Contacts of the helix formed by residues 394 - 405 (chain D) in PDB entry 2UZ1
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 ALA 394 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393D GLY* 1.3 75.6 - - - +
395D LEU* 1.3 70.0 + - - +
396D THR 3.1 1.9 + - - +
397D TYR* 3.1 12.9 + - + -
398D LEU* 3.0 30.4 + - + +
421D MET* 4.1 4.0 - - + -
480D ALA* 3.4 20.0 - - + -
1556D TPP 3.2 38.8 + - - +
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Residues in contact with LEU 395 (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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394D ALA* 1.3 72.3 - - - +
396D THR* 1.3 62.6 + - - +
398D LEU* 3.2 7.7 + - + +
399D TRP* 2.9 40.7 + - + +
475D ASN* 4.1 6.3 - - - +
479D GLY* 3.5 28.3 - - - -
480D ALA* 3.5 15.3 - - + +
483D HIS* 3.5 24.7 - - + +
546D LEU* 3.9 10.1 - - + +
548D PRO 5.0 1.3 - - - +
550D PRO* 3.7 15.5 - - + -
553D GLU* 3.5 35.9 - - - +
1556D TPP 2.9 15.3 + - - +
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Residues in contact with THR 396 (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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372D PRO* 6.4 0.4 - - - -
376D SER* 4.9 1.0 + - - -
392D ASP 3.6 17.9 - - - +
393D GLY* 4.3 2.5 - - - -
394D ALA 4.2 2.7 - - - -
395D LEU* 1.3 75.9 - - - +
397D TYR* 1.3 58.4 + - - +
399D TRP* 3.6 5.5 + - - +
400D LEU* 3.0 25.6 + - - +
445D VAL* 3.9 17.9 - - + +
446D THR 3.8 12.1 - - - +
447D GLY* 3.8 7.4 - - - -
473D MET* 3.4 40.7 + - + +
475D ASN* 5.4 0.2 + - - -
1556D TPP 2.8 21.8 + - - -
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Residues in contact with TYR 397 (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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112C LEU* 5.7 5.0 - - - +
239D TYR* 3.4 32.9 - + - -
282D LEU* 6.0 2.1 - - - +
391D ALA* 3.8 27.1 - - + -
392D ASP 3.8 5.1 + - - +
393D GLY 3.2 28.7 - - - -
394D ALA* 3.1 22.3 + - + -
396D THR* 1.3 77.2 - - - +
398D LEU* 1.3 79.7 + - + +
399D TRP 3.3 0.2 - - - -
400D LEU* 3.7 6.8 - - - +
401D SER* 2.8 32.3 + - - -
412D PHE* 5.8 1.4 - - + -
414D CYS* 3.4 17.3 - - - -
415D HIS* 3.6 24.0 - - + +
419D GLY* 6.1 0.3 - - - -
421D MET* 4.8 3.9 - - + +
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Residues in contact with LEU 398 (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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239D TYR* 4.2 8.3 - - - +
394D ALA* 3.0 25.4 + - + +
395D LEU* 3.6 9.2 - - + +
397D TYR* 1.3 106.4 - - + +
399D TRP* 1.3 59.1 + - - +
401D SER* 2.7 21.8 + - - +
402D GLU* 3.8 9.7 - - - +
480D ALA* 5.6 2.9 - - + -
550D PRO* 3.9 28.5 - - + +
552D GLU* 3.8 23.2 - - + +
553D GLU* 4.5 17.3 - - + +
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Residues in contact with TRP 399 (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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360D ILE* 3.9 19.1 - - + -
364D SER* 5.0 0.4 - - - -
371D HIS* 3.5 19.7 - + - -
372D PRO* 3.2 37.1 - - + +
373D PHE* 3.9 19.9 - + + -
376D SER* 3.7 17.3 + - - +
395D LEU* 2.9 35.9 + - + +
396D THR* 3.9 3.8 - - - +
398D LEU* 1.3 74.4 - - - +
400D LEU* 1.3 65.6 + - - +
402D GLU* 3.1 22.5 + - + +
403D VAL 4.1 1.6 + - - -
548D PRO* 3.5 24.2 + - + -
549D ILE 3.5 11.2 - - - -
550D PRO* 3.3 44.0 - - + +
551D PRO* 3.8 17.0 - - + -
