Contacts of the helix formed by residues 402 - 417 (chain D) in PDB entry 5UQ9
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 CYS 402 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D GLU* 5.1 7.0 - - - -
324D ARG* 5.9 0.7 - - - -
325D LYS* 3.5 52.1 - - + +
328D TYR* 4.3 18.8 - - - -
329D ALA* 4.1 10.1 - - + -
398D ALA* 3.2 19.3 + - - +
399D VAL 3.3 2.0 + - - +
400D GLU 3.1 0.8 - - - -
401D ASN* 1.3 79.5 - - - +
403D GLN* 1.3 58.4 + - - +
404D ASP* 3.6 1.6 - - - -
405D SER* 3.6 4.9 + - - -
406D TRP* 2.8 30.7 + - - +
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Residues in contact with GLN 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LYS* 2.8 41.1 + - - +
306C GLY 2.8 27.0 - - - +
307C PRO* 3.2 8.8 - - - +
308C GLN* 4.6 0.7 + - - +
399D VAL* 3.2 14.8 + - + +
400D GLU 3.4 11.2 + - - +
401D ASN 3.6 0.6 - - - -
402D CYS* 1.3 77.2 - - - +
404D ASP* 1.3 59.9 + - - +
406D TRP* 2.9 16.7 + - + +
407D ARG* 2.9 54.2 + - + +
430D TYR* 3.2 23.9 + - + -
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Residues in contact with ASP 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLN* 5.0 4.1 + - - +
400D GLU 5.4 2.6 - - - +
401D ASN 5.6 3.4 - - - +
402D CYS 5.3 0.2 - - - -
403D GLN* 1.3 78.8 + - - +
405D SER* 1.3 78.5 + - - +
407D ARG* 3.5 9.5 + - - +
408D ARG* 2.9 55.1 + - - +
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Residues in contact with SER 405 (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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322D ASP* 2.9 54.6 + - - +
325D LYS* 3.8 30.1 + - - +
401D ASN 5.3 0.7 + - - -
402D CYS* 3.6 3.9 + - - -
403D GLN 3.2 0.6 - - - -
404D ASP* 1.3 88.0 + - - +
406D TRP* 1.3 65.6 + - - +
408D ARG* 4.1 4.6 + - - -
409D ALA* 3.1 18.4 + - - +
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Residues in contact with TRP 406 (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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326D ALA* 3.5 29.6 - - + +
329D ALA* 3.5 22.2 - - + -
330D SER* 3.2 27.2 + - - -
333D ILE* 3.6 18.2 - - + -
399D VAL* 4.3 18.2 - - + -
402D CYS 2.8 20.2 + - - +
403D GLN* 2.9 14.3 + - + +
405D SER* 1.3 76.7 - - - +
407D ARG* 1.3 61.4 + - + +
409D ALA* 3.4 1.9 + - - +
410D VAL* 3.1 27.6 + - + +
423D PHE* 3.7 12.5 + - + +
426D ALA* 3.5 22.9 - - + -
427D LEU* 3.3 43.4 - - + +
430D TYR* 4.2 13.2 - + + -
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Residues in contact with ARG 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PRO* 3.7 33.5 - - - +
414C VAL* 2.9 42.0 + - + +
415C GLN* 3.8 17.0 + - - +
417C GLY* 3.5 2.2 - - - -
403D GLN* 2.9 49.2 + - - +
404D ASP* 4.1 6.3 - - - +
406D TRP* 1.3 73.7 - - - +
408D ARG* 1.3 60.4 + - - +
410D VAL* 4.3 0.2 - - - -
411D SER* 2.9 32.6 + - - -
427D LEU* 3.6 26.5 - - + +
430D TYR* 4.2 5.7 - - - -
431D ASP* 2.7 42.8 + - - -
434D ARG* 4.3 0.4 - - - +
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Residues in contact with ARG 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLN* 4.0 11.6 - - - +
318D SER* 5.1 7.3 + - - -
319D PHE* 4.5 6.7 - - + -
322D ASP* 2.8 34.6 + - - +
404D ASP* 2.9 48.8 + - - +
405D SER* 3.7 6.1 + - - +
406D TRP 3.3 0.2 - - - -
407D ARG* 1.3 77.9 - - - +
409D ALA* 1.3 60.9 + - - +
411D SER* 4.0 1.7 - - - -
412D THR* 2.8 36.3 + - - +
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Residues in contact with ALA 409 (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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204D LEU* 4.4 10.4 - - + +
319D PHE* 3.8 18.9 - - + -
322D ASP* 4.0 19.5 - - + +
323D ILE* 4.4 9.6 - - + +
326D ALA* 4.1 10.3 - - + -
405D SER 3.1 17.4 + - - +
406D TRP 3.9 3.4 - - - +
408D ARG* 1.3 73.4 - - - +
410D VAL* 1.3 64.1 + - + +
412D THR* 4.0 0.9 - - - -
413D GLY* 3.1 19.2 + - - -
420D MET* 3.9 7.2 - - - +
423D PHE* 5.7 1.1 - - + -
