Contacts of the helix formed by residues 383 - 400 (chain X) in PDB entry 2W6C
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 383 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380X ASP* 3.3 38.4 + - - +
381X ASP 3.5 0.8 - - - -
382X ASN* 1.3 76.0 - - - +
384X GLY* 1.3 55.3 - - - +
385X ILE* 2.8 32.4 - - - +
386X LYS* 3.0 28.8 - - + +
387X ASN* 2.9 32.2 + - - +
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Residues in contact with GLY 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346X LYS* 3.8 15.6 - - - +
347X ILE 3.3 33.8 + - - -
382X ASN 3.4 6.3 + - - -
383X ASN* 1.3 71.5 - - - +
385X ILE* 1.3 57.8 + - - -
388X ARG* 3.0 29.8 + - - +
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Residues in contact with ILE 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344X GLU* 5.4 5.2 - - - -
346X LYS* 3.9 32.5 - - + +
383X ASN* 2.8 17.9 - - - +
384X GLY* 1.3 70.8 - - - -
386X LYS* 1.3 62.1 + - + +
388X ARG* 3.6 26.0 - - - +
389X ASP* 2.8 51.6 + - - +
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Residues in contact with LYS 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X TYR 5.3 1.9 - - - +
377X ASP* 2.9 40.4 + - + +
380X ASP* 3.4 23.6 + - - +
383X ASN* 3.0 29.1 - - + +
385X ILE* 1.3 83.5 - - + +
387X ASN* 1.3 58.7 + - - +
389X ASP* 3.8 3.6 - - - +
390X GLY* 2.8 27.4 + - - -
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Residues in contact with ASN 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347X ILE* 2.8 34.4 + - + +
348X SER 3.7 1.2 + - - -
349X ARG* 3.2 43.1 + - - +
352X PHE* 3.5 20.7 - - + +
380X ASP 5.1 0.5 - - - +
381X ASP* 3.6 17.7 + - - +
382X ASN* 5.0 2.2 - - - +
383X ASN 2.9 20.4 + - - +
384X GLY 3.8 1.1 - - - +
386X LYS* 1.3 77.7 - - - +
388X ARG* 1.3 63.8 + - - +
390X GLY 3.3 0.5 + - - -
391X LEU* 3.0 25.8 + - - +
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Residues in contact with ARG 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339X PHE* 3.6 19.6 - - + -
344X GLU* 2.7 36.5 + - - +
345X SER* 3.1 25.3 + - - +
346X LYS* 5.1 0.4 - - - +
347X ILE* 4.0 10.3 - - + +
384X GLY 3.0 19.3 + - - +
385X ILE* 3.6 38.1 - - - +
387X ASN* 1.3 76.7 - - - +
389X ASP* 1.3 86.4 + - - +
391X LEU* 3.2 6.1 + - - +
392X ASP* 3.0 21.9 + - + +
435X TRP* 3.1 45.4 + - + +
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Residues in contact with ASP 389 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X ILE* 2.8 38.3 + - - +
386X LYS* 4.2 3.8 - - - +
388X ARG* 1.3 98.7 + - - +
390X GLY* 1.3 58.8 + - - +
392X ASP* 3.2 9.1 + - - +
393X ASP* 2.9 36.4 + - - +
435X TRP 4.7 4.9 - - - +
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Residues in contact with GLY 390 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352X PHE* 4.5 4.3 - - - -
375X TYR* 3.8 19.7 - - - -
386X LYS 2.8 21.2 + - - -
387X ASN 3.8 1.6 - - - -
389X ASP* 1.3 70.7 - - - +
391X LEU* 1.3 65.3 + - - +
393X ASP* 3.4 9.7 + - - +
394X ILE* 2.9 32.5 + - - +
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Residues in contact with LEU 391 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332X LEU* 3.7 19.7 - - + -
339X PHE* 4.0 22.9 - - + -
347X ILE* 4.1 7.4 - - + -
351X ASP 4.2 1.1 - - - +
352X PHE* 3.8 43.7 - - + +
355X GLY* 3.9 12.3 - - - -
356X VAL* 3.9 24.0 - - - +
359X SER* 4.7 5.4 - - - +
387X ASN 3.0 11.0 + - - +
388X ARG 3.5 4.9 - - - +
389X ASP 3.1 0.2 - - - -
390X GLY* 1.3 76.4 - - - +
392X ASP* 1.3 64.9 + - - +
394X ILE* 3.1 16.1 + - + +
395X VAL* 3.0 26.9 + - - +
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Residues in contact with ASP 392 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326X ASP* 4.0 20.3 - - - +
328X GLY* 3.4 8.3 + - - -
329X SER* 3.2 41.5 + - - -
332X LEU* 3.5 13.2 - - + +
339X PHE* 6.1 0.2 - - + -
388X ARG* 3.0 13.6 + - + +
389X ASP* 3.4 15.3 - - - +
391X LEU* 1.3 79.7 - - - +
