Contacts of the helix formed by residues 295 - 307 (chain B) in PDB entry 2W8D
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 GLY 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLN* 1.3 76.3 - - - +
296B LYS* 1.3 66.0 + - - +
297B TPO 3.1 1.4 + - - -
298B SER* 2.8 25.1 + - - -
299B ASP* 2.8 26.6 + - - -
314B GLY 4.0 4.2 + - - -
315B SER* 4.3 7.9 - - - -
350B TRP* 3.4 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 3.6 13.0 + - - +
293B GLY 3.4 20.6 + - - +
294B GLN* 3.2 10.6 - - - +
295B GLY* 1.3 75.0 - - - +
297B TPO 1.3 80.5 + - - +
299B ASP* 3.1 13.7 + - - +
300B ALA* 3.2 10.7 + - - +
350B TRP* 4.7 2.2 - - + -
472B HIS* 3.7 38.8 - - + +
473B TYR* 3.3 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TPO 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 4.4 8.0 + - - +
253B GLU* 2.9 5.9 + - - +
295B GLY 3.1 0.4 + - - -
296B LYS* 1.3 89.9 - - - +
298B SER* 1.3 63.3 + - - +
300B ALA* 3.3 5.5 + - - +
301B GLU* 3.2 23.3 + - + +
343B HIS* 6.2 0.3 - - - -
349B PHE* 4.5 7.8 - - - -
350B TRP* 3.1 32.3 + - - -
352B ARG* 4.0 12.2 + - - +
407B ILE* 4.0 27.1 - - + -
409B LEU* 5.9 0.2 - - - +
412B HIS* 2.7 37.6 + - - -
469B TYR* 5.3 0.2 + - - -
471B ASP* 3.4 18.7 - - - +
472B HIS* 3.2 6.4 + - - -
1636B MG 1.9 51.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY* 2.8 22.2 + - - -
297B TPO 1.3 77.3 + - - -
299B ASP* 1.3 59.7 + - - +
301B GLU* 3.3 12.5 + - - -
302B PHE* 2.9 24.6 + - - +
315B SER* 3.9 1.4 + - - -
317B PHE* 3.1 44.2 - - - +
350B TRP* 3.5 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 3.9 13.7 - - - -
293B GLY* 2.8 26.3 + - - -
294B GLN 3.5 0.3 + - - -
295B GLY* 2.8 34.6 + - - -
296B LYS 3.1 9.5 + - - +
298B SER* 1.3 78.6 + - - +
300B ALA* 1.3 62.0 + - - +
302B PHE* 3.2 6.2 + - - +
303B MSE 3.1 30.4 + - - +
310B PRO* 3.6 27.9 - - + +
311B LEU 5.0 0.5 - - - +
314B GLY 4.8 2.0 - - - +
315B SER* 4.6 0.2 - - - -
316B VAL* 3.8 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 3.8 3.4 - - + +
296B LYS 3.2 6.0 + - - +
297B TPO 3.4 9.9 - - - +
299B ASP* 1.3 76.0 - - - +
301B GLU* 1.3 59.5 + - - +
303B MSE 3.2 13.9 + - - +
304B MSE 2.9 34.5 + - - +
469B TYR* 3.9 21.3 - - + -
471B ASP* 3.8 26.0 - - + +
523B ASP* 4.5 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 5.9 0.2 - - - -
297B TPO 3.2 14.3 + - + +
298B SER* 3.5 13.2 - - - +
300B ALA* 1.3 76.8 - - - +
302B PHE* 1.3 63.5 + - - +
304B MSE 3.2 3.0 + - - +
305B GLU* 3.0 32.2 + - - +
317B PHE* 3.8 12.1 - - + -
352B ARG* 2.9 35.5 + - - -
356B TYR* 2.4 29.9 + - - -
359B GLU* 5.1 0.2 - - - -
405B LYS* 2.5 23.1 + - - +
407B ILE* 3.7 15.3 - - + +
469B TYR* 4.1 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B SER 2.9 13.8 + - - +
299B ASP 3.2 8.7 + - - +
301B GLU* 1.3 75.8 - - - +
303B MSE 1.3 57.9 - - - +
306B ASN* 2.9 63.3 + - + +
308B LEU* 3.5 24.9 - - + -
309B TYR 3.8 7.9 - - - -
310B PRO 4.5 1.3 - - - -
316B VAL* 3.7 35.2 - - + -
317B PHE* 3.7 10.5 - + + -
320B LYS* 5.9 0.4 - - + -
325B LEU* 3.9 23.1 - - + -
355B MSE 4.1 11.9 - - + -
359B GLU* 3.9 6.3 - - - -
609B ILE* 3.4 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLN* 3.4 39.9 - - - +
292B THR* 3.8 7.4 - - + +
299B ASP 3.1 28.2 + - - +
300B ALA* 3.6 8.1 - - - +
301B GLU 3.1 0.2 - - - -
302B PHE* 1.3 75.6 - - + +
304B MSE 1.3 66.6 + - - +
305B GLU 3.2 0.2 - - - -
307B SER* 3.0 23.3 + - - +
308B LEU 3.1 24.5 - - - +
309B TYR* 4.3 1.1 - - - -
310B PRO* 3.8 18.8 - - + -
523B ASP* 3.5 41.2 - - + +
524B VAL* 3.7 23.9 - - + -
527B ALA* 4.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 3.5 32.9 + - + -
288B PHE* 5.3 0.7 - - + -
300B ALA 2.9 20.9 + - - +
301B GLU* 3.2 7.6 + - - +
303B MSE 1.3 74.4 - - - +
305B GLU* 1.3 68.8 + - - +
328B VAL* 4.0 4.5 - - - +
403B TYR* 4.5 1.3 + - - -
405B LYS* 5.5 2.0 - - - -
467B VAL* 4.6 0.4 - - + -
469B TYR* 2.8 71.6 - - + +
505B LEU* 4.6 2.9 - - + -
523B ASP* 4.1 12.1 - - - +
526B VAL* 3.6 39.0 - - + -
527B ALA* 3.3 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 4.8 1.0 - - - -
301B GLU* 3.0 23.5 + - - +
304B MSE 1.3 84.3 - - - +
306B ASN* 1.3 60.1 + - - +
327B SER* 3.3 5.1 - - - -
328B VAL* 2.9 36.2 + - - +
329B PRO* 3.8 21.5 - - + -
359B GLU* 3.5 34.6 - - + +
361B ILE* 4.7 1.8 - - + -
403B TYR* 2.5 30.4 + - - -
405B LYS* 2.8 43.3 + - - +
543B MSE 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 2.9 46.8 + - + +
305B GLU* 1.3 79.8 - - - +
307B SER* 1.3 70.0 + - - +
308B LEU* 3.4 26.0 + - + +
325B LEU* 3.7 16.7 - - - +
326B GLN 4.4 4.1 + - - +
327B SER* 2.9 23.3 + - - +
359B GLU* 2.7 29.3 + - - +
542B LEU 4.4 1.6 - - - +
543B MSE 3.9 16.7 - - - +
614B LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MSE 3.0 17.4 + - - -
306B ASN* 1.3 80.3 - - - +
308B LEU* 1.3 56.8 + - - +
524B VAL* 2.7 32.6 + - - -
527B ALA* 4.0 15.8 - - - +
528B PRO* 3.8 2.5 - - - +
543B MSE 3.8 20.5 - - - +
544B SER* 2.8 35.0 + - - -
545B GLY* 3.0 15.6 + - - -
----------------------------------------------------------
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