Contacts of the helix formed by residues 371 - 381 (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 HIS 371 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363D LYS 5.0 1.8 - - - -
364D SER* 3.2 28.8 + - - -
365D SER 3.5 24.5 + - - +
366D SER* 2.8 18.9 + - - +
369D ALA 3.2 2.5 + - - -
370D LEU* 1.3 74.0 - - - +
372D PRO* 1.4 74.2 - - + +
373D PHE* 2.8 38.1 - - + +
374D HIS* 3.0 12.2 + - + +
375D ALA* 2.9 21.0 + - - +
399D TRP* 3.5 21.5 - + - -
544D VAL* 4.1 0.9 - - - -
545D ALA* 4.8 2.2 - - - -
548D PRO* 3.5 31.2 - - + +
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Residues in contact with PRO 372 (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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370D LEU 3.9 0.4 - - - +
371D HIS* 1.4 93.6 - - + +
373D PHE* 1.3 56.8 + - - +
375D ALA* 3.7 5.8 - - + +
376D SER* 2.8 33.7 + - - -
396D THR* 6.4 0.7 - - - -
399D TRP* 3.2 41.5 - - + +
473D MET* 5.4 1.9 - - + +
544D VAL* 3.3 28.9 - - + -
545D ALA* 3.6 13.7 - - + +
548D PRO* 4.0 12.8 - - + +
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Residues in contact with PHE 373 (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* 3.8 35.9 - + - -
360D ILE* 3.5 23.6 - - + -
361D ALA* 3.7 20.9 - - + -
364D SER* 3.5 20.9 - - - +
371D HIS* 2.8 25.5 + - + +
372D PRO* 1.3 73.1 - - - +
374D HIS* 1.3 59.5 + - - +
376D SER* 3.3 6.0 + - - -
377D GLN* 3.0 56.6 + - + +
399D TRP* 3.9 15.4 - + + -
402D GLU* 4.1 18.6 - - + -
403D VAL* 3.8 20.4 - - + -
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Residues in contact with HIS 374 (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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361D ALA* 4.7 5.8 - - + -
364D SER* 3.2 38.3 + - - -
365D SER* 4.0 0.4 - - - -
366D SER* 2.7 38.8 + - - +
370D LEU* 3.9 8.3 - - + -
371D HIS* 3.0 16.6 + - + +
373D PHE* 1.3 81.4 - + - +
375D ALA* 1.3 63.0 + - - +
377D GLN* 3.2 24.6 + - - +
378D VAL* 3.1 26.7 + - - +
521D VAL* 4.0 11.6 - - + +
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Residues in contact with ALA 375 (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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370D LEU* 3.9 22.3 - - + +
371D HIS 2.9 12.9 + - - +
372D PRO 3.7 7.6 - - - +
374D HIS* 1.3 76.5 - - - +
376D SER* 1.3 62.1 + - - +
378D VAL* 3.3 8.2 + - - -
379D ILE* 3.4 5.7 + - - +
473D MET* 3.7 27.8 - - + -
524D PHE* 3.2 31.4 - - + -
544D VAL* 4.1 5.2 - - + -
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Residues in contact with SER 376 (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 2.8 21.1 + - - -
373D PHE* 3.4 7.0 - - - -
375D ALA* 1.3 77.0 - - - +
377D GLN* 1.3 57.3 + - - +
379D ILE* 3.1 10.4 + - - +
380D ALA* 2.9 26.2 + - - +
396D THR 4.9 1.0 + - - -
399D TRP* 3.7 7.4 - - - +
400D LEU* 3.6 34.2 + - - +
403D VAL* 3.7 26.7 - - - +
473D MET* 4.5 4.8 - - - +
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Residues in contact with GLN 377 (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* 2.9 31.6 + - - +
361D ALA* 4.9 4.0 - - - +
373D PHE* 3.0 38.4 + - + +
374D HIS* 3.2 35.0 + - - +
376D SER* 1.3 72.3 - - - +
378D VAL* 1.3 66.1 + - + +
380D ALA* 3.2 9.5 + - - +
381D LYS* 3.2 23.6 + - - +
403D VAL* 4.0 7.9 - - + -
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Residues in contact with VAL 378 (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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374D HIS 3.1 15.8 + - - +
375D ALA* 3.4 8.5 - - - +
376D SER 3.2 0.2 - - - -
377D GLN* 1.3 76.5 - - + +
379D ILE* 1.3 59.0 + - - +
381D LYS* 3.0 40.1 - - - +
382D HIS* 3.3 6.4 - - - -
521D VAL* 4.0 33.9 - - + +
524D PHE* 3.6 28.9 - - + -
525D SER* 3.8 24.5 - - - +
528D LEU* 4.1 9.2 - - + -
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Residues in contact with ILE 379 (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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375D ALA 3.4 5.1 + - - +
376D SER* 3.1 7.0 + - - +
378D VAL* 1.3 76.9 - - - +
380D ALA* 1.3 66.1 + - - +
382D HIS* 2.9 18.5 + - - +
383D VAL* 3.5 19.1 - - + +
389D VAL* 5.1 4.5 - - + -
400D LEU* 4.4 15.5 - - + -
404D MET* 6.2 0.4 - - - -
443D ILE* 4.9 11.0 - - + -
445D VAL* 3.9 28.0 - - + -
471D ILE* 3.8 23.1 - - + -
473D MET* 3.4 31.6 - - + -
524D PHE* 3.7 17.7 - - + -
528D LEU* 3.9 8.5 - - + -
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Residues in contact with ALA 380 (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 2.9 14.4 + - - +
377D GLN* 3.2 11.4 + - - +
379D ILE* 1.3 76.5 - - - +
381D LYS* 1.3 63.0 + - - +
382D HIS 2.9 1.4 + - - -
383D VAL* 3.0 22.1 + - - +
403D VAL* 3.8 28.0 - - + +
404D MET* 6.0 0.7 - - - -
406D ARG* 6.5 0.2 - - + -
407D VAL* 3.4 28.8 - - + +
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Residues in contact with LYS 381 (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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377D GLN 3.2 8.4 + - - +
378D VAL* 3.0 42.4 - - - +
380D ALA* 1.3 77.2 - - - +
382D HIS* 1.3 79.6 + - + +
383D VAL 3.5 1.0 + - - +
521D VAL* 5.9 1.6 - - - +
525D SER* 2.7 34.4 + - - -
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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