Contacts of the strand formed by residues 268 - 276 (chain D) in PDB entry 1DVM
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 268 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D LYS* 5.9 2.6 - - - +
207D LYS* 3.9 40.3 + - + +
208D PHE 3.3 5.2 - - - +
209D ASN* 3.3 31.9 + - - +
267D THR* 1.3 75.9 - - - +
269D LEU* 1.3 63.5 + - - +
270D PRO* 4.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LYS* 4.4 0.9 - - - -
208D PHE* 2.8 26.6 + - - +
210D TYR* 3.9 28.9 - - + +
267D THR* 3.0 51.4 + - + +
268D ARG* 1.3 74.1 - - - +
270D PRO* 1.3 67.5 - - + +
271D ARG* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ASN* 3.3 12.6 - - - +
207D LYS* 4.3 26.0 - - + +
268D ARG 4.0 6.1 - - - +
269D LEU* 1.3 83.3 - - + +
271D ARG* 1.3 86.5 + - - +
348D ALA* 3.9 6.1 - - + -
349D PRO* 3.0 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 3.2 1.4 - - - -
206D ASN 3.0 28.0 + - - -
208D PHE* 3.1 20.2 - - + +
210D TYR* 5.9 1.7 - - + -
269D LEU* 3.0 53.4 + - + +
270D PRO* 1.3 114.7 + - - +
272D LEU* 1.3 61.5 + - - +
273D LEU 3.7 0.4 - - - -
348D ALA* 3.6 6.1 - - - -
349D PRO* 3.9 15.4 - - - +
350D GLU* 3.3 42.5 + - - +
352D ILE* 3.7 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 5.7 7.2 - - - +
203D ALA* 4.2 13.0 - - + -
204D GLN* 4.2 4.9 - - - +
205D THR* 3.2 31.6 - - + -
271D ARG* 1.3 72.1 - - - +
273D LEU* 1.3 71.7 + - - +
274D VAL* 4.5 9.0 - - + +
348D ALA* 3.8 7.1 - - + +
350D GLU 3.2 7.5 + - - +
351D GLU* 3.4 25.6 - - + +
352D ILE 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PHE* 3.8 13.7 - - + -
203D ALA* 3.3 6.2 - - - +
204D GLN 3.0 31.4 + - - +
208D PHE* 3.5 35.0 - - + -
224D LEU* 3.6 25.8 - - + -
226D LEU* 3.4 33.2 - - + -
237D ILE* 5.5 0.9 - - + -
271D ARG* 3.7 2.4 - - + -
272D LEU* 1.3 75.0 - - - +
274D VAL* 1.3 77.1 + - - +
275D LEU* 4.0 10.1 - - + +
352D ILE* 3.4 15.5 - - + +
354D ILE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D HIS* 3.8 20.6 - - + +
187D ARG* 4.1 10.1 - - - +
201D MET* 3.7 33.9 - - + -
202D MET 3.6 5.4 - - - +
203D ALA* 4.0 9.9 - - + -
272D LEU* 4.5 17.3 - - + +
273D LEU* 1.3 78.3 - - - +
275D LEU* 1.3 62.1 + - - +
276D PRO* 4.7 0.2 - - - -
351D GLU* 5.8 2.9 - - + -
352D ILE 3.0 6.8 + - - +
353D ILE* 4.0 22.6 - - + +
354D ILE* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D TRP* 5.0 4.3 - - + -
179D PHE* 4.6 3.6 - - + -
201D MET* 4.1 2.2 - - - -
202D MET* 2.8 55.8 + - + +
226D LEU* 4.4 15.7 - - + -
235D MET* 5.3 1.3 - - - -
237D ILE* 3.3 36.8 - - + -
273D LEU* 4.0 13.4 - - + +
274D VAL* 1.3 75.3 - - - +
276D PRO* 1.3 86.2 - - + +
278D PHE* 4.9 2.0 - - + -
328D VAL* 4.3 10.3 - - + -
354D ILE* 4.0 12.1 - - + -
358D PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D PHE* 4.2 2.7 - - + -
199D VAL* 3.8 18.4 - - + -
200D PRO 3.6 0.9 - - - +
201D MET* 3.4 24.9 - - + -
202D MET* 4.5 0.6 - - - +
275D LEU* 1.3 102.1 - - + +
277D LYS* 1.3 60.8 + - - +
278D PHE* 3.4 14.6 - - + -
328D VAL* 4.3 1.2 - - - +
354D ILE* 3.2 26.2 - - + +
358D PHE* 3.8 22.7 - - + -
379D PRO* 4.0 16.6 - - + -
----------------------------------------------------------
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