393X ASP* 1.3 64.9 + - - +
395X VAL* 3.2 1.4 + - - -
396X GLY* 3.1 18.7 + - - -
435X TRP* 4.2 10.4 - - + +
436X MET 4.0 6.6 - - - +
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Residues in contact with ASP 393 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325X LYS* 4.9 7.4 + - - +
326X ASP* 4.8 9.0 - - - +
375X TYR* 3.8 17.6 - - + -
389X ASP* 2.9 23.6 + - - +
390X GLY* 3.7 6.5 - - - +
392X ASP* 1.3 80.2 - - - +
394X ILE* 1.3 56.3 + - - +
396X GLY* 4.6 1.1 - - - +
397X ASP* 2.8 39.4 + - - +
517X ARG* 3.9 24.3 + - - +
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Residues in contact with ILE 394 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352X PHE* 4.3 9.6 - - + -
356X VAL* 4.7 5.2 - - + -
359X SER* 4.0 25.1 - - - +
360X VAL* 4.7 1.6 - - + -
371X VAL* 3.4 24.2 - - + -
375X TYR* 3.4 40.6 - - + -
390X GLY 2.9 19.8 + - - +
391X LEU* 3.1 24.2 + - + +
393X ASP* 1.3 75.7 - - - +
395X VAL* 1.3 65.6 + - - +
398X HIS* 3.0 24.9 + - + +
524X TRP* 4.0 18.5 - - + -
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Residues in contact with VAL 395 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287X ILE* 4.4 6.1 - - + -
288X PHE* 4.0 15.7 - - + -
328X GLY* 3.7 26.7 - - - +
331X PHE* 4.4 8.5 - - + -
332X LEU* 3.9 19.3 - - + -
359X SER* 3.3 29.2 - - - +
391X LEU 3.0 16.2 + - - +
392X ASP 3.9 0.2 - - - +
394X ILE* 1.3 77.9 - - + +
396X GLY* 1.4 51.4 + - - +
399X ASN* 2.9 58.6 + - - +
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Residues in contact with GLY 396 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X PHE* 6.0 0.4 - - - -
327X GLU* 3.9 13.5 - - - -
328X GLY* 3.8 18.7 - - - -
392X ASP 3.1 12.0 + - - -
393X ASP* 4.0 1.1 - - - -
395X VAL* 1.4 75.4 - - - +
397X ASP* 1.3 62.2 + - - +
400X VAL* 3.0 10.2 + - - +
401X ILE* 2.8 31.8 + - - +
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Residues in contact with ASP 397 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X TYR* 2.3 33.4 + - - +
393X ASP* 2.8 28.0 + - - +
394X ILE 4.1 0.2 - - - +
396X GLY* 1.3 72.7 - - - +
398X HIS* 1.3 63.7 + - - +
401X ILE* 4.0 11.4 - - - +
402X CYS* 2.8 36.2 + - - +
403X PRO* 3.3 3.1 - - - +
517X ARG* 2.9 44.6 + - - -
520X MET* 3.6 6.5 - - - +
524X TRP* 3.6 11.2 - - + +
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Residues in contact with HIS 398 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X PRO* 3.8 18.1 - - + +
289X ARG* 3.0 22.6 + - - -
359X SER* 3.6 21.0 + - - -
360X VAL* 5.0 0.2 - - + -
362X HIS* 3.8 24.5 - + - -
394X ILE* 3.0 16.5 + - + +
395X VAL 4.2 0.4 - - - +
397X ASP* 1.3 80.2 - - - +
399X ASN* 1.3 74.5 + - - +
403X PRO* 3.2 20.7 - - - +
524X TRP* 3.4 48.5 - + + +
528X LEU* 5.9 0.4 - - + -
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Residues in contact with ASN 399 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X CYS* 3.4 12.0 - - - +
232X PRO* 3.7 6.5 - - - +
233X TRP* 3.0 31.2 + - + -
287X ILE 4.9 0.6 + - - -
288X PHE* 3.6 34.5 - - + +
289X ARG* 2.6 30.7 + - - +
359X SER* 4.6 5.7 + - - +
395X VAL* 2.9 43.7 + - - +
398X HIS* 1.3 88.0 - - - +
400X VAL* 1.3 60.1 + - - +
403X PRO* 3.8 3.4 - - - +
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Residues in contact with VAL 400 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X SER* 3.9 29.6 - - - +
227X GLY 4.6 0.6 + - - +
231X CYS* 4.6 4.9 - - - -
233X TRP* 4.8 2.5 - - + +
288X PHE* 3.8 28.3 - - + -
323X VAL* 4.1 7.6 - - + -
327X GLU* 3.6 44.2 - - + +
396X GLY* 3.0 8.9 + - - +
398X HIS 3.6 0.6 - - - -
399X ASN* 1.3 86.9 - - + +
401X ILE* 1.3 67.7 + - - +
403X PRO* 3.5 4.8 - - - +
404X LEU* 3.1 25.9 + - + +
440X HIS* 4.5 2.9 - - + -
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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
------------------------------------------------------------
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