Contacts of the helix formed by residues 902 - 920 (chain B) in PDB entry 1P48
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 ARG 902 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER 3.0 16.2 + - - -
208A VAL* 3.9 20.0 - - - +
401A ALA* 4.6 3.6 - - - +
402A ARG* 3.7 39.5 - - + +
404A GLU* 3.8 8.1 - - - +
513B SER* 2.9 30.3 + - - -
514B ARG* 4.8 3.0 - - - +
708B VAL* 4.1 4.7 - - + -
709B GLY 2.8 27.4 + - - -
710B ASP* 3.2 22.1 + - - +
711B GLN 4.3 0.2 - - - -
712B GLY* 3.5 26.9 - - - +
901B ALA* 1.3 81.5 - - + +
903B SER* 1.3 61.0 + - - +
904B GLU* 2.7 32.8 + - - +
905B ARG* 2.9 19.8 + - + -
906B LEU* 3.1 8.9 - - - +
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Residues in contact with SER 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP 4.5 0.3 - - - -
13A SER* 3.8 12.1 + - - -
377A GLU 3.8 0.5 + - - -
378A THR* 3.6 14.2 - - - -
379A GLU* 4.0 18.1 + - - +
403A SER* 4.3 3.1 - - - -
404A GLU* 3.0 45.5 + - - +
879B GLU* 5.4 0.7 - - - -
902B ARG* 1.3 66.5 - - - +
904B GLU* 1.3 55.8 + - - +
905B ARG 2.9 6.1 - - - -
906B LEU* 3.7 12.0 - - - +
907B ALA* 2.8 31.2 + - - +
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Residues in contact with GLU 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 3.8 0.9 - - - -
403A SER* 3.0 40.5 + - - +
513B SER* 3.2 15.9 - - - -
877B GLU* 3.7 15.2 - - + +
878B THR 3.7 12.1 - - - +
897B THR* 4.6 0.2 + - - -
902B ARG* 2.7 40.3 + - - +
903B SER* 1.3 73.8 - - - +
905B ARG* 1.3 103.9 + - - +
908B LYS* 2.8 33.2 + - - +
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Residues in contact with ARG 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B SER* 3.4 8.7 + - - -
710B ASP 2.9 23.2 + - - -
711B GLN* 3.9 14.5 - - - +
873B HIS* 2.8 33.3 + - - -
874B ARG 3.0 16.6 + - - -
875B SER* 2.8 24.7 + - - +
877B GLU* 3.5 7.0 - - - +
897B THR* 3.2 25.2 - - - +
898B GLY* 3.8 7.4 - - - -
899B ALA 3.4 20.6 - - - +
901B ALA 3.3 18.8 - - - +
902B ARG* 2.9 6.0 + - + +
904B GLU* 1.3 107.2 + - + +
906B LEU* 1.3 64.4 + - - +
907B ALA 3.2 1.3 - - - -
908B LYS* 3.2 16.3 + - - +
909B LEU* 3.4 16.5 + - + +
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Residues in contact with LEU 906 (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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11A TYR* 3.5 39.3 - - + +
12A ASP 3.4 21.1 - - - +
379A GLU* 5.1 0.4 - - - +
683B LEU* 5.4 0.9 - - + -
900B PRO* 3.5 23.6 - - + +
901B ALA* 3.3 31.0 - - - +
902B ARG 3.1 27.7 + - - +
903B SER* 4.0 11.4 - - - +
905B ARG* 1.3 77.9 - - - +
907B ALA* 1.3 60.0 + - - +
909B LEU* 4.1 14.6 - - + -
910B ASN* 2.7 37.5 + - - +
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Residues in contact with ALA 907 (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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379A GLU* 3.8 30.7 + - + +
879B GLU* 4.2 14.8 - - - +
881B THR* 3.4 28.4 - - + +
903B SER 2.8 24.7 + - - +
904B GLU 4.6 0.9 - - - +
905B ARG 3.2 0.2 - - - -
906B LEU* 1.3 73.2 - - - +
908B LYS* 1.3 64.1 + - + +
910B ASN* 3.7 1.7 + - - +
911B GLN* 3.1 21.1 + - - +
914B ARG* 4.5 1.4 + - - -
