Contacts of the helix formed by residues 984 - 1005 (chain B) in PDB entry 3O33
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 984 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980B ASN* 3.7 9.7 + - - +
981B GLU* 2.6 36.6 + - - -
982B PRO 3.1 1.6 + - - -
983B ASP* 1.3 81.5 - - - +
985B GLU* 1.3 65.2 + - - +
986B VAL* 4.0 3.5 + - - +
987B ALA* 3.1 17.2 + - - +
988B ASN* 2.9 22.7 + - - -
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Residues in contact with GLU 985 (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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984B SER* 1.3 73.8 - - - +
986B VAL* 1.3 61.6 + - + +
988B ASN* 3.4 7.3 + - - +
989B ALA* 3.0 27.0 + - - +
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Residues in contact with VAL 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B ALA* 4.8 14.4 - - + -
924B PHE* 3.9 12.5 - - + -
976B CYS* 3.5 9.8 - - - -
980B ASN* 3.4 35.4 - - + +
984B SER* 3.3 3.0 + - - +
985B GLU* 1.3 76.5 - - + +
987B ALA* 1.3 60.5 + - - +
989B ALA* 3.1 8.3 + - - +
990B GLY 2.9 23.9 + - - -
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Residues in contact with ALA 987 (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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976B CYS* 4.0 13.7 - - - +
977B ALA* 5.6 4.0 - - - +
980B ASN* 4.1 11.4 - - + +
981B GLU 3.3 14.4 - - - +
982B PRO* 4.9 1.3 - - + -
983B ASP 4.3 5.6 - - - +
984B SER* 3.1 25.5 + - - +
986B VAL* 1.3 79.8 - - - +
988B ASN* 1.3 61.8 + - - +
990B GLY* 3.2 2.6 + - - -
991B ILE* 3.1 31.3 + - + +
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Residues in contact with ASN 988 (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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983B ASP* 3.1 47.3 + - - +
984B SER 2.9 15.1 + - - +
985B GLU* 3.8 6.0 - - - +
987B ALA* 1.3 73.4 - - - +
989B ALA* 1.3 64.8 + - - +
991B ILE* 3.3 16.3 + - - +
992B LYS* 3.0 25.2 + - - +
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Residues in contact with ALA 989 (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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920B MET* 4.2 28.5 - - + +
923B ALA* 5.9 2.2 - - + -
924B PHE* 4.1 14.6 - - + -
985B GLU 3.0 14.3 + - - +
986B VAL* 3.1 12.5 + - - +
988B ASN* 1.3 76.4 - - - +
990B GLY* 1.3 63.2 + - - +
992B LYS* 3.3 7.6 + - - +
993B LEU* 3.0 26.5 + - - +
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Residues in contact with GLY 990 (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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924B PHE* 3.6 21.5 - - - -
973B PHE* 3.7 11.1 - - - -
976B CYS* 3.7 12.3 - - - -
986B VAL 2.9 10.7 + - - -
987B ALA 3.2 4.4 + - - -
989B ALA* 1.3 78.3 - - - +
991B ILE* 1.3 56.9 + - - +
993B LEU* 3.4 1.8 + - - +
994B GLU* 2.9 30.6 + - - +
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Residues in contact with ILE 991 (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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977B ALA* 6.1 5.6 - - + -
983B ASP 6.3 0.9 - - - +
987B ALA* 3.1 18.3 + - + +
988B ASN* 3.3 19.0 + - - +
990B GLY* 1.3 72.4 - - - +
992B LYS* 1.3 66.4 + - - +
994B GLU* 3.4 14.6 + - - +
995B ASN* 3.0 42.7 + - - +
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Residues in contact with LYS 992 (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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918B HIS* 4.7 15.5 + - + +
920B MET* 3.9 31.0 - - + -
988B ASN 3.0 14.0 + - - +
989B ALA* 3.5 9.4 - - - +
991B ILE* 1.3 80.1 - - - +
993B LEU* 1.3 61.9 + - - +
995B ASN* 3.4 7.7 + - - +
996B TYR* 3.1 22.5 + - - +
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Residues in contact with LEU 993 (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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915B LEU* 3.6 34.4 - - + +
918B HIS* 3.6 34.9 - - + +
920B MET* 4.2 11.9 - - + +
921B SER* 3.9 15.5 - - - -
924B PHE* 3.5 33.2 - - + -
945B LEU* 5.3 2.7 - - + -
972B ILE* 6.0 0.2 - - + -
973B PHE* 3.7 20.0 - - + -
989B ALA 3.0 15.0 + - - +
990B GLY* 3.8 2.2 - - - +
992B LYS* 1.3 76.7 - - - +
994B GLU* 1.3 58.1 + - - +
996B TYR* 3.3 4.8 + - - +
997B PHE* 2.9 27.9 + - - +
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Residues in contact with GLU 994 (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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970B ARG* 5.4 4.7 - - - +
973B PHE* 3.6 43.1 - - + +
974B GLN* 6.1 1.2 - - - +
990B GLY 2.9 18.2 + - - +
991B ILE* 3.7 17.5 - - - +
992B LYS 3.3 0.2 - - - -
993B LEU* 1.3 74.4 - - - +
995B ASN* 1.3 65.7 + - - +
997B PHE* 3.2 1.6 + - - +
998B GLU* 2.9 45.7 + - + +
