Contacts of the strand formed by residues 330 - 346 (chain D) in PDB entry 4XLN
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 330 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D ARG* 3.2 37.6 + - - -
226D PRO* 3.9 15.3 - - - -
249D TYR* 5.3 4.3 - - - -
326D GLU* 4.0 1.2 - - - +
327D GLU* 4.1 5.2 + - - +
328D GLY* 3.1 18.2 + - - +
329D ASP* 1.3 82.5 - - - +
331D VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 331 (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 4.0 0.7 - - - +
224D ARG* 3.4 3.9 - - - -
225D ILE* 2.9 52.9 + - + +
226D PRO 4.4 0.2 - - - -
227D LEU* 3.9 17.5 - - + -
230D TRP* 3.5 34.1 - - + -
324D ALA* 4.8 1.8 - - + -
325D GLU 3.3 17.7 - - - +
326D GLU* 3.6 22.9 - - + -
330D SER* 1.3 74.7 - - - +
332D HIS* 1.3 62.8 + - - +
333D LEU* 3.6 22.5 + - + +
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Residues in contact with HIS 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ALA* 3.3 32.8 - - + +
223D LEU 4.0 7.2 + - - -
224D ARG* 3.4 35.3 + - - +
254D GLU* 4.6 14.6 + - - -
282D TYR* 6.1 0.4 - + - -
323D GLU 3.7 1.0 - - - +
325D GLU* 2.9 67.6 + - + +
327D GLU* 4.7 0.4 - - - +
331D VAL* 1.3 72.3 - - - +
333D LEU* 1.3 68.8 + - - +
334D THR* 3.6 23.2 + - + +
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Residues in contact with LEU 333 (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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221D ALA 3.9 1.2 - - - +
222D ALA* 3.4 0.9 - - - -
223D LEU* 2.9 46.6 + - + +
230D TRP* 3.4 42.2 - - + +
236D TYR* 6.4 1.1 - - + -
322D VAL* 3.6 26.7 - - + -
323D GLU 3.2 13.9 - - - +
324D ALA* 3.9 5.6 - - - -
331D VAL* 3.6 18.6 - - + +
332D HIS* 1.3 88.0 + - - +
334D THR* 1.3 60.8 + - - +
335D LEU* 4.1 20.9 - - + +
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Residues in contact with THR 334 (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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220D ARG* 5.2 11.2 - - + +
221D ALA 3.7 8.3 - - - +
222D ALA* 4.0 20.6 - - + -
321D GLU 3.6 0.7 - - - +
323D GLU* 2.9 57.1 + - - +
325D GLU* 6.0 0.5 - - - +
332D HIS* 3.6 17.7 + - + +
333D LEU* 1.3 73.4 - - - +
335D LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ARG* 3.4 9.8 - - - +
221D ALA 2.9 36.7 + - - +
223D LEU* 5.5 3.1 - - + -
234D GLU 5.9 0.4 - - - +
236D TYR* 5.7 11.7 - - + -
242D LEU* 6.2 1.6 - - + -
283D PHE* 4.1 26.9 - - + -
313D LEU* 5.4 2.7 - - + -
319D ALA* 5.0 8.3 - - + -
320D LYS 4.6 2.7 - - - +
321D GLU 3.9 3.8 - - - -
322D VAL* 4.5 12.1 - - + -
333D LEU* 4.1 27.1 - - + +
334D THR* 1.3 84.4 - - - +
336D PHE* 1.3 60.5 + - - +
337D LEU* 3.7 30.2 + - + -
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Residues in contact with PHE 336 (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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218D LYS* 4.5 26.7 - - + -
219D GLU 3.8 8.5 - - - -
220D ARG* 4.2 32.5 - - + -
319D ALA* 3.9 0.2 - - - -
320D LYS* 2.9 49.0 + - + +
321D GLU* 3.5 30.7 + - + +
335D LEU* 1.3 70.3 - - - +
337D LEU* 1.3 61.6 + - - +
338D GLU* 3.7 27.8 + - + +
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Residues in contact with LEU 337 (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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217D ARG 3.5 2.4 - - - +
218D LYS* 3.6 0.7 - - - -
219D GLU* 2.9 46.4 + - + +
221D ALA* 3.7 14.4 - - + -
269D LEU* 5.3 1.8 - - + -
283D PHE* 3.5 44.4 - - + -
313D LEU* 4.6 6.7 - - + -
317D MET* 3.6 20.4 - - + -
318D THR 3.7 6.1 - - - +
319D ALA* 3.6 28.5 - - + -
335D LEU* 3.7 28.9 - - + +
336D PHE* 1.3 71.9 - - - +
338D GLU* 1.3 60.4 + - - +
339D TRP* 4.1 3.4 - - - -
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Residues in contact with GLU 338 (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 LEU* 5.3 0.7 - - - +
217D ARG 3.1 3.6 - - - -
