Contacts of the strand formed by residues 216 - 223 (chain C) in PDB entry 3MDY
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 GLY 216 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LYS* 5.1 1.1 - - - -
213C GLY* 2.8 33.1 + - - +
214C ARG 3.3 3.6 + - - -
215C TYR* 1.3 80.1 - - - +
217C GLU* 1.3 64.7 + - - -
231C LYS* 4.0 9.4 - - - -
232C VAL 3.2 16.4 - - - -
233C PHE* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLN* 3.4 31.1 + - - +
211C GLY 3.9 4.5 - - - -
212C LYS* 4.6 8.1 - - + +
216C GLY* 1.3 74.1 - - - -
218C VAL* 1.3 59.1 + - - +
219C TRP* 2.9 33.2 + - + +
230C VAL 3.7 0.5 - - - +
231C LYS* 3.3 2.4 - - - -
232C VAL* 2.8 37.7 + - + +
234C PHE* 6.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C LDN 3.8 52.5 - - + +
209C GLN* 3.5 4.7 - - - +
210C ILE* 2.7 47.0 + - + -
211C GLY* 3.0 19.5 + - - +
212C LYS 3.8 23.8 - - - +
213C GLY 3.9 2.5 - - - +
217C GLU* 1.3 76.6 - - - +
219C TRP* 1.3 62.0 + - - +
229C ALA* 4.5 0.4 - - + -
230C VAL 3.4 7.6 - - - +
231C LYS* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C MET* 3.7 43.7 - - + -
207C VAL 4.0 6.3 - - - -
208C LYS* 3.2 39.0 - - - -
209C GLN* 3.6 20.8 - - + +
210C ILE* 3.7 8.0 - - - +
217C GLU* 2.9 33.8 + - + +
218C VAL* 1.3 82.1 - - - +
220C MET* 1.3 61.8 + - - +
229C ALA* 3.2 5.2 - - - -
230C VAL 2.7 40.1 + - - +
232C VAL* 4.1 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C MET* 3.9 1.4 - - - -
207C VAL* 2.8 53.5 + - - +
208C LYS* 2.9 31.6 + - + +
210C ILE* 3.8 18.8 - - + +
219C TRP* 1.3 76.5 - - - +
221C GLY* 1.3 70.6 + - - +
222C LYS* 4.8 4.9 - - - -
227C LYS* 3.9 33.4 - - + +
228C VAL 3.4 8.1 - - - +
281C TYR* 3.5 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ILE* 4.1 12.6 - - - -
205C GLN 3.1 12.3 - - - -
206C MET* 4.3 1.6 - - - -
207C VAL* 4.2 1.1 - - - -
219C TRP 3.9 1.8 + - - -
220C MET* 1.3 79.3 - - - +
222C LYS* 1.3 63.6 + - - +
227C LYS* 3.3 5.4 - - - -
228C VAL* 2.8 38.8 + - - +
230C VAL* 4.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C GLN 4.2 1.4 - - - +
204C ILE* 3.7 3.7 - - - +
205C GLN* 2.9 62.1 + - + +
207C VAL* 4.1 20.1 - - + +
220C MET* 4.8 4.4 - - - -
221C GLY* 1.3 77.3 - - - +
223C TRP* 1.3 61.3 + - - +
224C ARG 3.9 1.5 + - - -
225C GLY* 4.3 22.2 - - - +
226C GLU 3.2 7.9 - - - +
227C LYS* 4.2 37.0 - - + +
228C VAL* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 3.6 26.7 - - + -
176C LEU* 3.9 34.3 - - + -
179C LEU* 4.6 16.2 - - + -
192C LEU* 6.6 0.4 - - + -
196C VAL* 6.1 4.5 - - + -
199C THR* 5.3 2.4 + - - -
200C ILE* 4.1 32.7 - - + +
203C GLN* 3.1 39.3 + - + +
204C ILE* 4.2 16.4 - - + +
221C GLY 4.3 0.2 - - - -
222C LYS* 1.3 72.6 - - - +
224C ARG* 1.3 116.8 + - + +
226C GLU* 2.8 25.6 + - - +
228C VAL* 4.9 4.9 - - + +
----------------------------------------------------------
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