Contacts of the helix formed by residues 400 - 415 (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 VAL 400 (chain X).
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Specific contacts
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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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Residues in contact with ILE 401 (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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323X VAL* 4.0 34.3 - - + -
324X ASN 4.3 11.7 - - - +
325X LYS 5.1 5.6 - - - +
327X GLU* 4.5 7.9 - - + +
396X GLY* 2.8 25.1 + - - +
397X ASP* 4.0 18.8 - - - +
400X VAL* 1.3 70.3 - - - +
402X CYS* 1.3 66.4 + - - +
404X LEU* 3.1 2.3 + - - +
405X MET* 2.9 36.1 + - + +
422X PHE* 5.0 4.0 - - + -
516X LEU* 4.6 14.6 - - + -
517X ARG* 4.2 19.5 - - + -
521X CYS* 4.1 9.2 - - - -
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Residues in contact with CYS 402 (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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397X ASP* 2.8 33.6 + - - +
401X ILE* 1.3 72.9 - - - +
403X PRO* 1.4 66.1 - - + +
405X MET* 3.4 0.6 + - - -
406X HIS 3.0 18.4 + - - -
520X MET 4.0 0.4 - - - -
521X CYS* 2.0 60.6 - - + -
524X TRP* 3.7 28.0 - - + -
525X ASN* 3.1 19.1 + - - +
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Residues in contact with PRO 403 (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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228X SER* 3.4 3.3 + - - +
230X ASN* 3.0 33.8 + - - +
231X CYS* 3.9 22.2 - - - -
232X PRO* 3.7 16.6 - - + -
397X ASP 3.3 3.8 - - - +
398X HIS 3.2 28.3 - - - +
399X ASN 3.8 7.4 - - - +
400X VAL 3.5 9.2 - - - +
402X CYS* 1.4 91.2 - - + +
404X LEU* 1.3 61.3 + - - +
406X HIS* 3.3 2.5 + - + -
407X PHE 3.1 10.2 + - - -
525X ASN* 4.5 3.6 - - - +
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Residues in contact with LEU 404 (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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224X LEU 4.5 0.9 - - - +
227X GLY 4.1 24.2 - - - +
228X SER* 3.6 16.1 + - - -
321X LEU* 3.9 26.2 - - + -
322X GLY 3.6 30.7 - - - +
323X VAL* 3.8 15.5 - - + -
400X VAL 3.1 18.6 + - - +
401X ILE 3.1 2.2 + - - +
403X PRO* 1.3 76.9 - - - +
405X MET* 1.3 64.0 + - + +
407X PHE* 2.9 5.2 + - - +
408X VAL* 2.7 36.4 + - + +
420X LEU* 4.2 20.4 - - + -
516X LEU* 6.0 0.2 - - + -
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Residues in contact with MET 405 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401X ILE* 2.9 29.8 + - + +
402X CYS* 3.8 5.4 - - - +
404X LEU* 1.3 78.4 - - + +
406X HIS* 1.3 66.0 - - - +
408X VAL* 3.1 14.3 - - + +
409X ASN* 2.9 48.4 + - - +
420X LEU* 3.9 28.5 - - + -
495X PHE* 4.4 8.7 - - + -
500X GLN* 5.7 2.7 - - + +
515X ARG* 5.7 0.9 - - - -
516X LEU* 3.9 42.0 - - + +
521X CYS* 4.5 9.9 - - + -
525X ASN* 4.8 0.9 - - - +
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Residues in contact with HIS 406 (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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230X ASN* 3.9 16.6 - - + +
306X GLU* 2.9 33.6 + - - -
309X LEU* 4.8 5.6 - - + -
402X CYS 3.0 14.8 + - - +
403X PRO* 3.6 8.7 - - + +
405X MET* 1.3 78.1 - - - +
407X PHE* 1.3 63.2 + - - +
409X ASN* 3.6 4.6 - - - +
410X LYS* 2.9 58.2 + - + +
525X ASN* 3.8 32.4 + - + +
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Residues in contact with PHE 407 (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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207X GLY* 4.7 4.3 - - - -
210X ILE* 4.5 21.1 - - + -
211X LEU* 5.3 1.8 - - + -
224X LEU* 4.1 17.3 - - + -
228X SER* 3.7 10.3 - - - +
229X PRO* 3.5 33.4 - - + -
230X ASN* 3.6 20.4 - - - +
309X LEU* 3.9 33.0 - - + -
319X ILE* 4.1 21.3 - - + -
