Contacts of the helix formed by residues 374 - 383 (chain D) in PDB entry 5E9W
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 TYR 374 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D PHE* 5.0 4.7 - - - -
321D SER* 3.7 16.8 - - - -
322D PHE* 3.7 29.2 - + - -
353D LEU* 4.7 21.6 + - + +
372D LEU* 3.9 11.4 + - + +
373D VAL* 1.3 71.4 - - - +
375D PHE* 1.3 64.5 + - - +
376D PRO* 3.5 35.2 - - + +
377D LEU* 2.9 33.4 + - + +
378D LEU* 3.1 9.9 + - - +
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Residues in contact with PHE 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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318D THR* 5.4 0.7 - - + -
320D ASN* 6.0 0.2 - - - +
321D SER* 4.3 3.5 + - - +
322D PHE* 5.3 6.1 - - + -
373D VAL* 3.2 11.7 + - + +
374D TYR* 1.3 72.9 - - - +
376D PRO* 1.3 73.9 - - + +
378D LEU* 3.0 31.8 + - + -
379D ASN* 2.8 30.6 + - + +
389D LEU* 3.9 17.7 - - + -
392D LYS* 3.6 42.8 - - + -
468D LEU* 4.3 27.4 - - + -
470D PHE* 3.7 23.8 - + + -
472D PHE* 3.8 17.7 - + - -
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Residues in contact with PRO 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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322D PHE* 4.3 13.5 - - + -
374D TYR* 3.5 41.1 - - + +
375D PHE* 1.3 96.1 - - + +
377D LEU* 1.3 54.7 + - - +
379D ASN* 3.5 8.8 + - + +
380D GLU* 3.1 30.8 + - - +
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Residues in contact with LEU 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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291D PHE* 4.0 11.9 - - + -
353D LEU* 3.7 40.2 - - + +
354D PHE* 3.7 31.0 - - + -
374D TYR* 2.9 26.3 + - + +
376D PRO* 1.3 77.0 - - - +
378D LEU* 1.3 58.9 + - - +
380D GLU* 3.1 8.5 + - + +
381D MET* 2.8 49.2 + - + +
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Residues in contact with LEU 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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287D CYS* 5.5 7.9 - - + -
291D PHE* 3.9 28.5 - - + -
301D LEU* 4.0 26.9 - - + -
314D PHE* 5.1 3.6 - - + -
318D THR* 5.3 0.9 - - + -
373D VAL* 4.2 15.5 - - + -
374D TYR 3.1 9.5 + - - +
375D PHE* 3.0 40.0 + - + +
377D LEU* 1.3 75.9 - - - +
379D ASN* 1.3 64.0 + - - +
381D MET* 3.4 3.7 + - - +
382D ALA* 3.0 24.8 + - - +
470D PHE* 4.5 17.9 - - + -
472D PHE* 4.2 15.0 - - + -
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Residues in contact with ASN 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 PHE* 2.8 22.8 + - + +
376D PRO* 3.5 10.3 + - + +
378D LEU* 1.3 78.9 - - - +
380D GLU* 1.3 64.7 + - - +
382D ALA* 3.5 9.0 + - - +
383D LYS* 3.5 34.7 + - - +
387D MET 5.3 0.7 - - - +
389D LEU* 3.4 35.7 + - - +
472D PHE* 3.5 18.3 - - + -
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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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376D PRO 3.1 13.5 + - - +
377D LEU* 3.1 14.3 + - + +
379D ASN* 1.3 81.4 - - - +
381D MET* 1.3 63.2 + - + +
383D LYS* 2.2 59.0 + - - +
384D LYS* 4.1 1.2 + - - +
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Residues in contact with MET 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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291D PHE* 4.3 10.3 - - - -
294D TYR* 3.9 25.4 - - + -
297D ALA* 3.7 11.0 - - + -
298D ASP* 3.5 39.6 - - + +
301D LEU* 3.5 17.5 - - + +
354D PHE* 4.0 16.8 - - - -
377D LEU* 2.8 43.5 + - + +
378D LEU 3.8 1.8 - - - +
380D GLU* 1.3 74.8 - - - +
382D ALA* 1.3 61.5 + - - +
384D LYS* 3.2 23.5 + - - +
385D TYR* 4.2 3.6 - - - -
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Residues in contact with ALA 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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301D LEU* 3.7 20.6 - - + +
305D CYS* 5.4 0.7 - - - -
314D PHE* 5.6 0.2 - - + -
378D LEU 3.0 17.9 + - - +
379D ASN 3.7 6.7 - - - +
380D GLU 3.2 0.2 - - - -
381D MET* 1.3 73.6 - - - +
383D LYS* 1.3 63.9 + - - +
384D LYS 3.1 0.2 - - - -
385D TYR* 3.1 14.4 + - - +
387D MET* 3.3 34.1 + - + +
472D PHE* 4.0 22.9 - - + -
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Residues in contact with LYS 383 (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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379D ASN* 3.5 29.4 - - - +
380D GLU* 2.2 54.2 + - - +
382D ALA* 1.3 74.9 - - - +
384D LYS* 1.3 63.6 + - - +
386D ASN* 2.9 14.8 + - - +
387D MET 4.0 17.5 + - - +
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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