Contacts of the helix formed by residues 363 - 368 (chain D) in PDB entry 4O9U
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 PRO 363 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B HIS 5.3 1.6 - - - +
314B GLU* 3.5 47.4 - - + +
448B LYS* 4.3 12.8 - - - +
359D GLU 4.0 12.6 - - - +
360D GLU 5.0 3.4 - - - +
361D ILE* 3.6 4.0 - - - +
362D ASN* 1.4 93.0 - - + +
364D GLU* 1.3 57.2 + - + +
365D PHE 3.5 0.7 - - - -
366D PRO* 4.4 8.8 - - + +
367D THR* 5.1 1.0 + - - -
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 6.2 2.7 - - + -
311B LYS* 2.8 30.4 + - - +
314B GLU* 5.2 2.6 - - - +
294D LYS* 3.2 33.4 + - - +
327D LYS* 2.9 32.2 + - - +
356D LYS* 5.6 0.7 - - - +
360D GLU 3.6 15.3 - - - +
361D ILE* 3.2 25.1 - - + +
362D ASN 3.0 1.0 - - - -
363D PRO* 1.3 79.5 - - + +
365D PHE* 1.3 59.1 + - - +
366D PRO 3.7 0.7 - - - -
367D THR* 2.7 26.6 + - - +
368D VAL* 3.1 17.9 - - + +
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Residues in contact with PHE 365 (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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296D VAL* 3.7 34.1 - - + -
298D VAL* 4.6 3.1 - - + -
329D ALA* 3.9 4.7 - - + -
361D ILE* 3.2 35.9 - - + -
362D ASN* 3.4 20.0 - - - +
364D GLU* 1.3 74.6 - - - +
366D PRO* 1.4 65.9 - - + +
367D THR 2.9 5.2 - - - -
368D VAL* 2.7 28.7 + - + +
371D ALA* 4.3 10.1 - - + -
397D LEU* 3.6 27.8 - - + -
398D ASP* 3.0 28.3 - - + +
399D VAL* 4.3 9.4 - - - -
401D LYS* 4.9 0.9 - - + -
402D ALA* 3.3 32.6 - - + +
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Residues in contact with PRO 366 (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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362D ASN 4.3 6.5 - - - +
363D PRO* 4.4 8.5 - - + +
364D GLU 3.8 2.0 - - - -
365D PHE* 1.4 92.7 - - + +
367D THR* 1.3 63.2 + - + +
368D VAL 3.6 0.2 - - - -
401D LYS* 3.3 40.1 - - + +
403D LYS* 3.4 31.0 - - - +
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Residues in contact with THR 367 (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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310B HIS* 3.6 40.2 + - + +
347B GLU 5.1 4.0 - - - +
348B ALA 4.8 9.9 - - - +
294D LYS* 3.6 21.1 + - - +
363D PRO 5.1 0.9 + - - -
364D GLU* 2.7 27.3 + - - +
366D PRO* 1.3 83.6 - - + +
368D VAL* 1.3 64.1 + - - +
369D ASP* 3.2 9.9 + - - +
403D LYS* 5.1 9.1 - - - +
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Residues in contact with VAL 368 (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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294D LYS* 3.2 30.3 - - + +
296D VAL* 3.6 37.2 - - + +
361D ILE* 6.1 0.2 - - + -
364D GLU* 3.1 21.7 + - + +
365D PHE* 2.7 21.7 + - + +
367D THR* 1.3 75.2 - - - +
369D ASP* 1.3 64.2 + - - +
370D VAL 3.4 22.0 - - - +
371D ALA* 4.0 7.0 - - + +
402D ALA* 3.9 2.5 - - + +
403D LYS* 3.5 20.9 + - - +
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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