Contacts of the strand formed by residues 245 - 255 (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 LEU 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B PRO 5.1 0.9 - - - +
244B PRO* 1.3 76.8 - - + +
246B VAL* 1.3 60.9 + - - +
247B PHE* 4.3 13.0 - - + -
294B ILE* 4.3 15.5 - - + -
295B ASN 3.0 18.8 + - - +
296B ILE* 3.3 9.2 - - + +
297B VAL 2.9 23.2 + - - -
352B LYS* 4.7 7.9 - - + -
353B VAL* 3.7 22.0 - - + +
478B PHE* 3.8 30.3 - - + -
479B LEU* 4.0 12.6 - - + -
482B PHE* 3.7 42.6 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B PRO* 4.5 2.9 - - + -
245B LEU* 1.3 77.5 - - - +
247B PHE* 1.3 72.3 + - - +
248B VAL* 4.2 2.2 - - + -
297B VAL* 3.4 20.6 - - + +
299B LEU* 3.9 18.4 - - + -
346B ALA* 3.8 28.9 - - + +
349B PHE* 4.1 18.2 - - + -
351B PRO* 3.6 24.5 - - + -
353B VAL 2.9 12.9 + - - +
354B ILE* 3.4 6.1 - - + +
355B ILE* 2.9 25.5 + - - +
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.3 13.2 - - + -
246B VAL* 1.3 81.4 - - - +
248B VAL* 1.3 58.9 + - - +
280B ILE* 3.9 40.2 - - + -
283B ALA* 5.4 1.8 - - + -
284B ILE* 4.2 8.3 - - + -
296B ILE* 3.8 20.6 - - + -
297B VAL 2.8 10.1 + - - +
298B GLY* 3.4 0.5 - - - -
299B LEU* 2.8 32.3 + - - +
355B ILE* 3.1 33.0 - - + -
475B LEU* 4.0 29.4 - - + -
478B PHE* 4.4 4.9 - + - -
479B LEU* 3.8 38.8 - - + -
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B VAL* 4.2 2.9 - - + -
247B PHE* 1.3 80.3 - - - +
249B GLY* 1.3 63.1 + - - +
280B ILE* 4.0 5.7 - - - +
299B LEU* 3.2 26.5 - - + +
301B PRO* 4.8 0.2 - - + -
339B LEU* 3.8 17.9 - - + -
342B ALA* 3.6 30.7 - - + +
343B LEU* 4.3 14.4 - - + +
346B ALA* 4.2 15.7 - - + -
354B ILE* 4.5 5.8 - - + -
355B ILE 2.8 7.3 + - - +
356B ASN* 2.9 15.5 - - + +
357B ALA 2.8 25.3 + - - -
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL* 1.3 75.4 - - - +
250B LYS* 1.3 66.4 + - - -
251B GLY 3.3 3.3 + - - -
276B GLY 3.7 17.0 - - - -
277B ALA* 3.7 7.1 - - - +
280B ILE* 3.9 3.3 - - - +
299B LEU 2.9 10.9 + - - -
300B ALA* 3.7 8.0 - - - +
301B PRO* 3.4 18.4 - - - +
339B LEU* 4.2 4.0 - - - -
357B ALA 3.4 7.2 - - - -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLY* 1.3 68.7 - - - -
251B GLY* 1.3 59.3 + - - +
252B ILE* 3.6 8.3 - - + -
273B ASP* 3.1 25.0 + - - +
274B MET* 3.4 12.6 - - - -
276B GLY 3.7 1.6 + - - -
277B ALA 3.2 15.6 + - - +
334B GLU* 3.2 7.5 + - - -
335B GLY* 3.7 19.3 - - - -
338B ILE* 4.1 15.3 - - + -
339B LEU* 3.9 15.2 - - + +
357B ALA 3.1 7.9 + - - -
358B ALA* 3.5 31.4 - - + -
359B THR* 3.1 16.6 + - - +
360B LEU* 4.3 5.6 + - + +
489B ZN 2.2 37.4 - - - -
500B PLU 3.2 5.7 + - - -
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLY 3.3 1.4 + - - -
250B LYS* 1.3 73.7 - - - +
252B ILE* 1.3 61.3 + - - +
253B THR 3.2 4.6 + - - -
274B MET* 3.8 8.5 - - - -
277B ALA* 3.9 4.9 - - - -
301B PRO 3.1 22.1 + - - -
302B LEU* 3.1 41.0 - - - +
303B CYS 3.2 5.6 + - - -
338B ILE* 3.8 1.8 - - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B VAL* 4.1 5.4 - - + -
250B LYS* 3.6 13.2 - - - -
251B GLY* 1.3 71.9 - - - +
253B THR* 1.3 62.2 + - - +
254B PHE 3.3 29.6 - - - +
255B ASP* 3.7 5.8 - - + -
273B ASP* 3.0 48.8 + - - +
274B MET* 3.0 2.6 + - - -
303B CYS* 3.3 26.5 - - - +
305B ASN* 4.4 4.9 - - + +
334B GLU* 3.6 32.8 - - + +
335B GLY* 5.0 0.4 - - - -
338B ILE* 3.8 21.5 - - + -
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 3.3 17.4 - - - +
178B MET* 3.5 24.4 - - + +
179B THR* 3.9 2.5 - - - -
180B PRO* 3.6 34.5 - - + +
183B PHE* 5.2 2.7 - - + -
251B GLY 4.0 8.7 - - - +
252B ILE* 1.3 71.8 - - - +
254B PHE* 1.3 60.4 + - - +
270B MET 4.2 0.7 - - - -
271B ARG* 3.4 15.8 - - - +
274B MET* 3.8 13.0 - - + -
302B LEU* 4.3 9.6 - - + -
303B CYS 3.0 8.7 + - - -
304B GLU* 3.3 25.6 + - - +
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Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 3.7 17.7 - - + -
252B ILE* 3.2 6.5 - - - +
253B THR* 1.3 81.1 + - - +
255B ASP* 1.3 61.5 + - - +
256B SER* 3.7 32.3 - - - -
267B MET* 3.6 42.2 - - + -
268B ASP* 4.4 7.0 - - - -
270B MET* 3.6 9.2 - - + -
271B ARG* 3.8 21.3 - - + -
303B CYS 4.4 0.2 + - - -
304B GLU* 3.6 14.3 - - + +
305B ASN 3.0 27.5 + - - +
306B MET* 4.3 13.5 - - - -
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 3.7 3.4 - - + -
254B PHE* 1.3 80.5 - - - +
256B SER* 1.3 56.6 + - - +
257B GLY 3.0 10.9 + - - -
262B LYS* 3.3 14.8 - - - +
267B MET* 4.3 0.3 - - - +
270B MET* 3.3 26.9 + - + +
273B ASP* 3.1 21.5 - - + +
305B ASN* 3.0 25.0 - - - +
332B ASP* 3.1 2.6 - - - +
334B GLU* 3.4 7.6 - - - -
488B ZN 2.1 31.6 - - - -
489B ZN 2.7 11.1 - - - -
500B PLU 3.0 5.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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