Contacts of the strand formed by residues 209 - 214 (chain E) in PDB entry 3VZC
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 209 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLY* 1.3 73.1 - - - -
210E LEU* 1.3 64.6 + - - +
211E ALA* 5.9 2.9 - - + -
245E VAL* 6.5 0.4 - - - -
251E VAL* 4.5 23.3 - - + +
252E VAL 5.1 0.4 - - - +
255E GLU* 3.6 35.2 + - + +
328E ARG 3.8 1.0 - - - +
329E LEU* 3.4 8.3 - - - +
330E GLU* 2.8 68.8 + - + +
332E LYS* 4.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLY 4.2 0.6 + - - -
209E ARG* 1.3 77.1 - - - +
211E ALA* 1.3 85.1 + - - +
212E TYR* 4.8 0.7 - - + -
251E VAL* 3.8 2.3 - - - +
252E VAL* 2.9 43.8 + - + +
257E PHE* 3.8 20.4 - - + -
260E VAL* 4.2 23.8 - - + -
287E LEU* 4.6 13.0 - - + -
289E TYR* 3.7 35.0 - - + -
327E PHE* 4.7 9.6 - - + -
328E ARG 3.4 9.9 - - - +
329E LEU* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ARG* 4.3 4.0 - - + -
210E LEU* 1.3 85.2 - - - +
212E TYR* 1.3 62.6 + - - +
245E VAL* 3.9 25.1 - - + -
249E TRP* 3.6 20.6 - - + -
250E THR 3.2 10.5 - - - +
251E VAL* 4.4 7.6 - - + -
327E PHE* 3.3 1.6 - - - -
328E ARG* 2.8 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E LEU* 4.8 2.7 - - + -
211E ALA* 1.3 78.6 - - - +
213E LEU* 1.3 59.7 + - - +
214E PRO* 3.6 14.4 - - + +
217E ARG* 5.3 0.4 + - - -
249E TRP* 3.7 9.3 - - - -
250E THR* 2.8 63.1 + - + +
252E VAL* 3.8 26.2 - - + -
287E LEU* 3.7 27.1 - - + -
289E TYR* 4.5 7.0 + + - -
320E VAL* 5.8 0.2 - - - +
322E VAL* 3.6 40.7 - - + +
324E VAL* 3.5 17.7 - - + -
326E ALA 3.4 13.7 - - - +
327E PHE* 4.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E TYR* 1.3 74.7 - - - +
214E PRO* 1.3 79.7 - - + +
217E ARG* 3.8 19.1 - - + -
218E VAL* 4.0 10.1 - - - +
237E HIS* 3.7 41.5 - - + -
248E HIS* 4.0 21.8 - - + +
249E TRP* 3.8 27.3 - - + +
324E VAL* 3.3 3.8 - - - +
325E VAL* 3.0 40.2 + - + -
326E ALA* 2.9 16.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 5.0 0.9 - - - +
212E TYR* 3.6 27.5 - - + +
213E LEU* 1.3 99.1 - - + +
215E VAL* 1.3 66.6 + - - +
216E GLY* 3.0 6.5 + - - +
217E ARG* 3.3 55.2 + - + +
218E VAL* 3.9 2.9 + - - +
248E HIS 4.9 0.4 - - - +
250E THR* 4.2 0.7 - - - +
322E VAL* 4.4 8.1 - - + -
323E PRO 3.6 11.7 - - - +
324E VAL* 4.2 2.7 - - + -
325E VAL 4.8 0.2 - - - -
----------------------------------------------------------
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