LEU* 3.5 23.1 + - + +
796B TRP 5.0 0.7 - - - +
797B LEU* 1.4 68.5 - - - +
799B GLY* 1.4 57.3 + - - +
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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
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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