Contacts of the helix formed by residues 1004 - 1009 (chain B) in PDB entry 4UN5
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 LEU1004 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B LEU* 3.8 19.3 - - + -
998B ILE* 5.8 3.1 - - + -
1001B TYR* 3.1 29.9 + - + +
1003B LYS* 1.3 78.2 - - + +
1005B GLU* 1.3 62.4 + - - +
1006B SER* 3.2 3.6 - - - -
1007B GLU* 3.0 14.4 + - + +
1008B PHE* 3.0 42.9 + - + +
1038B PHE* 4.1 23.8 - - + -
1039B TYR* 4.6 14.6 - - + +
1042B ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954B LYS* 4.3 28.5 - - - +
998B ILE* 4.8 14.2 - - + +
1001B TYR 4.4 0.2 + - - -
1002B PRO* 3.2 29.0 - - + +
1003B LYS 3.0 1.6 + - - +
1004B LEU* 1.3 78.6 - - - +
1006B SER* 1.3 58.2 + - - +
1008B PHE* 5.2 0.4 - - - -
1009B VAL* 2.8 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LYS 3.6 13.4 + - - -
1005B GLU* 1.3 79.5 - - - +
1007B GLU* 1.3 80.4 + - - +
1009B VAL 4.3 5.7 - - - +
1011B GLY 5.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1007 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918B LYS* 4.2 26.5 + - - -
922B VAL* 4.1 26.6 - - + +
923B GLU 5.7 0.2 - - - +
957B THR* 5.3 2.3 + - - -
1004B LEU* 3.0 19.5 + - + +
1006B SER* 1.3 100.4 + - - +
1008B PHE* 1.3 75.7 + - + +
1009B VAL 5.1 0.6 - - - -
1039B TYR* 4.0 16.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1008 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B LEU* 3.5 33.2 - - + -
922B VAL* 4.0 17.9 - - + -
955B VAL 3.5 1.2 - - - +
956B ILE* 3.3 15.8 - - + -
957B THR* 3.2 47.8 + - - +
958B LEU* 3.7 19.7 - - + -
962B LEU* 4.5 4.9 - - + -
997B LEU* 4.5 18.6 - - + -
998B ILE* 4.7 10.8 - - + -
1004B LEU* 3.0 44.5 + - + +
1007B GLU* 1.3 90.8 - - + +
1009B VAL* 1.3 63.2 + - + +
1010B TYR 4.0 0.2 + - - -
1039B TYR* 5.7 4.9 - + - -
1042B ILE* 6.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1009 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B ARG* 5.0 6.3 - - - -
954B LYS* 4.0 30.5 - - + -
955B VAL 3.4 10.8 - - - +
956B ILE* 4.3 15.9 - - + -
998B ILE* 4.6 9.2 - - + -
1005B GLU* 2.8 51.4 + - + +
1006B SER* 4.3 6.8 - - - +
1007B GLU 5.1 0.4 - - - -
1008B PHE* 1.3 81.7 - - - +
1010B TYR* 1.3 75.6 + - - +
1011B GLY 3.6 6.4 + - - +
----------------------------------------------------------
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