Contacts of the strand formed by residues 253 - 266 (chain E) in PDB entry 5IXM
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 SER 253 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232E HIS* 3.5 23.4 - - - -
233E TYR 3.3 3.6 - - - -
234E GLN* 3.9 13.4 + - - -
251E LYS* 3.1 31.1 - - - +
252E ASP* 1.3 80.7 - - - +
254E VAL* 1.3 64.5 + - - +
255E ASN* 4.4 3.9 + - - -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E THR 3.8 0.9 - - - +
232E HIS* 3.6 5.0 + - - -
233E TYR* 2.9 49.8 + - + +
235E GLN* 4.3 5.2 - - - +
251E LYS* 3.7 22.4 - - + +
253E SER* 1.3 79.3 + - - +
255E ASN* 1.3 76.8 + - - +
256E ARG* 4.8 1.1 - - + +
299E ASP* 3.6 35.7 - - - +
300E ILE* 3.7 29.2 - - + -
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Residues in contact with ASN 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E THR 3.7 3.2 - - - +
232E HIS* 3.4 27.7 + - - +
253E SER* 4.4 3.7 + - - -
254E VAL* 1.3 79.5 - - - +
256E ARG* 1.3 62.1 + - - +
257E VAL* 4.2 6.3 - - + -
295E ARG* 3.8 23.0 + - - +
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Residues in contact with ARG 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E HIS* 4.8 0.6 + - - -
229E LEU* 3.6 6.2 + - - +
231E THR* 2.9 76.9 + - - +
233E TYR* 4.6 3.1 - - + -
254E VAL* 5.1 1.1 - - + -
255E ASN* 1.3 75.0 - - - +
257E VAL* 1.3 62.8 + - - +
258E LEU* 4.1 22.1 - - + +
295E ARG* 4.2 15.9 - - + +
297E GLN* 2.7 48.1 + - + -
300E ILE* 4.3 15.3 - - + +
324E LEU* 2.4 36.7 + - - +
325E ASP* 3.4 12.5 + - - +
327E ILE* 3.7 20.8 - - - +
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Residues in contact with VAL 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 4.0 25.8 - - + -
229E LEU 3.4 4.0 - - - +
230E ALA* 4.4 15.0 - - + -
231E THR 5.0 1.3 - - - +
255E ASN* 4.2 5.8 - - + -
256E ARG* 1.3 79.6 - - - +
258E LEU* 1.3 72.4 + - - +
259E PRO* 4.1 5.0 - - + +
295E ARG* 5.6 3.0 - - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 4.1 2.5 - - - -
229E LEU* 2.9 50.3 + - + +
256E ARG* 4.1 23.1 - - + +
257E VAL* 1.3 80.6 - - - +
259E PRO* 1.3 71.1 - - - +
260E GLN 4.0 0.3 + - - -
292E VAL* 4.5 6.1 - - + -
293E PRO* 3.5 36.8 - - + +
294E TYR 4.7 0.9 - - - +
295E ARG* 3.7 24.7 - - + -
297E GLN* 4.4 0.7 - - - +
327E ILE* 3.9 38.1 - - + +
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Residues in contact with PRO 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LYS 3.5 8.7 - - - +
228E LEU* 4.0 13.9 - - + -
257E VAL* 4.1 6.1 - - + +
258E LEU* 1.3 87.0 - - - +
260E GLN* 1.3 61.4 + - - +
291E TYR* 4.1 2.9 - - + +
292E VAL* 3.9 4.0 - - - +
293E PRO* 3.1 45.4 - - + +
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Residues in contact with GLN 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E GLU* 3.7 2.8 + - - +
226E ALA* 3.6 4.9 - - - +
227E LYS* 2.9 66.5 + - + +
229E LEU* 4.2 15.3 - - + +
259E PRO* 1.3 76.7 - - - +
261E PHE* 1.3 63.7 + - - +
262E LYS* 3.8 12.1 - - - +
290E LEU* 3.8 17.7 - - + +
291E TYR 3.5 3.6 - - - -
292E VAL* 3.7 20.7 - - + +
318E ASP* 2.9 43.4 + - - +
319E ARG* 4.7 4.5 + - - -
327E ILE* 6.0 0.2 - - - +
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Residues in contact with PHE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E THR* 3.8 26.0 - - + -
225E GLU 3.7 7.2 - - - -
226E ALA* 5.1 4.3 - - + +
260E GLN* 1.3 75.0 - - - +
262E LYS* 1.3 68.6 + - - +
263E VAL* 4.0 23.8 - - + -
289E TYR* 3.9 31.0 - + - -
290E LEU* 3.6 2.6 - - - +
291E TYR* 2.9 47.5 + + + +
602E C8E 6.3 0.2 - - - -
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Residues in contact with LYS 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E ASN* 3.9 2.7 - - - +
224E THR* 3.7 1.9 - - - +
225E GLU* 2.9 68.7 + - + +
260E GLN* 3.8 10.8 - - - +
261E PHE* 1.3 79.3 - - - +
263E VAL* 1.3 64.2 + - - +
264E ASP* 4.7 8.7 - - + -
288E GLN* 3.6 32.5 + - + +
289E TYR 3.3 10.3 - - - +
290E LEU* 3.8 9.6 - - + -
316E PHE 4.9 4.2 + - - -
318E ASP* 3.8 36.9 + - - +
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Residues in contact with VAL 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E ILE* 4.4 15.9 - - + -
223E ASN 3.5 9.4 - - - +
224E THR* 4.3 13.5 - - + +
261E PHE* 4.0 24.0 - - + -
262E LYS* 1.3 74.4 - - - +
264E ASP* 1.3 63.0 + - - +
265E GLY 4.3 0.2 - - - -
287E ALA 3.9 0.7 - - - +
288E GLN* 3.2 4.2 - - - +
289E TYR* 2.9 52.7 + - + +
602E C8E 4.2 24.4 - - + +
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Residues in contact with ASP 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E SER 4.2 0.5 - - - +
222E ILE* 3.5 3.5 - - - -
223E ASN* 2.9 48.9 + - + +
262E LYS* 4.3 7.5 - - + +
263E VAL* 1.3 76.3 - - - +
265E GLY* 1.3 73.9 + - - +
266E LYS* 5.6 0.2 - - - +
286E ARG* 3.4 32.7 + - - +
287E ALA 3.1 10.5 - - - +
288E GLN* 3.0 31.9 - - + +
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Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E SER 3.5 7.4 - - - -
222E ILE* 4.1 10.5 - - - -
264E ASP* 1.3 80.1 + - - +
266E LYS* 1.3 61.4 + - - +
286E ARG* 3.3 2.9 - - - -
287E ALA 2.9 35.8 + - - -
602E C8E 4.2 13.1 - - - +
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Residues in contact with LYS 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E GLY* 3.1 2.6 - - - -
221E SER* 2.9 44.0 + - - +
265E GLY* 1.3 76.0 - - - +
267E VAL* 1.3 74.9 + - - +
268E VAL* 4.0 18.7 - - + +
284E GLU* 3.8 25.7 + - + -
285E PRO 3.5 11.2 - - - +
286E ARG* 4.5 18.2 - - + +
340E ARG* 6.1 0.4 - - - +
133F GLN* 5.7 3.0 + - - -
137F ARG* 6.0 1.8 - - - +
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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