Contacts of the strand formed by residues 308 - 319 (chain B) in PDB entry 5E9W
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 LEU 308 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS* 5.7 0.2 - - - -
278B PHE* 3.3 18.4 - - + +
279B ASP 4.0 3.8 - - - -
280B ILE 4.0 1.6 - - - -
281B CYS* 3.7 14.1 - - + +
304B ALA 3.6 22.4 + - - +
305B CYS* 3.3 14.5 + - - +
306B GLU 3.3 1.8 - - - +
307B ARG* 1.3 78.1 - - - +
309B SER* 1.3 67.3 + - - +
310B PRO* 3.8 1.4 - - - +
312B GLY 4.3 0.9 - - - -
313B TYR 3.5 41.1 - - - +
314B PHE* 3.8 3.8 - - + +
387B MET* 3.6 31.0 - - + -
474B LYS* 3.2 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS* 3.7 20.5 - - - +
278B PHE 2.9 18.4 + - - -
279B ASP* 4.3 13.3 + - - -
307B ARG 3.3 1.6 + - - -
308B LEU* 1.3 77.1 - - - +
310B PRO* 1.3 70.1 - - - +
311B GLY 3.3 0.2 + - - -
312B GLY* 2.8 28.4 + - - -
474B LYS* 3.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 5.3 1.7 - - - +
308B LEU 3.8 1.8 - - - +
309B SER* 1.3 90.1 - - - +
311B GLY* 1.3 59.3 + - - +
312B GLY 3.4 0.2 + - - -
474B LYS* 3.8 12.6 - - + +
475B GLN 4.1 1.6 - - - +
476B GLN* 4.0 48.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 5.0 1.3 - - - +
194B LYS* 2.8 43.0 + - - +
310B PRO* 1.3 72.0 - - - +
312B GLY* 1.3 64.3 + - - +
313B TYR* 3.3 9.9 - - - -
473B GLU* 3.8 7.9 - - - -
474B LYS 2.8 19.1 + - - -
475B GLN 4.9 0.2 - - - -
476B GLN 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 5.2 1.6 - - - -
279B ASP* 3.2 20.4 - - - -
308B LEU* 4.3 8.7 - - - +
309B SER* 2.8 19.8 + - - -
310B PRO 3.2 1.2 + - - -
311B GLY* 1.3 82.2 - - - +
313B TYR* 1.3 60.1 + - - -
473B GLU* 3.4 4.0 - - - -
474B LYS* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.6 30.3 - + + -
190B LYS* 3.8 31.1 - - + +
191B VAL* 3.6 27.6 - - + -
194B LYS* 2.5 27.1 + - - -
279B ASP 3.0 9.0 + - - +
280B ILE* 3.3 7.8 - - + +
281B CYS 2.8 27.7 + - - +
308B LEU* 3.5 8.0 - - - +
311B GLY 3.3 12.3 - - - -
312B GLY* 1.3 75.0 - - - -
314B PHE* 1.3 60.0 + - - +
315B ILE* 3.9 17.3 - - + -
390B VAL* 4.1 8.3 - - + -
471B ALA* 5.3 0.2 - - + -
472B PHE 3.3 14.1 - - - +
473B GLU* 3.9 23.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B CYS* 3.5 9.9 - - - +
283B CYS* 3.9 22.9 - - + -
287B CYS* 3.8 17.7 - - - -
300B MET* 6.4 0.7 - - + -
301B LEU* 3.5 28.3 - - + -
304B ALA* 3.8 23.8 - - + +
305B CYS* 3.5 27.1 - - - -
308B LEU* 3.8 5.5 - - + +
313B TYR* 1.3 72.4 - - - +
315B ILE* 1.3 62.9 + - - +
378B LEU* 4.9 3.1 - - + -
382B ALA* 5.6 0.4 - - + -
387B MET* 3.9 9.9 - - + -
470B PHE* 3.6 25.9 - + - -
471B ALA* 3.2 2.3 - - - -
472B PHE* 2.8 59.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.4 15.0 - - + +
184B ILE* 4.3 25.6 - - + -
187B PHE* 3.9 29.8 - - + -
215B TRP* 5.0 1.1 - - + -
280B ILE* 4.0 17.0 - - + -
281B CYS 3.0 14.5 + - - +
282B SER* 3.9 11.2 - - - +
283B CYS* 2.9 28.1 + - - +
284B GLN* 3.8 12.3 + - - +
313B TYR* 4.0 13.0 - - + -
314B PHE* 1.3 79.5 - - - +
316B GLY* 1.3 59.1 + - - +
470B PHE* 3.4 11.7 - - - +
471B ALA* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.0 3.0 - - - +
283B CYS 3.1 13.2 - - - -
284B GLN* 3.8 8.5 - - - +
315B ILE* 1.3 77.6 - - - +
317B THR* 1.3 65.4 + - - +
469B VAL* 3.3 5.7 - - - +
470B PHE* 2.9 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 5.9 2.2 - - + -
180B LYS* 5.2 4.5 - - + -
183B LEU* 4.4 5.2 - - + -
283B CYS 3.4 4.5 + - - +
284B GLN* 3.0 20.6 + - - +
285B PHE* 3.1 54.7 + - + -
286B VAL 4.2 2.1 + - - -
287B CYS* 5.2 1.0 + - - +
316B GLY* 1.3 80.1 - - - +
318B THR* 1.3 65.9 + - - +
395B PHE* 3.6 28.0 - - + -
467B TYR* 4.7 1.3 - - - -
468B LEU 3.3 4.9 - - - -
469B VAL* 3.8 11.0 - - + -
470B PHE* 3.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B CYS* 4.2 6.7 - - + +
288B HIS* 3.0 33.2 + - - +
317B THR* 1.3 75.7 - - - +
319B PRO* 1.3 81.1 - - - +
373B VAL* 4.1 20.5 - - + +
375B PHE* 5.4 1.3 - - + -
378B LEU* 5.3 2.7 - - + -
467B TYR* 3.4 7.5 - - - -
468B LEU* 2.9 44.1 + - + +
470B PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B HIS* 3.3 18.4 - - + +
318B THR* 1.3 104.4 - - - +
320B ASN* 1.3 62.2 + - - +
321B SER* 3.5 3.9 + - - -
324B LEU* 3.8 13.2 - - + +
358B TYR* 3.4 26.5 - - - +
370B GLU* 3.5 12.6 - - - +
373B VAL* 4.4 11.4 + - + +
466B ILE* 3.7 15.7 - - + +
467B TYR* 3.5 23.8 - - + -
468B LEU* 4.4 1.4 - - - +
----------------------------------------------------------
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