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Residues in contact with LEU 400 (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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376D SER* 3.6 18.6 + - - +
379D ILE* 4.4 25.6 - - + -
389D VAL* 4.0 12.3 - - + -
391D ALA* 3.8 28.3 - - + -
396D THR 3.0 18.3 + - - +
397D TYR* 3.3 5.6 + - - +
399D TRP* 1.3 75.3 - - - +
401D SER* 1.3 64.0 + - - +
403D VAL* 3.0 37.6 + - + +
404D MET* 3.3 20.1 - - + +
412D PHE* 4.3 5.6 - - + -
445D VAL* 3.9 26.2 - - + -
473D MET* 6.0 0.2 - - + -
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Residues in contact with SER 401 (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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239D TYR* 4.3 12.5 + - - -
256D LEU* 3.6 26.6 - - - +
258D GLN* 3.1 27.0 + - - +
397D TYR 2.8 16.2 + - - -
398D LEU* 2.7 23.2 + - - +
400D LEU* 1.3 77.7 - - - +
402D GLU* 1.3 63.3 + - - +
404D MET* 3.2 18.2 + - - -
405D SER* 4.1 4.2 + - - -
412D PHE* 5.3 4.5 - - - -
552D GLU* 4.6 3.1 - - - +
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Residues in contact with GLU 402 (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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258D GLN* 3.8 8.4 - - - +
259D ASN* 4.9 1.4 + - - -
356D ARG* 2.8 49.4 + - - -
357D TYR* 3.7 19.2 - - - +
360D ILE* 3.2 26.2 - - + +
373D PHE* 4.1 12.1 - - + -
398D LEU 3.8 9.0 - - - +
399D TRP* 3.1 19.0 + - + +
400D LEU 3.0 1.2 - - - -
401D SER* 1.3 78.4 + - - +
403D VAL* 1.3 58.2 + - - +
404D MET 3.5 0.2 - - - -
405D SER* 4.9 4.1 + - - -
406D ARG* 5.3 1.2 - - - +
551D PRO* 3.5 21.7 - - + +
552D GLU* 4.2 7.3 + - - +
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Residues in contact with VAL 403 (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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357D TYR* 4.3 11.2 - - + +
373D PHE* 3.8 22.4 - - + -
376D SER* 3.7 38.6 - - - +
377D GLN* 4.0 17.9 - - + +
380D ALA* 3.8 16.6 - - + +
399D TRP 4.8 0.2 - - - +
400D LEU* 3.0 25.7 + - + +
402D GLU* 1.3 79.5 - - - +
404D MET* 1.3 67.3 + - - +
405D SER 3.4 2.1 + - - -
406D ARG* 3.9 13.3 - - + +
407D VAL* 3.6 15.6 - - - +
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Residues in contact with MET 404 (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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242D LEU* 3.9 23.4 - - + +
256D LEU* 4.4 3.6 - - + -
379D ILE* 6.2 0.2 - - - -
380D ALA* 6.0 0.2 - - - -
383D VAL* 4.3 10.1 - - + -
389D VAL* 4.4 11.9 - - + -
400D LEU* 3.3 33.2 - - + +
401D SER* 3.2 14.1 + - - +
403D VAL* 1.3 81.6 - - - +
405D SER* 1.3 63.6 + - - +
406D ARG 3.4 0.2 - - - -
407D VAL* 3.3 32.3 - - + +
409D PRO* 3.7 33.7 - - + +
412D PHE* 3.7 40.4 - - + -
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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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242D LEU* 4.8 4.3 - - - -
253D ARG* 2.9 29.3 + - - +
254D GLY 4.9 0.4 - - - -
255D GLY* 3.9 16.3 - - - -
256D LEU* 2.8 35.2 + - - +
259D ASN* 3.5 16.3 + - - -
353D ALA* 6.0 3.8 - - - -
401D SER 4.1 3.5 + - - -
402D GLU 4.9 3.3 + - - -
403D VAL 3.4 0.8 - - - -
404D MET* 1.3 79.3 - - - +
406D ARG* 1.3 57.3 + - - +
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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