Contacts of the strand formed by residues 303 - 314 (chain B) in PDB entry 4LEY
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 GLU 303 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASN* 3.3 21.7 + - - +
297B LEU* 3.9 19.3 - - + +
298B ILE 3.4 4.9 - - - -
299B ARG* 3.3 39.6 + - - -
301B PRO 4.6 1.8 - - - +
302B GLU* 1.3 75.7 - - - +
304B ILE* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.7 32.3 - - + +
170B THR* 5.4 1.1 - - - -
171B VAL* 4.1 9.6 - - + -
209B PRO 4.2 7.4 - - - +
210B ASN* 3.5 10.1 - - - +
212B PHE* 3.5 33.9 - - + -
296B LEU 3.4 2.8 - - - +
297B LEU* 3.6 5.4 - - - +
298B ILE* 2.9 43.4 + - + +
300B ASN* 3.8 27.1 - - + -
302B GLU* 4.1 15.3 - - + +
303B GLU* 1.3 78.9 - - - +
305B SER* 1.3 64.2 + - - +
306B VAL* 4.1 1.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASN 2.7 10.7 + - - +
211B GLU* 3.2 27.4 + - - +
212B PHE* 2.9 25.1 + - - +
285B GLU* 5.9 0.7 - - - -
295B THR* 4.3 13.9 - - - -
296B LEU 3.3 7.6 - - - -
297B LEU* 4.9 4.9 - - - +
304B ILE* 1.3 74.3 - - - +
306B VAL* 1.3 62.9 + - - +
307B ASP* 4.2 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 4.0 28.3 - - + -
175B VAL* 4.6 8.5 - - + -
212B PHE* 3.4 18.2 - - + +
214B VAL* 4.4 9.4 - - + -
294B VAL 3.4 2.3 - - - +
295B THR* 3.4 1.9 - - - -
296B LEU* 2.9 48.0 + - + +
298B ILE* 4.3 16.4 - - + -
304B ILE* 4.5 3.6 - - + +
305B SER* 1.3 78.3 - - - +
307B ASP* 1.3 66.7 + - - +
308B ILE* 3.4 24.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE 2.9 9.8 + - - -
213B ASP* 3.5 21.5 - - - +
214B VAL* 3.0 31.7 + - - +
291B SER* 5.6 1.2 + - - -
293B ALA* 3.8 16.9 - - + +
294B VAL 4.0 3.4 - - - -
295B THR* 3.0 29.7 + - - +
305B SER* 4.9 3.9 + - - -
306B VAL* 1.3 71.9 + - - +
308B ILE* 1.3 60.7 + - - +
309B ILE* 3.5 8.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 4.7 5.8 - - + -
178B LEU* 4.3 19.3 - - + -
214B VAL* 3.5 14.6 - - + -
216B PHE* 4.0 27.4 - - + -
266B PHE* 3.7 31.3 - - + -
270B ILE* 3.8 14.4 - - + -
293B ALA* 3.3 2.3 - - - -
294B VAL 2.9 41.3 + - - +
296B LEU* 4.1 17.0 - - + -
306B VAL* 3.8 21.1 - - + -
307B ASP* 1.3 71.0 - - - +
309B ILE* 1.3 60.3 + - - +
310B LEU 3.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 4.5 2.2 - - - +
213B ASP* 4.1 24.0 - - + -
214B VAL 2.9 14.1 + - - +
215B MET* 3.6 24.1 - - + +
216B PHE* 2.9 28.2 + - - -
266B PHE* 4.7 1.3 - - - -
292B PRO* 3.7 23.3 - - + +
293B ALA* 3.8 12.6 - - + -
307B ASP* 3.8 17.9 - - + +
308B ILE* 1.3 72.3 - - - +
310B LEU* 1.3 62.8 + - - +
311B ALA* 3.4 1.3 + - + -
348B VAL* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.7 25.4 - - + -
192B VAL* 5.5 0.9 - - + -
216B PHE 3.8 6.7 - - - +
218B LEU* 5.5 2.9 - - + -
262B MET* 4.0 31.2 - - + +
263B LEU* 3.9 42.8 - - + +
266B PHE* 3.9 28.6 - - + -
292B PRO 3.2 7.2 + - - +
308B ILE 3.6 3.6 + - - -
309B ILE* 1.3 70.0 - - - +
311B ALA* 1.3 70.1 + - - +
348B VAL* 3.8 5.4 - - - +
349B PRO* 3.2 33.5 - - + +
363B TRP* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 3.6 32.3 - - + -
216B PHE 2.9 9.8 + - - +
217B LYS* 3.3 11.6 - - + -
218B LEU* 2.9 27.1 + - - +
309B ILE 4.4 2.7 - - - +
310B LEU* 1.3 79.4 - - - +
312B LEU* 1.3 66.5 + - - +
346B TYR* 4.5 5.8 - - + -
347B LEU 3.5 8.1 - - - +
348B VAL* 4.1 8.5 - - + -
363B TRP* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 3.4 4.0 - - + +
220B VAL* 3.8 24.7 - - + -
223B ILE* 5.8 3.1 - - + -
237B VAL* 4.1 16.2 - - + -
257B LEU* 4.0 11.0 - - + -
262B MET* 3.6 31.0 - - + -
310B LEU* 5.4 0.9 - - + -
311B ALA* 1.3 77.2 - - - +
313B GLU* 1.3 60.8 + - - +
314B SER* 5.4 0.6 - - - -
345B PHE 3.6 0.9 - - - +
346B TYR* 3.1 9.3 - - - -
347B LEU* 2.9 45.6 + - + +
363B TRP* 3.6 48.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 4.7 2.3 - - - +
217B LYS* 2.5 36.8 + - + -
218B LEU 2.9 11.4 + - - +
219B GLU* 3.3 35.6 + - + +
220B VAL* 3.1 24.0 + - - +
223B ILE* 6.1 0.2 - - - -
312B LEU* 1.3 73.2 - - - +
314B SER* 1.3 63.9 + - - +
315B LYS* 4.3 12.1 - - + -
344B PRO* 3.7 21.3 - - + +
345B PHE 3.6 3.4 - - - -
346B TYR* 3.0 33.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLU* 5.3 0.7 - - - -
220B VAL 5.1 2.7 + - - -
223B ILE* 4.2 23.7 - - - +
312B LEU 4.0 1.1 + - - -
313B GLU* 1.3 74.1 - - - +
315B LYS* 1.3 60.5 + - - +
316B GLY* 3.3 8.7 + - - -
344B PRO* 3.1 5.2 - - - +
345B PHE* 2.9 75.0 + - - -
347B LEU* 6.0 1.1 - - - -
----------------------------------------------------------
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