Contacts of the strand formed by residues 215 - 229 (chain A) in PDB entry 3C0M
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 TYR 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLN* 3.2 48.9 - - + -
213A SER 2.4 23.8 + - - +
214A GLY 1.3 68.5 - - - -
216A ASP* 1.3 61.1 + - - +
217A VAL* 3.7 2.4 + - - +
282A ARG* 3.4 20.8 - - - +
283A PRO* 4.1 6.2 - - - +
441A LEU* 4.2 29.6 - - + +
464A VAL* 4.5 18.6 - - + -
465A THR* 3.5 5.6 - - - +
466A PRO* 3.2 44.4 - - + -
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 1.3 70.1 - - - +
217A VAL* 1.3 61.1 + - - +
218A THR* 3.6 1.7 + - - +
280A SER* 3.9 21.5 + - - +
281A VAL 3.4 4.8 - - - +
282A ARG* 3.3 28.6 + - - +
463A SER 3.2 3.6 - - - +
464A VAL* 3.7 0.6 - - - -
465A THR* 2.7 43.3 + - - +
466A PRO 4.7 0.5 - - - +
467A ALA* 3.9 20.7 - - - +
468A ALA 4.2 6.4 + - - -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 5.3 2.5 - - + -
215A TYR 3.7 1.3 + - - +
216A ASP* 1.3 73.4 - - - +
218A THR* 1.3 59.7 + - - +
280A SER* 3.1 1.6 - - - -
281A VAL* 2.6 41.1 + - + +
283A PRO* 4.1 21.1 - - + -
293A VAL* 6.1 5.8 - - + -
414A ILE* 3.8 15.2 - - + +
441A LEU* 4.4 18.2 - - + -
443A LEU* 4.4 21.8 - - + -
462A LEU* 4.6 17.0 - - + -
463A SER 3.4 6.7 - - - +
464A VAL* 4.6 12.3 - - + -
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 4.6 4.0 - - + +
217A VAL* 1.3 73.9 - - - +
219A LEU* 1.3 63.2 + - - +
220A ARG* 3.2 38.8 + - - +
278A SER* 5.2 2.1 - - - -
279A GLN 3.1 10.8 + - - -
280A SER* 2.9 21.8 + - - +
461A SER 3.7 0.9 - - - +
462A LEU* 3.2 6.2 - - - +
463A SER* 2.6 61.1 + - - +
465A THR* 4.9 7.0 - - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 1.3 73.4 + - - +
220A ARG* 1.3 63.3 + - - +
277A LEU* 3.2 31.8 - - + +
278A SER* 3.9 0.9 - - - -
279A GLN* 3.0 27.7 + - + +
295A ILE* 3.9 29.8 - - + -
297A LEU* 5.9 0.7 - - + -
411A ALA* 4.7 6.7 - - + -
412A GLY 5.9 0.2 - - - +
414A ILE* 4.2 14.5 - - + +
447A LEU* 6.0 0.2 - - + -
460A VAL* 3.7 28.3 - - + -
461A SER 3.2 16.8 - - - +
462A LEU* 3.2 28.9 - - + -
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 3.2 37.1 + - - +
219A LEU* 1.3 78.4 - - - +
221A GLY* 1.3 58.7 + - - +
277A LEU* 3.3 13.9 - - - +
278A SER* 5.7 0.2 - - - -
459A ASN 3.3 2.9 - - - +
460A VAL* 3.3 2.4 - - - -
461A SER* 2.9 44.4 + - - +
463A SER* 3.9 18.6 + - - -
465A THR* 5.9 1.0 - - - +
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Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 1.3 78.1 - - - +
222A ASP* 1.3 61.4 + - - +
276A SER* 3.3 4.9 - - - -
277A LEU* 2.9 37.8 + - - +
458A ASN 3.3 13.5 - - - -
459A ASN* 3.4 7.9 - - - -
460A VAL* 4.1 3.4 - - - -
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Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLY* 1.3 75.6 - - - +
223A THR* 1.3 69.2 + - - +
274A THR* 4.6 13.7 - - - +