218D LYS* 3.1 39.1 + - + +
317D MET* 4.9 0.2 - - - -
318D THR* 2.9 49.9 + - - +
320D LYS* 3.2 40.1 + - + +
336D PHE* 3.7 27.1 - - + +
337D LEU* 1.3 74.7 - - - +
339D TRP* 1.3 61.0 + - - +
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Residues in contact with TRP 339 (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 LEU* 3.4 7.8 - - - +
217D ARG* 2.9 71.5 + - + +
218D LYS* 4.9 1.2 + - - -
219D GLU* 4.3 16.2 - - + -
262D LYS* 4.7 11.0 - - - -
264D LEU* 3.5 29.9 - - + +
269D LEU* 4.3 11.9 - - + -
271D TYR* 5.6 0.2 - - - -
316D HIS* 3.7 20.6 + + - +
317D MET* 3.5 50.5 - - + +
318D THR* 4.5 1.8 - - - +
337D LEU 4.1 7.4 - - - -
338D GLU* 1.3 78.2 - - - +
340D THR* 1.3 89.4 + - - +
341D GLU* 2.9 34.6 + - + +
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Residues in contact with THR 340 (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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214D ASP* 4.6 18.2 - - + -
215D TYR 3.2 7.6 - - - +
216D LEU* 4.6 15.9 - - + -
316D HIS* 3.6 24.9 + - - +
339D TRP* 1.3 91.4 - - - +
341D GLU* 1.3 61.1 + - - +
342D PRO* 3.9 5.9 - - - +
384D VAL* 6.5 0.2 - - + -
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Residues in contact with GLU 341 (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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214D ASP* 4.6 1.1 - - - -
215D TYR* 2.9 38.7 + - + +
217D ARG* 3.3 34.0 + - + +
262D LYS* 4.8 11.9 + - - -
264D LEU* 5.2 2.1 - - - +
316D HIS* 5.6 3.8 - - + +
339D TRP* 2.9 40.7 + - + +
340D THR* 1.3 71.7 - - - +
342D PRO* 1.3 73.2 - - + +
343D LYS 4.0 0.2 + - - -
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Residues in contact with PRO 342 (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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212D ARG* 5.2 15.0 - - - +
213D VAL 3.6 7.0 - - - +
214D ASP* 4.4 8.3 - - - +
215D TYR* 5.7 0.2 - - - -
316D HIS* 5.7 4.0 - - + -
340D THR 3.9 7.0 - - - +
341D GLU* 1.3 95.2 - - + +
343D LYS* 1.3 70.6 + - - +
344D ASP* 6.1 0.4 - - - +
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Residues in contact with LYS 343 (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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212D ARG* 3.2 6.2 - - - +
213D VAL* 2.9 49.4 + - + -
215D TYR* 4.1 13.0 - - + -
342D PRO* 1.3 81.3 + - - +
344D ASP* 1.3 92.8 + - - +
345D TYR* 3.9 24.9 - - + +
380D GLU* 4.5 12.1 - - - +
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Residues in contact with ASP 344 (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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210D ARG* 3.8 24.7 + - + -
211D VAL 4.0 0.2 - - - -
212D ARG* 3.2 44.6 + - - +
342D PRO* 6.1 0.3 - - - +
343D LYS* 1.3 94.6 + - - +
345D TYR* 1.3 68.4 + - - +
346D LYS 4.3 0.7 + - - -
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Residues in contact with TYR 345 (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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210D ARG* 3.8 4.0 - - - +
211D VAL* 2.9 56.1 + - + +
212D ARG 4.7 0.2 - - - -
213D VAL* 3.6 30.3 - - + -
215D TYR* 2.3 39.1 + - - -
343D LYS* 3.9 15.3 - - + +
344D ASP* 1.3 79.1 - - - +
346D LYS* 1.3 62.1 + - - +
347D VAL* 3.6 2.0 + - + -
367D ILE* 5.5 4.5 - - + -
377D VAL* 3.9 40.8 - - + -
378D ILE 4.5 6.2 + - - -
380D GLU* 4.3 7.5 + - + +
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Residues in contact with LYS 346 (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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209D ARG 4.2 9.4 - - - +
210D ARG* 4.8 5.2 - - + +
344D ASP 4.2 0.8 + - - -
345D TYR* 1.3 71.1 - - - +
347D VAL* 1.3 72.0 + - - +
351D MET* 3.5 13.4 - - - +
377D VAL* 6.5 0.4 - - - -
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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