Contacts of the helix formed by residues 994 - 1013 (chain B) in PDB entry 5W0N
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 THR 994 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B PRO 4.5 6.1 - - - +
993B LEU* 1.3 78.4 - - - +
995B PRO* 1.3 73.2 - - + +
996B LYS* 2.9 11.0 + - - +
997B PHE* 2.7 37.9 + - + +
998B LEU* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 995 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B LEU 4.5 1.8 - - - +
994B THR* 1.3 85.8 - - - +
996B LYS* 1.3 64.5 + - + +
998B LEU* 3.9 8.5 - - + +
999B ASN* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 996 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B THR* 2.9 10.6 - - - +
995B PRO* 1.3 79.9 - - + +
997B PHE* 1.3 64.1 + - - +
999B ASN* 3.2 15.8 + - - +
1000B ILE* 3.4 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 997 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B LEU* 3.8 23.6 - - + -
994B THR* 2.7 25.0 + - + +
996B LYS* 1.3 71.2 - - - +
998B LEU* 1.3 64.7 + - - +
1000B ILE* 3.0 35.7 + - + +
1001B LEU* 3.1 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 998 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B LEU* 4.1 26.0 - - + -
994B THR 2.9 20.2 + - - +
995B PRO* 3.9 7.9 - - + +
997B PHE* 1.3 78.8 - - - +
999B ASN* 1.3 65.1 + - + +
1001B LEU* 3.0 17.9 + - + +
1002B ASP* 3.0 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 999 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B PRO 3.2 13.6 + - - +
996B LYS* 3.5 11.4 - - - +
997B PHE 3.2 0.8 - - - -
998B LEU* 1.3 79.5 - - + +
1000B ILE* 1.3 62.4 + - + +
1002B ASP* 3.4 16.3 + - - +
1003B GLN* 3.1 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1000 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B LYS 3.4 10.7 + - - +
997B PHE* 3.0 32.3 + - + +
999B ASN* 1.3 77.3 - - + +
1001B LEU* 1.3 67.4 + - + +
1003B GLN* 3.1 17.2 + - - +
1004B VAL* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1001 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B LEU* 4.3 15.3 - - + -
997B PHE* 3.1 50.3 + - + +
998B LEU* 3.0 21.4 + - + +
1000B ILE* 1.3 79.4 - - + +
1002B ASP* 1.3 64.3 + - - +
1004B VAL* 3.3 8.9 + - + +
1005B CYS* 3.1 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1002 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998B LEU* 3.0 45.7 + - - +
999B ASN* 3.6 17.9 + - - +
1000B ILE 3.3 0.2 - - - -
1001B LEU* 1.3 77.9 - - - +
1003B GLN* 1.3 63.5 + - + +
1005B CYS* 3.4 5.4 + - - +
1006B ILE* 3.1 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1003 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B ASN* 3.1 39.0 + - - +
1000B ILE* 3.1 19.2 + - - +
1002B ASP* 1.3 76.6 - - + +
1004B VAL* 1.3 58.3 + - + +
1006B ILE* 3.3 8.2 + - + +
1007B GLN* 2.8 36.3 + - + +
1010B LYS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1004 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000B ILE* 3.0 28.5 + - + +
1001B LEU* 3.3 11.6 + - + +
1003B GLN* 1.3 77.3 - - + +
1005B CYS* 1.3 65.8 + - - +
1007B GLN* 3.2 9.7 + - + +
1008B CYS* 3.1 30.5 + - - -
1150B THR* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B LEU* 3.1 23.5 + - - +
1002B ASP* 3.8 6.7 - - - +
1004B VAL* 1.3 78.2 - - - +
1006B ILE* 1.3 64.1 + - + +
1008B CYS* 3.3 17.9 + - - +
1009B TYR 3.6 3.3 + - - -
1146B TYR* 3.9 20.0 - - + +
1147B LEU* 5.1 11.7 - - + -
1150B THR* 3.3 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ASP* 3.1 27.8 + - + +
1003B GLN* 3.8 7.0 - - + +
1005B CYS* 1.3 74.2 - - + +
1007B GLN* 1.3 66.3 + - - +
1009B TYR* 3.0 5.2 + - - +
1010B LYS* 3.0 44.2 + - + +
1146B TYR* 4.4 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1007 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B GLN* 2.8 23.2 + - + +
1004B VAL* 3.2 10.3 + - + +
1006B ILE* 1.3 78.0 - - - +
1008B CYS* 1.3 57.2 + - - +
1010B LYS* 3.6 30.0 - - - +
1011B ASP* 2.8 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1008 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A ILE* 6.1 0.9 - - - -
1004B VAL* 3.1 26.2 + - - -
1005B CYS 3.4 9.6 - - - +
1006B ILE 3.2 0.4 - - - -
1007B GLN* 1.3 75.7 - - - +
1009B TYR* 1.3 61.3 + - - +
1012B PHE* 3.1 37.1 + - - +
1149B TYR* 3.8 6.4 - - - +
1150B THR* 3.9 33.4 - - - +
1153B VAL* 3.9 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1009 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B CYS 3.6 2.5 + - - +
1006B ILE 3.0 8.5 + - - +
1008B CYS* 1.3 77.5 - - - +
1010B LYS* 1.3 73.5 + - + +
1013B SER* 2.8 61.1 + - - -
1145B LYS* 4.3 26.8 + - + +
1146B TYR* 3.8 38.6 - + + -
1149B TYR* 3.6 41.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1010 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006B ILE* 3.0 37.4 + - + +
1007B GLN* 3.6 28.2 - - - +
1009B TYR* 1.3 88.4 - - + +
1011B ASP* 1.3 66.8 + - - +
1012B PHE 3.5 0.2 + - - -
1013B SER* 4.4 8.6 + - - +
1055B LYS* 5.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1011 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A THR* 4.3 20.5 - - + +
1007B GLN* 2.8 51.0 + - - +
1010B LYS* 1.3 75.9 - - - +
1012B PHE* 1.3 85.3 + - + +
1055B LYS* 3.6 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1012 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A THR* 3.7 33.0 - - + -
1016A ILE* 4.3 10.1 - - + -
1017A ILE* 3.4 34.1 - - + -
1008B CYS* 3.1 29.5 + - - +
1009B TYR 3.3 1.8 + - - -
1011B ASP* 1.3 95.9 - - + +
1013B SER* 1.3 62.2 + - - +
1054B PHE* 3.1 31.6 - + + -
1055B LYS* 2.9 34.1 + - + +
1149B TYR* 4.3 1.6 - - - -
1153B VAL* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1013 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B TYR* 2.8 60.6 + - - -
1010B LYS* 4.4 6.1 + - - +
1011B ASP 3.8 0.2 - - - -
1012B PHE* 1.3 77.1 - - - +
1014B PRO* 1.3 73.6 + - - +
1015B THR* 5.2 0.2 - - - +
1055B LYS* 3.2 19.6 + - - -
1149B TYR* 3.6 15.1 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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