275A THR 2.9 13.5 - - - +
276A SER* 4.8 0.9 - - - -
277A LEU* 3.6 4.2 - - - +
457A PHE* 3.8 2.8 - - - -
458A ASN* 2.9 53.5 + - - +
459A ASN* 2.5 30.1 - - - +
460A VAL* 5.2 0.6 - - - +
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASP* 1.3 79.5 - - - +
224A ALA* 1.3 63.5 + - - +
225A THR* 5.7 0.7 - - - +
274A THR* 3.1 6.9 - - - -
275A THR* 2.5 57.5 + - + +
277A LEU* 4.3 12.1 - - + -
409A GLN* 2.8 48.8 - - - +
410A PHE* 4.5 4.7 - - + -
456A GLY 3.2 14.3 + - - -
457A PHE* 4.6 7.9 - - - -
458A ASN* 5.3 1.8 - - - +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR* 1.3 84.5 + - - +
225A THR* 1.3 64.2 + - - +
226A ASN 4.3 0.4 - - - -
272A SER* 4.5 10.1 - - - +
273A THR 3.3 12.3 - - - +
274A THR* 4.1 9.6 - - + +
275A THR* 4.5 0.7 - - - +
407A GLU 4.1 0.5 - - - +
408A SER* 3.5 2.4 - - - -
409A GLN* 3.4 25.6 + - - +
456A GLY 4.7 1.8 + - - -
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR* 5.7 0.3 - - - +
224A ALA* 1.3 74.6 + - - +
226A ASN* 1.3 64.6 + - - +
227A TRP* 3.7 4.9 + - + -
255A LEU* 4.1 15.5 - - + -
256A SER* 4.5 11.8 + - - +
257A ILE* 4.7 13.9 - - + -
271A GLY 3.6 1.9 - - - +
272A SER* 3.3 4.5 - - - -
273A THR* 2.9 41.7 + - - -
275A THR* 4.3 11.6 + - - -
406A ALA* 4.5 5.8 - - + -
407A GLU 3.1 15.5 - - - +
408A SER* 3.3 21.7 - - - -
409A GLN 5.3 0.7 + - - -
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 4.3 0.6 - - - +
225A THR* 1.3 71.8 - - - +
227A TRP* 1.3 63.7 + - - +
271A GLY* 3.4 16.9 - - - +
272A SER* 3.9 14.5 - - - +
405A SER 4.2 0.2 - - - +
406A ALA* 3.4 1.6 - - - -
407A GLU* 2.8 51.9 + - + +
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Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A THR* 4.3 8.7 - - + -
226A ASN* 1.3 81.6 - - - +
228A SER* 1.3 79.5 + - - +
229A LYS* 3.8 29.2 - - + -
247A TRP* 4.9 4.0 - + - -
257A ILE* 3.7 47.7 - - + +
258A GLU 5.6 3.8 - - - -
259A ILE* 5.2 9.0 - - + -
268A GLN* 3.3 26.5 - - + -
270A GLY* 3.6 23.1 + - - -
271A GLY 2.9 51.4 + - - +
273A THR* 4.3 16.2 - - + +
404A PHE* 3.5 20.6 - + + -
405A SER 3.2 10.3 - - - +
406A ALA* 3.9 7.0 - - + -
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A TRP* 1.3 84.5 - - - +
229A LYS* 1.3 68.1 + - - +
230A THR* 5.5 3.6 - - - +
269A ASN 3.7 11.0 + - - -
270A GLY* 3.9 2.9 - - - -
404A PHE* 3.5 3.5 - - - -
405A SER* 2.8 41.4 + - - +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A TRP* 3.8 18.2 - - + -
228A SER* 1.3 77.9 + - - +
230A THR* 1.3 61.2 + - - +
231A ASN* 3.0 11.3 - - - +
247A TRP* 4.3 8.1 - - + -
259A ILE* 5.7 1.6 - - - -
265A TRP* 2.7 57.5 + - + +
268A GLN* 3.5 15.0 + - - -
269A ASN* 2.9 50.2 + - - +
306A TYR* 3.7 23.1 - - + +
403A ASP 2.9 13.2 - - - +
404A PHE* 4.2 7.2 - - + -
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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