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Residues in contact with LYS 908 (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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877B GLU* 2.7 34.7 + - - +
878B THR 2.8 25.5 + - - -
880B ASP* 2.8 20.1 + - - +
881B THR* 4.3 8.5 - - - +
882B PHE 5.6 0.2 - - - +
883B ILE* 3.7 25.8 - - + -
884B ALA* 3.6 7.6 - - + +
895B ILE* 5.4 2.0 - - + -
897B THR* 3.3 31.2 - - + +
904B GLU 2.8 24.1 + - - +
905B ARG 3.2 2.2 + - - +
906B LEU 3.1 0.6 - - - -
907B ALA* 1.3 77.5 - - + +
909B LEU* 1.3 65.1 + - - +
911B GLN* 3.2 8.2 + - - +
912B LEU* 3.0 27.6 + - + +
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Residues in contact with LEU 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B PRO* 4.2 19.1 - - + -
651B LEU* 4.0 16.4 - - + -
679B PHE* 3.4 29.2 - - + -
683B LEU* 3.9 31.9 - - + -
895B ILE* 5.8 0.2 - - + -
897B THR* 3.5 23.3 - - + -
898B GLY 4.9 0.7 - - - +
899B ALA 4.5 2.7 - - - +
900B PRO* 4.3 8.1 - - + -
905B ARG* 3.6 16.4 - - + +
906B LEU* 3.1 25.0 + - + +
908B LYS* 1.3 75.4 - - - +
910B ASN* 1.3 62.1 + - - +
912B LEU* 3.3 6.8 + - + -
913B LEU* 3.1 18.7 + - - +
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Residues in contact with ASN 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 17.4 - - + +
11A TYR* 3.0 57.2 + - - +
33A ILE* 5.6 0.2 - - - +
378A THR* 5.9 0.2 - - - -
379A GLU* 3.1 32.5 + - - +
683B LEU* 5.0 0.2 - - - +
906B LEU* 2.7 25.9 + - - +
907B ALA 3.9 0.4 - - - +
909B LEU* 1.3 70.2 - - - +
911B GLN* 1.3 64.7 + - - +
913B LEU* 3.0 18.8 + - - +
914B ARG* 3.1 28.4 + - - +
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Residues in contact with GLN 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 4.8 4.0 + - - -
881B THR* 4.0 19.0 + - + +
884B ALA* 3.5 21.3 - - + -
885B ASP* 2.8 27.6 + - - +
907B ALA 3.1 18.7 + - - +
908B LYS 3.4 5.6 - - - +
910B ASN* 1.3 78.0 - - - +
912B LEU* 1.3 58.3 + - - +
914B ARG* 3.2 31.5 + - - +
915B ILE* 2.9 35.2 + - + +
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Residues in contact with LEU 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 4.6 4.3 - - + +
647B PRO* 4.1 16.6 - - + -
679B PHE* 3.5 42.8 - - + -
884B ALA* 3.5 30.5 - - + +
887B VAL* 4.0 6.7 - - + -
888B VAL* 3.8 19.5 - - + -
895B ILE* 4.2 19.3 - - + -
908B LYS* 3.0 18.6 + - + +
909B LEU* 3.5 9.4 - - + +
910B ASN 3.2 0.2 - - - -
911B GLN* 1.3 76.9 - - - +
913B LEU* 1.3 58.0 + - - +
915B ILE* 3.6 5.1 - - + +
916B GLU* 2.9 30.8 + - - +
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Residues in contact with LEU 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.6 6.1 - - - -
9A SER 3.8 23.1 - - - +
10A VAL* 4.4 2.2 - - + -
11A TYR* 4.0 11.4 - - + -
679B PHE* 3.9 10.7 - - + -
680B ALA* 3.8 36.6 - - + +
683B LEU* 3.8 21.8 - - + -
909B LEU 3.1 13.0 + - - +
910B ASN* 3.0 27.7 + - - +
912B LEU* 1.3 78.6 - - - +
914B ARG* 1.3 61.9 + - + +
916B GLU* 3.5 5.3 + - - +
917B GLU* 3.1 24.4 + - - +
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Residues in contact with ARG 914 (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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8A ARG* 4.1 28.2 + - - +