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Residues in contact with ASN 995 (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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991B ILE* 3.0 38.3 + - - +
992B LYS* 3.7 7.5 - - - +
994B GLU* 1.3 83.0 - - - +
996B TYR* 1.3 64.1 + - - +
998B GLU* 3.9 5.9 - - - +
999B GLU* 3.1 38.1 + - - +
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Residues in contact with TYR 996 (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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914B PHE* 3.3 42.4 + + - -
915B LEU* 3.6 19.5 - - + -
918B HIS* 3.4 34.4 - + + +
992B LYS 3.1 14.2 + - - +
993B LEU 3.3 8.3 - - - +
995B ASN* 1.3 77.8 - - - +
997B PHE* 1.3 60.9 + - - +
999B GLU* 3.2 15.0 + - + +
1000B LEU* 3.0 53.9 + - + +
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Residues in contact with PHE 997 (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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911B LEU* 3.9 24.9 - - + -
915B LEU* 3.9 22.4 - - + -
966B VAL* 4.3 6.3 - - + -
969B PHE* 3.4 43.7 - + + -
970B ARG* 4.1 9.6 - - + -
973B PHE* 3.9 22.0 - + + -
993B LEU 2.9 17.0 + - - +
994B GLU 3.5 4.0 - - - +
996B TYR* 1.3 76.7 - - - +
998B GLU* 1.3 76.6 + - - +
1000B LEU* 3.1 11.1 + - + +
1001B LEU* 2.8 61.9 + - + +
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Residues in contact with GLU 998 (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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970B ARG* 3.0 47.4 + - - +
994B GLU* 2.9 37.5 + - + +
995B ASN* 3.9 7.0 - - - +
997B PHE* 1.3 84.4 - - - +
999B GLU* 1.3 63.6 + - + +
1001B LEU* 3.3 11.6 + - - +
1002B LYS* 3.1 36.2 + - - +
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Residues in contact with GLU 999 (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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995B ASN* 3.1 29.4 + - - +
996B TYR* 3.5 14.7 + - + +
998B GLU* 1.3 77.3 - - + +
1000B LEU* 1.3 63.9 + - + +
1002B LYS* 3.2 23.3 + - + +
1003B ASN* 3.3 19.6 + - - +
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Residues in contact with LEU1000 (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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911B LEU* 3.8 18.8 - - + +
914B PHE* 3.4 57.4 - - + -
915B LEU* 4.4 4.7 - - + -
996B TYR* 3.0 47.5 + - + +
997B PHE* 3.1 11.0 + - - +
999B GLU* 1.3 78.2 - - + +
1001B LEU* 1.3 56.9 + - - +
1003B ASN* 3.0 17.1 + - + +
1004B LEU* 3.0 32.4 + - + +
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Residues in contact with LEU1001 (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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911B LEU* 3.8 29.1 - - + +
966B VAL* 3.7 37.9 - - + -
970B ARG* 3.8 13.9 - - - +
997B PHE* 2.8 31.1 + - + +
998B GLU* 3.6 10.5 - - - +
1000B LEU* 1.3 76.4 - - - +
1002B LYS* 1.3 58.0 + - + +
1004B LEU* 3.9 1.6 - - - +
1005B TYR* 3.0 56.3 + - + +
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Residues in contact with LYS1002 (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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998B GLU* 3.1 23.4 + - - +
999B GLU* 3.5 16.6 - - + +
1000B LEU 3.2 0.6 - - - -
1001B LEU* 1.3 77.8 - - + +
1003B ASN* 1.3 65.1 + - - +
1005B TYR 4.7 3.4 - - - -
1006B PRO* 3.5 26.0 - - - +
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Residues in contact with ASN1003 (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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999B GLU* 3.3 14.2 + - - +
1000B LEU* 3.0 20.4 + - + +
1002B LYS* 1.3 83.6 - - - +
1004B LEU* 1.3 65.6 + - + +
1006B PRO* 3.5 13.0 - - - +
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Residues in contact with LEU1004 (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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873B LEU* 4.1 26.2 - - + -
907B LYS* 3.0 52.0 + - + +
910B ARG* 4.2 26.2 - - + +
911B LEU* 3.7 36.3 - - + +
914B PHE* 5.6 3.1 - - + -
1000B LEU* 3.0 14.4 + - + +
1001B LEU* 4.5 1.3 - - - +
1003B ASN* 1.3 77.5 - - + +
1005B TYR* 1.3 69.5 + - + +
1006B PRO* 3.3 10.5 - - - +
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Residues in contact with TYR1005 (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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904B ASP* 2.7 30.9 + - - -
907B LYS* 3.3 36.6 - - + +
911B LEU* 4.9 2.0 - - + -
962B PRO* 3.7 19.1 - - + +
965B PHE* 3.5 30.4 - + - -
966B VAL* 5.3 2.0 - - + -
1001B LEU* 3.0 44.5 + - + +
1002B LYS* 3.9 3.4 - - - +
1004B LEU* 1.3 86.8 - - + +
1006B PRO* 1.3 63.2 - - - +
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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