Contacts of the strand formed by residues 236 - 249 (chain D) in PDB entry 3CMT
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 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4286A LYS* 5.1 11.1 + - - +
232D LYS* 3.2 6.1 - - - +
233D GLU* 2.7 50.7 + - + +
235D GLU* 1.3 87.3 - - - +
237D VAL* 1.3 64.1 + - - +
238D VAL* 3.6 4.4 + - + +
1256D LYS* 6.2 2.6 - - - +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ARG* 4.0 0.7 - - - +
230D ALA* 4.0 17.5 - - + -
231D VAL 3.7 2.9 - - - +
232D LYS* 4.2 16.6 - - + -
235D GLU 3.9 3.1 + - - +
236D ASN* 1.3 75.0 - - - +
238D VAL* 1.3 60.2 + - - +
239D GLY 3.9 16.8 - - - +
264D TYR* 3.8 12.9 - - + -
1253D ALA* 5.2 2.9 - - - +
1254D PRO 4.2 6.6 - - - +
1255D PHE* 3.7 49.7 + - + +
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D VAL* 2.9 31.5 + - + +
232D LYS 4.7 0.9 - - - +
233D GLU* 3.9 31.2 - - + -
236D ASN* 3.6 4.9 + - + +
237D VAL* 1.3 73.9 - - - +
239D GLY* 1.3 57.1 + - - +
263D LEU* 3.8 12.0 - - + +
264D TYR* 3.1 33.5 + - + +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ALA* 3.7 4.5 - - - -
231D VAL* 2.8 40.2 + - - +
237D VAL* 3.9 3.6 - - - +
238D VAL* 1.3 80.0 - - - +
240D SER* 1.3 56.2 + - - -
262D ILE 3.1 13.9 - - - -
263D LEU* 4.1 2.5 - - - -
264D TYR* 3.5 21.0 + - - -
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Residues in contact with SER 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D SER 4.9 1.4 + - - -
70D SER 5.7 1.8 - - - -
227D ARG* 3.0 28.5 + - - +
229D GLY 3.7 4.3 - - - -
231D VAL* 4.0 2.7 - - - -
239D GLY* 1.3 70.5 - - - -
241D GLU* 1.3 62.2 + - - +
242D THR* 3.3 10.8 + - - -
261D GLN* 3.6 0.9 - - - -
262D ILE* 2.8 44.5 + - - -
264D TYR* 2.7 25.5 + - - -
502D ADP 3.3 13.4 + - - -
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ARG* 3.6 4.0 - - - -
228D ILE* 2.8 43.3 + - + -
229D GLY* 2.8 31.7 + - - +
230D ALA 4.4 3.9 - - - +
231D VAL* 3.4 13.8 - - + +
240D SER* 1.3 72.2 - - - +
242D THR* 1.3 58.7 + - - +
259D GLU* 5.6 3.0 - - + +
260D PHE* 3.8 9.9 + - - +
261D GLN* 3.2 38.2 + - - +
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Residues in contact with THR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D SER 4.2 5.9 + - - +
225D ILE* 3.8 28.3 - - + -
226D ARG 3.5 6.2 + - - +
227D ARG* 4.8 1.2 - - - -
228D ILE* 4.4 3.6 - - - +
240D SER* 3.3 18.6 + - - -
241D GLU* 1.3 75.5 + - - +
243D ARG* 1.3 65.0 + - - +
244D VAL 4.4 0.2 - - - -
259D GLU* 3.2 6.6 - - - +
260D PHE* 2.7 72.6 + - + +
262D ILE* 3.7 14.0 - - + +
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ASP 3.6 1.9 - - - +
225D ILE* 3.5 0.9 - - - -
226D ARG* 2.9 41.4 + - + +
228D ILE* 3.6 41.1 - - + +
242D THR* 1.3 75.4 - - - +
244D VAL* 1.3 66.3 + - - +
245D LYS* 4.1 22.5 - - - +
257D GLN* 3.3 30.7 + - - +
258D ALA 3.3 4.5 - - - +
259D GLU* 2.4 42.8 + - + -
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 4.3 18.8 - - + +
50D ALA* 5.5 0.2 - - - +
75D LEU* 4.3 6.7 - - + -
223D LEU* 3.7 36.3 - - + -
224D ASP 3.3 7.0 - - - +
225D ILE* 3.8 22.7 - - + -
243D ARG* 1.3 76.6 - - - +
245D LYS* 1.3 65.7 + - - +
246D VAL* 4.1 1.6 + - - +
257D GLN* 3.3 5.7 - - - +
258D ALA* 2.8 38.0 + - + +
260D PHE* 3.7 31.2 - - + -
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Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.4 4.5 - - - -
224D ASP* 2.8 53.5 + - + +
226D ARG* 5.9 5.3 - - - +
243D ARG* 4.1 19.5 - - - +
244D VAL* 1.3 73.3 - - - +
246D VAL* 1.3 61.4 + - - +
247D VAL* 3.3 13.3 + - + -
255D PHE* 6.0 4.9 - - + +
256D LYS 4.0 3.6 - - - +
257D GLN* 3.4 34.1 - - + +
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Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 4.3 9.4 - - + -
50D ALA* 4.1 28.5 - - + +
51D LEU* 4.4 7.2 - - + +
222D ARG 3.7 5.2 - - - +
223D LEU* 4.0 17.9 - - + -
244D VAL 5.2 0.7 - - - +
245D LYS* 1.3 71.2 - - - +
247D VAL* 1.3 60.5 + - - +
248D LYS 3.6 19.1 - - - +
249D ASN* 3.9 26.9 - - + +
254D PRO* 4.5 3.1 - - + -
255D PHE* 2.7 36.3 + - - +
256D LYS 3.0 21.5 + - - +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TYR* 3.5 26.5 - - + +
222D ARG* 2.8 30.9 + - + +
224D ASP* 3.6 23.8 - - + +
245D LYS* 3.3 13.4 + - + +
246D VAL* 1.3 74.1 - - - +
248D LYS* 1.3 60.8 + - + +
254D PRO* 4.5 1.4 - - - +
255D PHE* 3.5 31.4 - - + -
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Residues in contact with LYS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D LYS 2.7 29.8 + - - +
217D PHE* 2.8 25.9 + - - +
219D ALA 3.0 19.8 + - - +
220D SER 4.8 1.6 - - - +
221D VAL* 3.2 4.2 - - - -
222D ARG* 2.9 47.2 + - + +
246D VAL* 3.6 9.4 - - - +
247D VAL* 1.3 81.6 - - + +
249D ASN* 1.3 69.0 + - - +
250D LYS* 4.5 19.0 - - - +
254D PRO* 4.4 2.0 - - - -
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Residues in contact with ASN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.2 28.5 + - - +
220D SER 3.5 2.0 - - - -
221D VAL* 3.6 9.7 - - - +
246D VAL* 3.9 12.3 - - + +
248D LYS* 1.3 81.7 - - - +
250D LYS* 1.3 59.5 + - - +
251D ILE* 3.0 27.8 + - - +
252D ALA* 3.1 32.2 + - - +
253D ALA 3.3 12.3 + - - -
254D PRO* 3.8 25.7 - - + +
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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