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Residues in contact with VAL 410 (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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414C VAL* 3.8 26.2 - - + -
406D TRP* 3.1 31.6 + - + +
407D ARG 3.8 3.6 - - - +
408D ARG 3.3 0.2 - - - -
409D ALA* 1.3 75.7 - - + +
411D SER* 1.3 59.8 + - - +
413D GLY 3.3 0.2 + - - -
414D VAL* 2.9 36.9 + - + +
420D MET* 3.3 9.0 - - + +
423D PHE* 4.3 23.3 - - + +
424D THR* 3.9 23.1 - - + -
427D LEU* 3.9 18.4 - - + -
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Residues in contact with SER 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C SER* 3.2 36.5 + - - +
414C VAL* 4.5 4.0 - - - +
415C GLN* 4.4 13.7 + - - +
407D ARG 2.9 17.5 + - - -
408D ARG* 4.1 2.7 - - - -
410D VAL* 1.3 77.8 - - - +
412D THR* 1.3 62.4 + - - +
414D VAL* 3.4 5.2 + - - +
415D GLN* 3.1 32.8 + - - +
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Residues in contact with THR 412 (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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208D VAL* 4.1 9.6 - - + -
310D PHE* 3.9 22.0 - - + -
312D PHE* 4.3 11.1 - - + -
319D PHE* 3.5 33.9 - - + -
408D ARG* 2.8 27.5 + - - +
409D ALA 4.0 0.2 - - - -
411D SER* 1.3 77.8 - - - +
413D GLY* 1.3 57.9 + - - +
415D GLN* 3.2 10.8 + - - +
416D ALA* 2.8 28.9 + - - +
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Residues in contact with GLY 413 (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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431C ASP* 5.1 0.2 - - - +
204D LEU* 4.2 12.9 - - - +
208D VAL* 5.2 0.2 - - - -
409D ALA 3.1 13.3 + - - -
410D VAL 3.7 2.2 - - - -
412D THR* 1.3 77.1 - - - +
414D VAL* 1.3 60.7 + - - +
416D ALA* 4.0 7.4 - - - -
417D GLY 3.1 3.3 + - - -
418D ILE* 3.0 30.8 + - - +
420D MET* 3.8 21.1 - - - -
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Residues in contact with VAL 414 (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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407C ARG* 2.5 51.3 + - + +
410C VAL* 3.7 23.1 - - + -
411C SER* 3.5 18.4 - - - +
427C LEU* 3.6 24.5 - - + -
431C ASP* 5.5 0.7 - - - -
410D VAL* 2.9 28.8 + - + +
411D SER* 3.6 6.7 - - - +
412D THR 3.2 0.2 - - - -
413D GLY* 1.3 76.8 - - - +
415D GLN* 1.3 61.3 + - - +
417D GLY 3.3 0.9 + - - -
418D ILE 5.2 0.9 - - - -
420D MET* 4.3 8.7 - - + -
424D THR* 4.9 5.6 - - + -
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Residues in contact with GLN 415 (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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407C ARG* 4.3 13.6 - - + +
408C ARG* 5.9 3.6 - - - +
411C SER* 3.5 23.7 + - - +
307D PRO* 3.5 19.3 - - - +
310D PHE* 3.5 25.2 - - + +
411D SER* 3.1 24.2 + - - +
412D THR* 3.9 6.7 - - - +
414D VAL* 1.3 76.6 - - + +
416D ALA* 1.3 59.9 + - - +
417D GLY 3.3 0.2 - - - -
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Residues in contact with ALA 416 (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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434C ARG* 4.6 1.2 + - - -
207D ASP 5.8 0.4 - - - +
208D VAL* 3.9 10.8 - - + -
307D PRO* 3.5 11.9 - - - +
310D PHE* 3.4 32.1 - - + +
412D THR 2.8 17.2 + - - +
413D GLY* 3.8 1.6 - - - +
414D VAL 3.2 0.6 - - - -
415D GLN* 1.3 76.7 - - - +
417D GLY* 1.3 61.2 + - - +
418D ILE* 3.7 26.6 - - + +
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Residues in contact with GLY 417 (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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407C ARG* 3.4 22.4 - - - +
431C ASP* 3.5 7.3 - - - +
434C ARG* 2.9 31.7 + - - -
435C HIS* 3.1 15.4 - - - -
307D PRO* 3.7 1.3 - - - +
413D GLY 3.1 3.4 + - - -
414D VAL 3.3 2.2 + - - -
415D GLN 3.3 3.8 + - - -
416D ALA* 1.3 80.7 - - - +
418D ILE* 1.3 61.3 + - - +
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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