Contacts of the strand formed by residues 210 - 214 (chain A) in PDB entry 3CMM
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 PHE 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY 3.4 20.0 - - - -
209A ASN* 1.3 75.6 - - - +
211A VAL* 1.3 64.5 + - - +
227A LEU* 4.3 17.9 - - + -
228A PHE 3.4 3.6 - - - -
229A LYS* 3.9 35.2 - - + -
257A GLU* 3.3 11.7 + - - +
258A VAL* 2.9 38.3 + - - +
260A VAL* 3.7 37.9 - - + -
210C PHE* 3.7 26.7 - + - -
226C THR* 5.8 1.8 - - + -
227C LEU* 3.6 35.9 - - + -
260C VAL* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 4.2 11.7 - - + -
210A PHE* 1.3 77.6 - - - +
212A ARG* 1.3 57.9 + - - +
213A PHE* 3.5 33.0 - - + -
227A LEU* 3.3 9.0 - - - +
228A PHE* 3.0 36.6 + - + +
230A VAL* 3.9 19.7 - - + -
238A PHE* 4.3 3.8 - - + -
240A ILE* 4.6 0.2 - - + -
255A PHE* 3.2 38.1 - - + -
256A THR 3.3 14.4 - - - +
257A GLU* 3.8 2.5 - - - +
258A VAL 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A VAL* 1.3 74.7 - - - +
213A PHE* 1.3 70.3 + - - +
214A SER* 4.3 15.2 + - - -
225A GLY* 4.3 14.2 - - - +
226A THR 3.8 14.4 - - - +
227A LEU* 4.0 9.2 - - + -
254A ILE 3.7 0.2 - - - +
255A PHE* 3.3 6.8 - - - +
256A THR* 2.8 72.3 + - - +
258A VAL* 3.5 19.4 - - + +
848A GLU* 5.1 2.6 + - - -
263C LYS* 3.2 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.1 14.8 - - + -
189A ILE* 4.5 7.0 - - + -
195A VAL* 4.1 23.3 - - + -
211A VAL* 3.5 26.9 - - + -
212A ARG* 1.3 83.2 + - - +
214A SER* 1.3 63.2 + - - +
216A VAL* 4.1 14.8 - - + -
222A LEU* 3.6 34.2 + - + +
223A ASN* 3.1 31.7 - - - +
225A GLY 4.9 1.1 + - - +
226A THR 4.6 0.8 + - - -
228A PHE* 3.9 17.7 - + - -
238A PHE* 4.4 2.9 - + - -
240A ILE* 3.8 20.6 - - + -
254A ILE 3.4 13.0 - - - -
255A PHE* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 4.3 15.6 + - - -
213A PHE* 1.3 74.7 + - - +
215A GLU* 1.3 72.8 + - - +
216A VAL* 2.9 8.3 + - - +
223A ASN* 3.0 10.2 + - - -
253A GLY* 3.2 0.9 - - - -
254A ILE* 2.8 49.1 + - - -
256A THR* 6.0 0.7 - - - -
263C LYS* 5.2 2.9 + - - -
----------------------------------------------------------
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