Contacts of the strand formed by residues 295 - 305 (chain B) in PDB entry 1LCP
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 ASN 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR 3.3 2.7 - - - -
235B LYS* 3.4 10.8 - - - +
236B GLY 3.3 7.3 + - - -
237B SER* 3.1 29.2 + - - +
239B ASN 3.5 12.7 + - - -
240B ALA* 3.4 21.0 + - - -
242B GLU* 2.9 29.2 + - + +
243B PRO 4.7 2.1 + - - +
244B PRO* 3.3 6.9 - - + +
245B LEU* 3.0 27.2 + - - +
294B ILE* 1.3 73.5 - - - +
296B ILE* 1.3 64.4 + - - +
503B MRD 3.6 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE 4.0 0.2 - - - +
233B HIS* 3.5 2.9 - - - -
234B TYR* 2.9 54.0 + - + +
244B PRO* 4.4 0.2 - - - -
245B LEU* 3.3 14.1 - - + +
247B PHE* 3.8 25.4 - - + -
284B ILE* 4.0 23.6 - - + +
287B ALA* 3.8 27.1 - - + -
294B ILE* 3.8 28.5 - - + -
295B ASN* 1.3 80.1 - - - +
297B VAL* 1.3 68.5 + - - +
479B LEU* 4.1 10.5 - - + -
503B MRD 3.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE 3.3 8.5 - - - +
233B HIS* 3.9 22.0 - - + +
244B PRO* 4.1 9.9 - - + -
245B LEU 2.9 7.1 + - - +
246B VAL* 3.4 13.4 - - + -
247B PHE* 2.8 28.2 + - - +
284B ILE* 4.1 3.1 - - - -
296B ILE* 1.3 80.5 - - - +
298B GLY* 1.3 62.6 + - - +
299B LEU* 3.8 26.7 - - + -
349B PHE* 4.1 22.4 - - + -
503B MRD 3.9 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 3.6 0.7 - - - +
231B GLU* 3.5 2.1 - - - -
232B ILE* 2.9 40.3 + - - +
247B PHE 3.4 4.7 - - - -
280B ILE* 4.3 5.8 - - - -
281B CYS* 5.9 1.1 - - - -
284B ILE* 3.5 23.2 - - - +
297B VAL* 1.3 74.8 - - - +
299B LEU* 1.3 67.4 + - - +
300B ALA 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 4.0 21.1 - - + -
230B LEU 3.5 2.0 - - - -
231B GLU* 3.9 17.7 - - + -
246B VAL* 3.9 9.4 - - + -
247B PHE 2.8 14.2 + - - +
248B VAL* 3.2 12.5 - - + +
249B GLY 2.9 25.3 + - - -
280B ILE* 4.1 2.7 - - - +
297B VAL* 3.8 18.6 - - + -
298B GLY* 1.3 83.3 - - - +
300B ALA* 1.3 60.7 + - - +
301B PRO* 4.1 2.5 - - - -
342B ALA* 3.9 10.1 - - + +
345B TYR* 4.0 15.5 - - + -
346B ALA* 3.7 37.9 - - + +
349B PHE* 4.2 4.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
183B PHE* 4.9 0.2 - - + -
229B PHE* 4.5 2.6 - - - -
230B LEU* 2.8 45.7 + - + +
249B GLY 3.7 2.7 - - - +
277B ALA* 3.9 27.4 - - + -
280B ILE* 5.0 0.7 - - + -
281B CYS* 4.4 15.7 - - - -
299B LEU* 1.3 76.0 - - - +
301B PRO* 1.3 67.7 - - - +
302B LEU* 3.4 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.7 35.4 - - + -
228B VAL 3.9 2.0 - - - +
229B PHE* 4.0 15.5 - - + -
248B VAL* 4.8 0.9 - - + -
249B GLY 3.4 12.3 - - - +
251B GLY* 3.1 26.3 + - - +
299B LEU 4.0 2.5 - - - +
300B ALA* 1.3 85.1 - - - +
302B LEU* 1.3 58.0 + - - +
338B ILE* 3.6 28.6 - - + +
339B LEU* 5.0 2.9 - - + +
342B ALA* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 3.7 20.4 - - + +
183B PHE* 3.7 45.5 - - + -
184B ALA* 4.7 1.1 - - + -
216B PHE* 3.6 2.8 - - - -
227B PRO* 3.3 4.0 - - - +
228B VAL* 2.9 56.6 + - + +
230B LEU* 3.9 13.0 - - + -
251B GLY* 3.1 26.2 - - - +
253B THR* 4.3 10.8 - - + -
274B MET* 4.8 1.1 - - + -
277B ALA* 4.4 4.0 - - + -
300B ALA* 3.5 19.3 - - + +
301B PRO* 1.3 73.2 - - - +
303B CYS* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 3.7 10.4 - - - +
216B PHE* 3.7 19.3 - - + -
219B VAL* 3.8 23.3 - - - -
220B ALA* 3.6 27.1 - - + +
225B GLU 5.6 2.0 - - - +
227B PRO* 3.9 7.2 - - + -
251B GLY 3.2 4.6 + - - -
252B ILE* 3.3 18.4 - - - +
253B THR* 3.0 27.1 + - - -
302B LEU* 1.3 75.8 - - - +
304B GLU* 1.3 70.1 + - - +
338B ILE* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 4.5 13.9 - - - +
176B ASN* 5.8 0.5 - - - -
179B THR* 5.2 2.1 - - - +
180B PRO* 4.7 0.2 - - - +
219B VAL 3.5 15.2 - - - +
220B ALA* 4.0 7.2 - - - +
223B SER* 2.7 34.4 + - - +
225B GLU* 3.6 32.3 + - + +
252B ILE* 4.8 0.7 - - - -
253B THR* 3.3 18.8 + - - +
254B PHE* 3.6 21.3 - - + +
303B CYS* 1.3 84.8 - - - +
305B ASN* 1.3 59.7 + - - +
306B MET* 3.7 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 3.9 20.9 + - + +
252B ILE* 4.5 2.2 - - + -
254B PHE 3.0 13.0 + - - +
255B ASP* 3.0 25.7 - - - +
256B SER* 2.7 34.0 + - - -
257B GLY 3.4 8.0 - - - -
258B GLY* 4.1 12.3 - - - -
304B GLU* 1.3 71.9 - - - +
306B MET* 1.3 58.3 + - - +
312B ASN* 5.8 4.0 + - - +
331B THR* 3.2 25.7 + - - +
334B GLU* 3.5 22.2 - - + +
----------------------------------------------------------
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