Contacts of the helix formed by residues 373 - 382 (chain D) in PDB entry 5I94
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 SER 373 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D GLN* 4.8 0.2 - - - +
282D CYS* 3.8 4.3 - - - -
372D PHE* 1.3 73.1 - - - +
374D ASN* 1.3 62.8 + - - +
375D ALA* 3.7 6.8 + - - +
376D THR* 2.6 33.3 + - - -
377D PHE* 3.0 15.6 + - - +
418D SER* 3.0 23.1 + - - -
420D GLU* 3.4 26.2 + - - -
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Residues in contact with ASN 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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372D PHE* 3.5 27.1 + - + -
373D SER* 1.3 74.0 - - - +
375D ALA* 1.3 64.6 + - - +
377D PHE* 3.3 17.2 + - - +
378D GLN* 3.0 40.4 + - - +
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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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251D GLN* 3.3 27.2 + - + +
373D SER* 4.0 5.4 - - - +
374D ASN* 1.3 81.9 - - - +
376D THR* 1.3 61.1 + - - +
378D GLN* 3.6 5.1 + - - +
379D SER* 3.2 25.5 + - - -
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Residues in contact with THR 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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249D ILE* 3.8 19.0 - - + +
251D GLN* 3.3 23.6 - - + +
252D LEU* 5.8 1.7 - - + +
282D CYS* 3.6 20.1 - - - -
284D GLN* 3.9 17.3 - - - +
373D SER* 2.6 29.9 + - - -
375D ALA* 1.3 72.4 - - - +
377D PHE* 1.3 67.6 + - - +
379D SER* 3.4 0.9 + - - -
380D GLU* 2.9 26.3 + - - +
418D SER* 3.6 11.2 - - - +
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Residues in contact with PHE 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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372D PHE* 3.8 19.7 - + + -
373D SER 3.0 13.3 + - - +
374D ASN* 3.3 19.1 - - - +
376D THR* 1.3 77.2 - - - +
378D GLN* 1.3 79.1 + - - +
380D GLU* 3.2 2.0 + - - +
381D ARG* 3.1 55.0 + - - +
411D ASP* 3.6 23.6 - - - -
414D PHE* 3.7 20.2 - - + -
415D GLN* 3.3 39.7 - - + -
418D SER* 3.2 10.3 + - - +
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Residues in contact with GLN 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 ASN* 3.0 34.4 + - - +
375D ALA* 3.9 4.9 - - - +
376D THR 3.4 0.2 - - - -
377D PHE* 1.3 88.8 - - - +
379D SER* 1.3 62.6 + - - +
381D ARG* 3.2 52.3 + - - +
382D GLU* 3.2 27.8 + - - +
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Residues in contact with SER 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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249D ILE* 3.9 20.2 - - - +
250D PRO* 3.8 11.2 - - - +
251D GLN* 2.6 31.8 + - - -
375D ALA 3.2 10.3 + - - -
376D THR 3.9 3.6 - - - -
378D GLN* 1.3 78.9 - - - +
380D GLU* 1.3 63.1 + - - +
381D ARG 3.3 0.9 + - - -
382D GLU* 3.5 13.8 + - - +
383D SER* 3.2 24.6 + - - -
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Residues in contact with GLU 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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248D TYR* 2.9 40.3 + - - -
249D ILE* 4.0 11.6 - - - +
284D GLN* 3.8 22.1 + - - +
376D THR* 2.9 19.5 + - + +
377D PHE* 3.7 5.2 - - - +
379D SER* 1.3 76.8 - - - +
381D ARG* 1.3 57.5 + - - +
383D SER* 4.1 1.5 - - - -
384D GLY* 3.3 18.8 + - - -
387D ASN* 4.9 7.4 + - - -
413D TYR* 6.0 0.9 - - - -
414D PHE* 3.4 36.4 - - + +
417D CYS* 5.2 7.4 - - + +
418D SER* 4.9 2.9 - - - +
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Residues in contact with ARG 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 PHE* 3.1 37.9 + - - +
378D GLN* 3.2 47.5 + - - +
380D GLU* 1.3 75.6 - - - +
382D GLU* 1.3 63.7 + - + +
383D SER 2.7 12.5 + - - -
384D GLY* 3.1 9.2 + - - -
388D PHE* 4.3 13.2 - - + -
411D ASP* 3.3 25.5 + - - +
414D PHE* 3.8 27.1 - - + -
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Residues in contact with GLU 382 (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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378D GLN* 3.2 31.9 + - - +
379D SER* 3.5 10.8 + - - +
381D ARG* 1.3 80.1 - - + +
383D SER* 1.3 62.1 + - - +
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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