Contacts of the strand formed by residues 207 - 211 (chain Z) in PDB entry 3EXG
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 ILE 207 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206Z HIS* 1.3 82.9 - - + +
208Z THR* 1.3 72.3 + - - +
209Z VAL* 4.0 2.0 + - + -
231Z VAL* 4.6 1.3 - - + -
232Z GLU 3.7 0.4 + - - -
233Z CYS* 3.6 29.8 - - - -
234Z GLU* 3.0 27.5 + - - +
256Z THR* 3.7 8.8 - - - +
258Z HIS* 3.8 13.7 - - + +
259Z LEU 4.6 0.2 - - - +
260Z VAL* 3.9 20.0 - - + -
323Z ILE* 3.4 44.6 - - + +
326Z THR* 4.6 9.0 - - + -
327Z LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Z ILE* 1.3 75.9 - - - +
209Z VAL* 1.3 65.6 + - - +
210Z VAL* 4.1 13.2 - - + -
234Z GLU 3.7 5.2 - - - +
236Z ILE* 3.7 21.1 - - + -
249Z ILE 4.9 1.6 - - - +
252Z SER* 2.9 35.1 + - - +
253Z VAL* 3.8 7.6 - - + +
256Z THR* 2.7 22.9 + - - +
258Z HIS 2.9 14.7 + - - -
259Z LEU* 3.6 9.1 - - + +
260Z VAL 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Z ILE* 4.4 6.3 - - + -
208Z THR* 1.3 78.6 - - - +
210Z VAL* 1.3 62.3 + - - +
219Z CYS* 3.6 30.1 - - + -
233Z CYS* 4.0 24.2 - - + -
234Z GLU 3.1 7.3 + - - +
235Z VAL* 3.5 10.7 - - + +
236Z ILE* 2.8 26.7 + - - +
260Z VAL* 3.3 11.9 - - + +
262Z VAL* 3.8 12.6 - - + -
319Z ILE* 4.5 8.5 - - + -
323Z ILE* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208Z THR* 4.1 8.3 - - + -
209Z VAL* 1.3 76.8 - - - +
211Z SER* 1.3 68.1 + - - +
236Z ILE* 3.5 12.3 - - + +
238Z MET* 3.6 23.6 - - + -
249Z ILE* 3.6 41.7 - - + -
259Z LEU* 3.7 24.5 - - + -
260Z VAL 2.8 12.3 + - - +
261Z THR* 3.3 11.4 - - + -
262Z VAL* 2.8 28.6 + - - +
275Z ILE* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209Z VAL 5.5 0.2 - - - -
210Z VAL* 1.3 83.8 - - - +
212Z HIS* 1.3 73.3 + - - +
215Z PRO* 3.8 3.8 - - - +
216Z VAL* 3.6 22.9 + - - -
219Z CYS* 4.1 12.6 - - - -
235Z VAL* 5.9 0.7 - - - -
236Z ILE 3.1 7.7 + - - +
237Z ASN* 3.5 3.1 - - - -
238Z MET* 3.0 33.5 + - - +
262Z VAL* 2.6 30.8 + - - +
----------------------------------------------------------
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