Contacts of the strand formed by residues 294 - 300 (chain B) in PDB entry 3DM6
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 GLN 294 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TRP* 3.8 24.5 - - - -
190B TYR 5.3 0.4 + - - -
288B MET* 4.5 0.5 - - - +
289B GLY* 2.7 41.9 + - - -
290B GLU* 2.7 28.3 + - - +
291B VAL* 2.6 51.5 + - + +
292B THR 4.4 0.2 - - - +
293B ASN* 1.3 74.7 - - - +
295B SER* 1.3 79.4 + - - +
296B PHE* 4.2 2.4 - - - +
373B PRO* 3.9 17.3 - - + -
374B PHE 3.4 4.5 - - - +
376B THR* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 4.1 19.9 - - - +
286B TYR* 4.0 8.3 - - - -
287B LEU 3.3 16.8 - - - -
288B MET* 4.9 0.4 - - - -
289B GLY 3.8 1.6 - - - +
293B ASN 4.0 0.4 + - - -
294B GLN* 1.3 91.0 + - - +
296B PHE* 1.3 63.6 + - - +
373B PRO* 3.4 4.3 - - - +
374B PHE* 2.9 46.0 + - - +
375B VAL 4.4 1.0 + - - -
376B THR* 4.4 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TRP* 3.5 54.5 - + + -
190B TYR 3.4 24.2 - - - -
191B THR* 3.8 9.9 - - - -
286B TYR* 3.1 10.2 - - - +
287B LEU* 2.9 61.2 + - + +
288B MET 3.8 12.1 - - - -
294B GLN* 4.2 8.3 - - - -
295B SER* 1.3 77.2 - - - +
297B ARG* 1.3 65.5 + - - +
298B ILE* 4.1 10.1 - - + -
354B PHE* 4.3 7.0 - + + -
370B VAL* 4.2 9.4 - - + -
371B GLU 3.6 12.6 - - - +
372B GLY* 4.2 1.8 - - - -
374B PHE* 4.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.9 8.5 + - - -
284B SER* 4.6 4.7 + - - -
285B LEU 3.2 11.7 - - - +
286B TYR* 3.1 47.1 + - + -
287B LEU 4.7 0.2 - - - +
296B PHE* 1.3 76.5 - - - +
298B ILE* 1.3 66.3 + - - +
299B THR* 4.1 15.7 + - - +
369B ALA 3.7 0.3 - - - +
370B VAL* 3.2 7.3 - - - +
371B GLU* 2.5 75.8 + - - +
374B PHE* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE 3.8 0.5 - - - +
284B SER* 3.3 1.6 - - - -
285B LEU* 2.9 49.7 + - + +
287B LEU* 4.1 6.7 - - + -
296B PHE* 4.1 10.3 - - + -
297B ARG* 1.3 77.4 - - - +
299B THR* 1.3 61.1 + - - +
300B ILE 4.2 0.8 + - - -
333B MET* 3.2 35.2 - - + -
337B ILE* 3.7 20.9 - - + -
341B PHE* 3.6 13.9 - - + -
354B PHE* 3.7 39.3 - - + -
369B ALA 3.4 3.6 - - - -
370B VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL* 3.8 28.0 - - + -
283B ILE 3.3 4.7 - - - +
284B SER* 2.6 27.9 + - - +
297B ARG* 4.1 17.7 + - - +
298B ILE* 1.3 72.0 - - - +
300B ILE* 1.3 61.0 + - - +
341B PHE* 3.6 5.0 - - - -
367B THR 5.2 4.7 - - - +
368B ALA* 3.3 13.5 - - - +
369B ALA* 2.7 44.0 + - + +
371B GLU* 4.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 5.7 2.5 - - + -
282B VAL* 3.4 8.3 - - - +
283B ILE* 2.6 58.3 + - + +
298B ILE 4.2 1.1 - - - +
299B THR* 1.3 73.6 - - - +
301B LEU* 1.3 66.3 + - - +
304B GLN* 3.2 33.4 - - + +
305B TYR* 4.1 12.6 - - + -
336B VAL* 3.4 14.4 - - + +
337B ILE* 3.3 35.9 - - + +
340B GLY* 4.5 0.9 - - - -
341B PHE* 3.3 31.9 - - + -
----------------------------------------------------------
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