321X LEU* 4.0 14.4 - - + -
403X PRO 3.1 6.0 + - - +
404X LEU 2.9 7.4 + - - +
406X HIS* 1.3 75.0 - - - +
408X VAL* 1.3 55.3 + - - +
410X LYS* 3.3 2.4 + - - +
411X TYR* 2.7 57.3 + + + +
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Residues in contact with VAL 408 (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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319X ILE* 5.3 0.9 - - + -
321X LEU* 4.4 15.3 - - + -
404X LEU* 2.7 24.5 + - + +
405X MET* 3.1 40.4 - - + +
407X PHE* 1.3 74.9 - - - +
409X ASN* 1.3 67.0 + - - +
411X TYR* 4.3 3.6 - - - +
412X THR* 2.9 24.3 + - - +
418X THR* 3.7 24.0 - - + -
420X LEU* 5.0 4.7 - - + -
495X PHE* 3.4 28.7 - - + -
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Residues in contact with ASN 409 (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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405X MET* 2.9 45.6 + - - +
406X HIS* 3.8 4.9 - - - +
408X VAL* 1.3 81.3 - - - +
410X LYS* 1.3 65.9 + - + +
412X THR 3.6 4.7 + - - -
413X LYS* 3.6 4.7 + - - +
495X PHE* 3.7 17.1 - - - -
497X THR* 3.6 33.0 - - + +
500X GLN* 4.1 18.3 + - - -
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Residues in contact with LYS 410 (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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306X GLU* 4.1 4.4 + - - -
309X LEU* 4.1 33.1 - - + +
310X ASN* 2.2 35.4 + - - +
314X PHE* 4.0 9.6 - - - -
406X HIS* 2.9 50.8 + - + +
407X PHE 3.8 2.9 - - - +
409X ASN* 1.3 76.7 - - + +
411X TYR* 1.3 67.1 + - - +
413X LYS* 3.5 16.2 + - + +
414X PHE* 4.0 5.4 - - - -
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Residues in contact with TYR 411 (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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210X ILE* 4.1 14.3 - - + +
309X LEU* 5.3 1.1 - - - +
314X PHE* 3.3 36.7 - + - -
315X LYS 2.7 23.6 + - - -
317X THR* 2.7 44.2 + - - +
319X ILE* 3.4 43.1 - - + -
407X PHE* 2.7 40.7 + + + +
408X VAL* 3.9 3.4 - - - +
410X LYS* 1.3 73.7 - - - +
412X THR* 1.3 62.1 + - - +
414X PHE 3.0 5.5 + - - -
415X GLY* 2.9 37.8 + - - -
416X ASN 4.5 0.2 - - - -
417X GLY 5.0 0.4 - - - -
418X THR* 4.2 6.5 - - - -
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Residues in contact with THR 412 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408X VAL* 2.9 17.6 + - - +
409X ASN 4.0 3.4 - - - -
411X TYR* 1.3 74.2 - - - +
413X LYS* 1.3 67.6 + - - +
414X PHE 3.0 1.2 + - - -
415X GLY* 3.5 12.8 + - - +
418X THR* 2.8 30.1 + - - +
495X PHE* 3.5 23.4 - - + +
496X THR* 4.2 2.0 - - - -
497X THR* 3.8 35.5 + - + +
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Residues in contact with LYS 413 (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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409X ASN 3.6 8.9 + - - +
410X LYS* 3.5 13.1 + - - +
411X TYR 3.2 1.4 + - - -
412X THR* 1.3 78.2 - - - +
414X PHE* 1.3 79.6 + - + +
497X THR* 4.4 13.3 - - + +
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Residues in contact with PHE 414 (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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309X LEU 4.2 5.4 - - - -
310X ASN 3.9 14.4 - - - -
311X SER 3.9 5.2 - - - -
312X GLY* 3.6 38.4 - - - -
314X PHE* 3.9 16.8 - + + -
316X LYS* 3.3 35.8 - - - +
410X LYS 4.0 5.2 - - - -
411X TYR 3.0 3.8 + - - -
413X LYS* 1.3 96.6 - - + +
415X GLY* 1.3 68.5 + - - +
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Residues in contact with GLY 415 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A NAG 4.2 5.7 - - - +
316X LYS* 4.6 5.6 - - - -
317X THR 4.1 0.9 - - - -
411X TYR* 2.9 38.5 + - - -
412X THR* 3.5 9.2 + - - +
414X PHE* 1.3 84.1 - - - +
416X ASN* 1.3 61.2 + - - -
417X GLY 3.5 3.4 + - - -
418X THR* 5.9 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