Contacts of the strand formed by residues 350 - 357 (chain E) in PDB entry 1EV2
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 350 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.9 33.4 - - - +
255E ARG* 3.3 17.0 + - - +
256E PRO* 5.1 0.2 - - - -
343E LEU* 3.7 36.6 - - + -
344E ALA 3.5 9.6 - - - +
345E GLY* 4.3 3.4 - - - -
349E GLY* 1.3 79.0 - - - +
351E SER* 1.3 68.3 + - - +
352E PHE* 4.5 7.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E ARG* 2.8 29.4 + - - +
256E PRO* 2.6 31.0 + - - +
257E ILE* 5.2 0.4 - - - -
258E LEU* 4.5 15.0 - - - -
343E LEU* 3.5 0.3 - - - -
344E ALA* 2.8 36.4 + - - +
350E ILE* 1.3 71.5 - - - +
352E PHE* 1.3 66.4 + - - +
353E HIS* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E LEU* 4.2 2.9 - - - +
341E THR* 3.7 20.6 - - + -
342E CYS 3.2 15.0 - - - +
343E LEU* 3.8 22.0 - - + -
350E ILE* 4.5 8.3 - - + -
351E SER* 1.3 81.3 - - - +
353E HIS* 1.3 74.8 + - - +
354E SER* 4.5 8.7 - - - -
174H THR* 4.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E LEU* 3.6 33.0 + - + +
259E GLN 3.4 14.6 + - - -
262E LEU 3.3 27.5 + - - +
263E PRO* 3.7 9.9 - - + +
341E THR* 3.5 1.1 - - - -
342E CYS 3.0 29.6 + - - -
351E SER* 6.1 1.1 - - - -
352E PHE* 1.3 87.1 - - - +
354E SER* 1.3 63.4 + - - +
172H ALA 5.8 0.6 + - - -
174H THR* 4.1 13.8 + - - -
219H GLU* 3.6 43.9 + - + +
220H SER* 3.6 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E PRO* 4.2 2.2 - - - -
339E GLU* 3.5 24.9 + - - -
340E TYR 3.2 9.6 - - - -
341E THR* 2.6 24.5 + - - +
352E PHE* 4.5 8.7 - - - -
353E HIS* 1.3 74.4 - - - +
355E ALA* 1.3 58.8 + - - +
208H LYS* 2.5 35.5 + - - +
219H GLU* 4.1 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E PRO* 3.6 21.3 - - + +
264E ALA 3.6 32.3 - - - +
265E ASN* 3.7 7.6 - - - +
276E PHE* 4.1 9.0 - - + -
339E GLU* 3.5 7.1 - - - +
340E TYR* 2.8 33.0 + - - +
354E SER* 1.3 75.6 - - - +
356E TRP* 1.3 63.4 + - - +
208H LYS* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E ASN* 3.1 29.7 + - - +
266E ALA 2.9 26.7 + - - +
276E PHE* 4.3 4.0 - - - -
338E GLY* 3.4 23.8 - - - -
339E GLU* 3.2 48.0 - - + -
355E ALA* 1.3 75.4 - - - +
357E LEU* 1.3 72.2 + - - +
358E THR* 4.0 7.1 + - - +
210H ARG* 4.8 12.3 - - + -
212H GLN* 6.2 3.4 - - + -
213H HIS* 3.9 29.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ALA* 3.4 15.0 - - + +
267E SER* 4.8 2.5 - - - +
274E VAL* 4.2 24.2 - - + -
276E PHE* 3.8 10.5 - - + -
329E ILE* 4.7 11.0 - - + -
332E VAL* 5.2 4.3 - - + -
336E ASP* 3.2 37.7 - - + +
337E ALA* 3.4 8.5 - - - +
338E GLY 2.9 26.9 + - - +
340E TYR* 3.7 26.5 - - + +
356E TRP* 1.3 78.7 - - - +
358E THR* 1.3 70.3 + - - +
359E VAL* 5.0 4.3 - - + +
----------------------------------------------------------
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