Contacts of the helix formed by residues 395 - 403 (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 PHE 395 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D PHE* 4.3 6.4 - + + -
176D ASN* 3.9 14.8 - - - -
179D MET* 3.5 32.1 - - + +
285D PHE* 4.2 9.0 - + - -
317D THR* 3.6 17.7 - - + -
394D THR* 1.3 72.3 - - - +
396D LEU* 1.3 57.6 + - - +
398D PHE* 3.7 1.0 - - - +
399D TYR* 2.9 30.8 + - - +
461D TRP* 5.4 1.8 - - - -
464D THR* 3.3 41.1 - - + +
465D SER* 4.6 2.9 + - - -
467D TYR* 2.9 46.3 + + + +
468D LEU 3.4 14.4 - - - -
469D VAL* 3.4 30.1 - - + -
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Residues in contact with LEU 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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394D THR* 3.1 7.7 + - - +
395D PHE* 1.3 78.6 - - - +
397D GLU* 1.3 59.7 + - + +
399D TYR* 3.1 7.7 + - + +
400D GLU* 2.9 59.0 + - + +
450D ARG 4.2 14.4 - - - +
451D LEU* 4.1 25.8 - - + -
452D PRO* 4.3 16.2 - - + -
461D TRP* 4.8 8.9 - - + -
465D SER* 5.1 13.8 + - - +
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Residues in contact with GLU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D LYS* 4.4 2.9 - - - +
393D LYS* 3.4 19.7 - - + +
394D THR* 2.9 47.8 + - - +
396D LEU* 1.3 79.1 - - + +
398D PHE* 1.3 63.5 + - - +
400D GLU* 3.3 6.9 + - - +
401D GLU* 3.1 24.6 + - - +
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Residues in contact with PHE 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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178D TRP* 5.7 0.4 - + - -
179D MET* 3.4 49.1 - - + -
182D VAL* 4.3 4.7 - - + -
183D LEU* 4.0 26.0 - - + -
186D GLU* 4.6 0.2 - - - -
391D TYR* 3.7 22.0 - + - -
393D LYS* 4.1 17.7 - - + +
394D THR 2.9 16.8 + - - +
395D PHE* 3.7 4.3 - - - +
397D GLU* 1.3 75.9 - - - +
399D TYR* 1.3 57.4 + - - +
401D GLU* 3.3 4.3 + - - +
402D LYS* 2.9 70.9 + - + +
469D VAL* 3.6 28.3 - - + -
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Residues in contact with TYR 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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175D PHE* 3.7 33.4 - + + -
178D TRP* 3.9 9.4 - + - -
179D MET* 4.5 5.4 - - - -
395D PHE 2.9 19.0 + - - +
396D LEU 3.4 4.7 - - - +
398D PHE* 1.3 77.7 - - - +
400D GLU* 1.3 86.7 + - - +
402D LYS* 3.1 4.9 + - - +
403D ILE* 3.0 63.3 + - + +
412D LEU* 4.4 3.4 - - + -
452D PRO* 4.4 7.2 - - + -
454D GLY* 4.0 9.7 - - - -
455D THR* 2.7 29.5 + - - -
461D TRP* 3.6 26.9 - + + -
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Residues in contact with GLU 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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396D LEU* 2.9 35.4 + - + +
397D GLU* 3.3 6.5 + - - +
399D TYR* 1.3 84.7 - - + +
401D GLU* 1.3 62.4 + - - +
403D ILE* 3.4 17.5 - - - +
404D LYS* 3.2 24.8 - - - +
452D PRO* 3.7 28.2 - - - +
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Residues in contact with GLU 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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186D GLU* 5.1 1.4 - - - +
391D TYR* 5.8 1.6 + - - -
393D LYS* 3.0 36.4 + - - +
397D GLU 3.1 15.6 + - - +
398D PHE* 3.8 4.7 - - - +
400D GLU* 1.3 77.5 - - - +
402D LYS* 1.3 90.3 + - + +
404D LYS* 3.5 23.3 + - - +
405D ASN* 4.4 2.4 + - - +
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Residues in contact with LYS 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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178D TRP* 3.8 20.6 - - + -
182D VAL* 3.4 28.0 - - + +
186D GLU* 3.2 29.3 + - - +
398D PHE* 2.9 60.4 + - + +
399D TYR 3.1 0.2 + - - -
401D GLU* 1.3 100.9 + - + +
403D ILE* 1.3 57.3 + - - +
404D LYS 3.2 0.7 - - - -
405D ASN* 3.2 24.1 + - - +
408D ASN* 3.4 16.7 + - - +
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Residues in contact with ILE 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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178D TRP* 3.8 19.5 - - + -
399D TYR* 3.0 54.0 + - + +
400D GLU* 3.4 30.3 - - - +
402D LYS* 1.3 73.6 - - - +
404D LYS* 1.3 62.6 + - + +
405D ASN 2.9 15.6 + - - +
406D ASN* 5.4 0.2 - - - -
409D LYS* 4.0 29.8 - - + +
412D LEU* 4.3 10.3 - - + -
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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