Contacts of the helix formed by residues 372 - 382 (chain D) in PDB entry 1Y8Q
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 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309D ASP 3.2 14.7 + - - -
310D GLN* 3.6 23.1 + - - -
311D GLN 3.9 7.4 - - - -
312D VAL* 3.8 14.0 - - - +
318D TYR* 4.2 2.7 - - - -
371D LYS* 1.3 77.6 - - - +
373D ARG* 1.3 65.4 + - - +
374D PHE* 3.8 2.8 - - - +
375D ASP* 3.1 31.7 + - - +
376D ILE* 2.9 22.4 + - - +
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Residues in contact with ARG 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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309D ASP* 3.0 42.7 + - - +
311D GLN 4.7 1.4 + - - -
318D TYR* 4.5 5.8 + - + +
321D LEU* 5.2 4.3 - - - -
349D PRO* 3.2 35.0 + - - +
352D MET* 3.3 25.0 - - + +
353D ASP* 3.0 20.8 + - - +
356D THR* 3.5 39.2 + - + +
371D LYS 3.9 0.6 + - - -
372D SER* 1.3 72.6 - - - +
374D PHE* 1.3 64.0 + - - +
376D ILE* 3.2 1.9 + - - +
377D LYS* 2.9 39.6 + - + +
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Residues in contact with PHE 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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20C ASP* 4.3 7.4 - - - -
23C ILE* 4.1 26.2 - - + -
24C ARG* 2.9 77.9 + - + +
307D LEU* 4.3 13.5 - - + -
309D ASP* 2.8 30.6 + - + +
310D GLN* 3.6 35.0 - - + -
372D SER* 3.8 2.5 - - - +
373D ARG* 1.3 78.6 - - - +
375D ASP* 1.3 76.2 + - - +
377D LYS* 3.5 8.8 + - - +
378D SER* 3.6 2.3 + - - -
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Residues in contact with ASP 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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310D GLN* 5.5 1.4 + - - +
371D LYS* 4.3 22.0 + - + +
372D SER* 3.1 28.3 + - - +
374D PHE* 1.3 92.2 - - - +
376D ILE* 1.3 65.4 + - - +
378D SER* 3.5 14.6 + - - -
379D MET* 3.1 26.1 + - + +
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Residues in contact with ILE 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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186D ILE* 4.3 20.4 - - + -
352D MET* 3.7 19.5 - - + -
355D VAL* 4.3 10.8 - - + +
356D THR* 3.7 26.9 - - + +
359D ALA* 4.8 1.3 - - + -
360D ASN* 3.6 21.3 - - - +
363D MET* 4.2 7.4 - - + -
371D LYS* 3.4 32.3 - - + +
372D SER 2.9 16.1 + - - +
373D ARG* 3.2 5.6 + - - +
375D ASP* 1.3 74.5 - - - +
377D LYS* 1.3 60.3 + - - +
379D MET* 3.2 6.7 + - - +
380D ALA* 2.8 28.6 + - + +
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Residues in contact with LYS 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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20C ASP* 3.4 22.4 + - - -
21C ARG* 5.0 2.7 - - - +
24C ARG* 3.2 16.1 - - - +
309D ASP* 5.5 3.6 + - - -
346D LYS* 4.3 16.4 + - + +
347D ASP* 5.7 4.6 + - - +
352D MET* 3.6 29.1 - - + +
373D ARG* 2.9 35.9 + - - +
374D PHE* 3.6 8.3 - - - +
375D ASP 3.3 0.2 - - - -
376D ILE* 1.3 76.4 - - - +
378D SER* 1.3 58.2 + - - +
380D ALA 4.7 0.2 - - - +
381D GLY* 2.8 29.3 + - - -
383D ILE* 3.4 20.6 - - + +
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Residues in contact with SER 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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24C ARG* 2.8 34.5 + - - +
374D PHE* 3.6 3.2 + - - -
375D ASP* 3.5 12.6 + - - -
376D ILE 3.2 0.2 - - - -
377D LYS* 1.3 78.5 - - - +
379D MET* 1.3 60.7 + - - +
382D ASN* 2.9 24.8 + - - -
383D ILE* 3.1 24.0 + - - +
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Residues in contact with MET 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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168D ARG* 4.0 11.8 + - - -
182D PRO* 5.4 0.4 - - - -
183D ILE* 4.5 25.5 - - + +
186D ILE* 3.7 29.8 - - + -
371D LYS* 3.3 38.6 - - + +
375D ASP* 3.1 30.2 + - + +
376D ILE* 3.2 2.8 + - - +
378D SER* 1.3 77.5 - - - +
380D ALA* 1.3 65.2 + - - +
382D ASN* 3.5 18.6 - - - +
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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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186D ILE* 3.8 22.4 - - + +
190D LYS* 2.8 34.2 + - + -
344D TRP* 3.7 25.7 - - + -
352D MET* 4.1 5.4 - - + -
355D VAL* 4.1 11.7 - - + -
376D ILE 2.8 20.2 + - - +
379D MET* 1.3 76.2 - - - +
381D GLY* 1.3 60.0 + - - +
382D ASN* 3.6 3.1 + - - -
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Residues in contact with GLY 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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344D TRP* 3.9 4.9 - - - -
346D LYS* 3.9 34.8 + - - +
377D LYS 2.8 19.8 + - - -
380D ALA* 1.3 74.5 - - - +
382D ASN* 1.3 74.1 + - - +
383D ILE* 3.0 6.1 + - - -
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Residues in contact with ASN 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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167D GLN* 3.5 16.9 + - - +
168D ARG* 2.7 32.6 + - - +
190D LYS* 4.5 7.1 - - - +
378D SER 2.9 11.9 + - - -
379D MET* 3.5 9.1 + - - +
380D ALA 3.4 11.3 + - - -
381D GLY* 1.3 78.8 + - - +
383D ILE* 1.3 64.3 + - - +
384D ILE* 3.5 15.6 + - - +
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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