Contacts of the strand formed by residues 185 - 187 (chain B) in PDB entry 3ENM
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 VAL 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.2 4.5 - - - -
136B LEU* 2.7 49.6 + - + +
162B ILE* 4.3 26.0 - - + -
180B VAL* 5.6 0.9 - - + -
181B LYS 3.4 17.7 - - - +
182B PRO* 2.9 8.1 + - + +
183B SER 3.3 1.2 - - - -
184B ASN* 1.3 87.0 - - - +
186B LEU* 1.3 61.9 + - - +
193B VAL* 3.6 29.4 - - + -
194B LYS 3.8 9.4 - - - +
195B MSE 4.3 15.5 - - + +
246B THR* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.5 24.0 - - + -
129B MSE 3.6 26.2 - - + -
130B GLU 5.1 0.2 - - - +
132B MSE 3.8 31.2 - - + -
134B THR 3.4 9.0 - - - +
135B SER* 3.8 21.3 - - - +
136B LEU* 5.1 0.4 - - - -
183B SER 4.5 3.8 - - - +
184B ASN 4.3 0.2 + - - -
185B VAL* 1.3 85.3 - - - +
187B ILE* 1.3 60.7 + - - +
193B VAL* 3.3 8.7 - - - +
194B LYS 2.8 36.7 + - - +
196B CYS* 4.0 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B MSE 3.9 4.0 - - - -
133B ASP* 3.2 15.4 + - - +
134B THR* 2.9 31.6 + - - +
136B LEU* 3.8 28.0 - - + -
139B PHE* 4.1 26.7 - - + -
154B ILE* 5.3 2.5 - - + -
158B ILE* 4.9 8.5 - - + -
185B VAL 4.4 0.2 + - - -
186B LEU* 1.3 75.8 - - - +
188B ASN* 1.3 65.3 + - - +
191B GLY 4.8 0.7 - - - -
192B GLN 3.2 13.5 - - - +
193B VAL* 3.8 21.1 - - + -
324B VAL* 4.2 10.5 - - + -
328B VAL* 3.6 31.2 - - + -
332B LEU* 5.7 0.4 - - + -
----------------------------------------------------------
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