10A VAL* 4.5 1.1 - - - +
20A GLU* 2.7 40.1 + - - -
31A ARG* 3.4 42.8 - - - +
33A ILE* 4.3 2.6 - - - +
379A GLU* 3.4 23.6 + - - +
881B THR* 5.8 1.6 - - - +
907B ALA 4.5 1.4 + - - -
910B ASN* 3.1 17.7 + - - +
911B GLN* 3.3 48.4 + - - +
913B LEU* 1.3 73.9 - - - +
915B ILE* 1.3 64.8 + - + +
917B GLU* 3.3 8.1 + - - +
918B GLU* 2.9 25.4 + - - +
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Residues in contact with ILE 915 (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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630B TYR* 3.8 35.2 - - + -
646B LEU* 4.4 2.7 - - + -
884B ALA 4.1 8.7 - - - +
885B ASP* 3.9 29.6 - - - +
888B VAL* 4.0 22.4 - - + -
911B GLN* 2.9 29.1 + - + +
912B LEU* 3.6 10.3 - - + +
914B ARG* 1.3 77.6 - - + +
916B GLU* 1.3 64.5 + - - +
918B GLU* 3.2 7.0 + - - +
919B LEU* 3.0 43.8 + - + +
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Residues in contact with GLU 916 (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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646B LEU* 3.0 35.4 - - + +
678B THR* 3.6 11.9 - - - +
679B PHE* 2.8 32.6 + - + +
680B ALA* 3.0 30.6 + - - +
912B LEU 2.9 16.9 + - - +
913B LEU* 3.7 6.9 - - - +
915B ILE* 1.3 76.5 - - - +
917B GLU* 1.3 63.9 + - - +
919B LEU* 3.4 3.5 + - - +
920B GLY* 3.1 23.5 + - - +
923B ALA* 5.5 0.5 - - - +
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Residues in contact with GLU 917 (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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6A TYR* 3.0 33.7 + - - +
8A ARG* 2.7 49.7 + - - +
913B LEU 3.1 17.7 + - - +
914B ARG 3.5 4.5 - - - +
916B GLU* 1.3 78.9 - - - +
918B GLU* 1.3 64.5 + - - +
919B LEU 3.5 0.2 + - - -
920B GLY* 3.5 8.8 + - - -
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Residues in contact with GLU 918 (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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628B PRO* 3.6 15.3 - - - +
630B TYR* 2.5 36.6 + - - +
914B ARG 2.9 16.6 + - - +
915B ILE* 3.6 5.6 - - - +
917B GLU* 1.3 81.9 - - - +
919B LEU* 1.3 60.9 + - + +
920B GLY 3.6 0.2 + - - -
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Residues in contact with LEU 919 (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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630B TYR* 3.4 26.2 - - + +
644B TYR* 3.5 54.7 - - + -
646B LEU* 4.9 3.4 - - + -
888B VAL* 4.6 2.7 - - + -
915B ILE* 3.0 36.6 + - + +
916B GLU 4.0 2.0 - - - +
918B GLU* 1.3 77.9 - - + +
920B GLY* 1.3 65.3 + - - +
921B ASP 3.3 0.7 + - - -
922B ASN* 2.9 28.4 + - + +
923B ALA* 3.7 20.6 - - + +
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Residues in contact with GLY 920 (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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916B GLU 3.1 15.6 + - - +
917B GLU* 3.5 7.1 + - - -
918B GLU 3.4 2.6 - - - -
919B LEU* 1.3 74.8 - - - +
921B ASP* 1.3 58.0 + - - -
922B ASN 3.0 5.7 + - - -
923B ALA* 3.2 19.4 + - - +
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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