Contacts of the strand formed by residues 351 - 357 (chain D) in PDB entry 2VKM
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 351 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D TYR* 3.4 45.4 + - + -
191D THR 3.4 14.4 - - - +
192D PRO* 4.6 0.9 - - + -
193D ILE* 3.7 4.6 - - - +
290D GLU* 2.8 49.8 + - - +
346D ASP* 2.9 63.3 + - + +
349D ARG* 3.2 54.4 - - - +
350D LYS* 1.3 76.9 - - - +
352D ILE* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D TRP 3.7 0.7 - - - +
190D TYR* 3.3 3.2 - - - -
191D THR* 2.9 42.7 + - + +
193D ILE* 3.6 17.9 - - + -
199D TYR* 3.7 33.0 - - + -
201D VAL* 3.9 21.5 - - + -
227D VAL* 4.0 7.6 - - + -
343D VAL* 3.6 23.1 - - + -
344D VAL 3.1 7.0 - - - +
345D PHE* 4.2 10.3 - - + -
351D ARG* 1.3 79.0 - - - +
353D GLY* 1.3 61.4 + - - +
354D PHE* 3.6 25.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 3.9 5.8 - - - -
189D TRP 3.2 8.3 - - - -
190D TYR* 3.3 24.8 - - - -
343D VAL* 3.2 11.8 - - - +
344D VAL* 2.7 37.7 + - - -
352D ILE* 1.3 73.5 - - - +
354D PHE* 1.3 62.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 3.3 4.1 - - - +
189D TRP 2.8 33.8 + - - +
191D THR* 4.0 9.0 - - + -
201D VAL* 5.8 0.7 - - + -
227D VAL* 4.4 11.9 - - + -
287D LEU* 3.5 22.2 - - + -
296D PHE* 4.1 8.1 - + + -
298D ILE* 3.9 31.4 - - + -
333D MET* 3.8 30.5 - - + -
337D ILE* 4.5 7.2 - - + -
341D PHE* 4.3 10.5 - + + -
342D TYR 3.5 2.7 - - - -
343D VAL* 4.2 24.0 - - + -
352D ILE* 3.6 29.6 - - + -
353D GLY* 1.3 76.2 - - - -
355D ALA* 1.3 61.6 + - - +
370D VAL* 3.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D TYR* 3.5 35.9 - - + -
185D THR 4.2 1.1 - - - +
187D SER 3.5 14.4 - - - +
188D LEU* 3.6 13.0 - - + -
341D PHE* 3.2 4.8 - - - +
342D TYR 2.7 33.6 + - - +
354D PHE* 1.3 77.3 - - - +
356D VAL* 1.3 60.2 + - - +
370D VAL* 3.7 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D TYR* 3.1 21.7 - - - +
185D THR* 3.1 34.2 + - - +
186D GLY* 6.1 1.1 - - - -
340D GLY 4.0 6.5 - - - +
341D PHE* 4.1 2.7 - - + -
355D ALA* 1.3 70.4 - - - +
357D SER* 1.3 64.3 + - - +
360D HIS* 3.5 31.4 - - + +
367D THR* 5.6 0.7 - - - -
368D ALA 3.7 7.9 - - - +
369D ALA* 3.6 31.6 - - - +
370D VAL* 3.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D GLN* 3.6 8.2 - - - +
154D LEU 5.5 0.2 - - - -
183D LEU 3.8 5.4 - - - -
185D THR 5.2 0.2 - - - -
339D GLU 4.4 1.8 - - - -
340D GLY 3.2 16.2 + - - -
341D PHE* 3.6 26.0 - - - -
342D TYR* 3.9 2.5 - - - +
355D ALA 3.2 4.5 + - - -
356D VAL* 1.3 74.7 - - - +
358D ALA* 1.3 59.2 + - - +
359D CYS* 2.9 35.3 + - - -
360D HIS* 2.9 29.5 + - - -
----------------------------------------------------------
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