Contacts of the helix formed by residues 132 - 139 (chain J) in PDB entry 3DUF
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 MET 132 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F LEU 4.3 14.4 - - - +
285F GLU* 4.3 32.3 - - + +
324F PHE* 6.5 0.9 - - + -
282H LEU* 5.3 6.3 - - + -
131J ALA* 1.3 76.7 - - - +
133J PRO* 1.3 66.1 - - + +
134J SER* 4.1 5.4 - - - +
135J VAL* 2.6 55.4 + - + +
136J ARG* 3.0 11.1 + - - +
153J GLY 4.5 6.5 - - - +
154J LYS* 4.1 14.1 - - - +
155J ASN* 4.4 6.1 - - - +
156J GLY* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F ILE* 3.4 39.5 - - + +
282F LEU* 5.1 0.9 - - - +
284F LEU* 5.3 3.8 - - + +
281H ILE* 3.3 42.0 - - + +
282H LEU* 6.2 0.2 - - + -
284H LEU* 3.7 26.9 - - + +
285H GLU 4.8 3.7 - - - +
286H ALA* 5.2 6.7 - - - +
324H PHE* 5.7 1.8 - - + -
131J ALA 3.7 0.6 - - - +
132J MET* 1.3 84.8 - - + +
134J SER* 1.3 61.3 + - - +
136J ARG* 3.8 4.4 + - + +
137J LYS* 3.4 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F ILE 3.9 6.3 + - - -
282F LEU* 2.6 49.7 + - - +
284F LEU 4.5 10.1 + - - -
132J MET* 2.8 4.2 + - - -
133J PRO* 1.3 79.8 - - - +
135J VAL* 1.3 63.9 + - - +
137J LYS* 4.2 3.1 - - - +
138J TYR* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J ALA* 4.5 0.4 - - + -
132J MET* 2.6 60.7 + - + +
134J SER* 1.3 69.6 - - - +
136J ARG* 1.3 58.8 + - - +
137J LYS 3.1 4.0 - - - -
138J TYR* 2.9 23.1 + - - +
139J ALA* 3.0 12.3 + - - +
146J ILE* 4.1 13.5 - - + -
154J LYS 3.5 17.3 - - - +
155J ASN 4.4 0.2 - - - +
156J GLY* 3.4 27.6 - - - +
159J LEU* 3.8 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H LEU 3.2 21.9 + - - -
283H SER* 3.3 21.0 + - - +
284H LEU 3.3 17.3 - - - +
285H GLU* 3.0 42.0 + - - +
130J ILE 3.8 10.9 - - - +
131J ALA* 3.6 28.6 + - - +
132J MET 3.0 10.5 + - - +
133J PRO* 3.8 10.8 - - + +
135J VAL* 1.3 78.4 - - - +
137J LYS* 1.3 57.4 + - - +
139J ALA* 4.1 5.8 - - - +
140J ARG* 3.6 24.8 + - - +
146J ILE* 3.7 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F LEU* 4.0 33.2 - - + +
285H GLU 4.9 0.4 - - - +
324H PHE* 3.6 32.1 - - + +
133J PRO 3.4 18.0 + - - +
134J SER 4.2 3.1 - - - +
135J VAL 3.1 1.0 - - - -
136J ARG* 1.3 76.6 - - - +
138J TYR* 1.3 68.2 + - - +
139J ALA 3.3 0.9 - - - -
140J ARG* 3.3 44.4 + - - +
141J GLU* 3.2 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER 3.3 13.9 + - - +
135J VAL* 2.9 9.4 + - - +
137J LYS* 1.3 81.9 - - - +
139J ALA* 1.3 60.9 + - - +
141J GLU* 3.4 23.6 - - - +
142J LYS* 2.9 60.8 + - + +
156J GLY* 4.7 12.8 - - - -
159J LEU* 3.4 40.4 - - + -
160J LYS* 2.9 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J VAL 3.0 13.9 + - - +
136J ARG* 4.3 8.7 - - - +
138J TYR* 1.3 79.1 - - - +
140J ARG* 1.3 61.8 + - - +
142J LYS* 3.2 8.0 + - - -
144J VAL* 2.9 51.0 + - + +
146J ILE* 4.7 13.7 - - + -
159J LEU* 3.9 23.3 - - + -
----------------------------------------------------------
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