Contacts of the strand formed by residues 215 - 219 (chain H) in PDB entry 3CII
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 ARG 215 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H MET* 4.6 5.1 - - - -
197H GLU* 4.4 16.6 + - - +
199H LYS* 4.9 27.6 - - + +
211H LEU* 3.9 5.1 - - - +
212H GLN* 3.2 31.9 + - - +
213H VAL 3.2 6.5 + - - +
214H ASN* 1.3 86.3 + - - +
216H LEU* 1.3 68.8 + - - +
217H LYS* 5.2 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H ILE* 4.6 9.4 - - + -
163H MET* 4.9 15.7 - - + -
175H ILE* 3.4 27.6 - - + -
194H PHE* 3.6 38.1 - - + -
196H HIS* 4.2 7.6 - - + -
197H GLU 3.7 20.4 + - - +
198H ILE* 3.7 10.9 - - + -
199H LYS* 3.0 31.5 + - - +
210H VAL 3.5 10.5 - - - +
211H LEU* 3.9 20.4 - - + -
215H ARG* 1.3 77.5 - - - +
217H LYS* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU 4.9 0.2 + - - -
157A ARG* 3.8 27.0 + - - +
158A ALA* 3.0 41.0 + - + +
161A GLU* 5.3 3.0 + - - +
162A ASP* 4.1 23.5 - - - +
198H ILE* 4.1 5.2 - - - -
199H LYS* 4.2 17.5 - - + +
209H ALA* 3.1 7.3 - - - +
210H VAL* 2.8 45.8 + - + +
212H GLN* 3.7 20.0 + - + +
215H ARG* 5.2 2.2 - - + +
216H LEU* 1.3 75.6 - - - +
218H SER* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 4.3 9.9 + - - -
179H ARG* 4.1 2.8 + - - -
186H TRP* 3.8 17.7 - - - -
198H ILE* 4.3 4.0 - - - -
199H LYS 3.7 24.0 - - - -
206H LEU* 3.0 48.7 + - - +
208H CYS 3.9 2.7 - - - -
217H LYS* 1.3 84.6 - - - +
219H ALA* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 4.8 1.3 - - - +
157A ARG* 4.5 12.6 - - - +
174H TRP* 4.0 20.0 - - + -
206H LEU* 3.7 8.1 - - - -
207H ASN 3.4 13.9 + - - -
208H CYS 2.8 25.3 + - - +
210H VAL* 4.0 20.2 - - + -
218H SER* 1.3 76.3 + - - +
220H GLN* 1.3 65.2 + - - +
221H CYS* 3.3 3.8 + - - -
223H SER* 5.3 1.6 - - - +
225H ILE* 4.6 6.3 - - + -
----------------------------------------------------------
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