Contacts of the strand formed by residues 427 - 432 (chain A) in PDB entry 2DB3
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 GLN 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A ILE* 3.0 26.3 + - - +
282A GLY* 3.1 36.6 - - - +
283A ARG 3.1 20.5 - - - +
284A ASP* 3.2 7.9 - - - +
306A LYS* 5.7 3.2 - - - +
394A ARG* 2.9 13.2 + - - +
395A PHE* 3.1 38.9 - - + -
396A VAL 2.9 27.0 + - - -
426A HIS* 1.3 76.8 + - - +
428A THR* 1.3 61.4 + - - +
429A LEU* 4.1 6.2 - - + +
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ASP* 2.9 14.6 + - - -
285A LEU 3.1 21.3 + - - -
396A VAL* 3.3 15.8 - - + +
398A LEU* 5.5 1.8 - - + -
417A MET* 5.0 5.5 - - - -
426A HIS* 3.2 28.9 + - - -
427A GLN* 1.3 71.6 - - - +
429A LEU* 1.3 63.3 + - - +
430A MET* 3.9 17.3 - - + -
446A PHE* 3.5 22.7 + - + +
447A LEU* 3.5 26.1 - - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE* 3.7 33.0 - - + -
283A ARG 3.7 16.2 - - - +
284A ASP* 4.3 0.2 - - - -
285A LEU* 3.5 24.0 - - + +
299A PHE* 4.5 2.0 - - + -
303A ILE* 3.7 30.3 - - + -
395A PHE* 4.7 5.8 - - + -
396A VAL 2.8 14.3 + - - +
397A VAL* 3.3 11.2 - - + +
398A LEU* 2.8 27.4 + - - +
427A GLN* 4.5 6.7 - - + +
428A THR* 1.3 89.4 - - - +
430A MET* 1.3 64.5 + - - +
431A PHE* 3.8 15.5 - - + -
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Residues in contact with MET 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU 2.9 12.1 + - - +
286A MET* 3.4 5.0 - - - +
287A ALA 2.7 31.5 + - - +
398A LEU* 3.6 23.8 - - + -
401A ALA* 3.5 15.7 - - + -
405A LEU* 3.9 12.8 - - + -
417A MET* 4.9 0.2 - - - -
428A THR* 3.9 12.3 - - + -
429A LEU* 1.3 79.6 - - - +
431A PHE* 1.3 59.7 + - - +
435A PHE* 4.4 10.3 - - + -
443A ALA* 3.4 48.5 - - + +
446A PHE* 4.1 11.2 - - + -
447A LEU* 3.8 24.9 - - + -
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE* 5.0 1.1 - - + -
275A SER* 3.7 11.7 - - - -
279A ILE* 4.2 4.7 - - + -
285A LEU* 3.6 21.8 - - + -
287A ALA* 3.3 26.5 - - + -
295A LYS* 4.0 30.3 - - + -
298A ALA* 3.9 15.7 - - + -
299A PHE* 3.7 39.0 - + + -
397A VAL* 4.6 3.8 - - + -
398A LEU 3.2 5.8 + - - +
399A ASP* 4.2 13.5 - - - +
400A GLU 2.9 24.7 + - - -
401A ALA* 2.9 5.3 + - - -
429A LEU* 3.8 21.3 - - + -
430A MET* 1.3 82.8 - - - +
432A SER* 1.3 65.3 + - - +
435A PHE* 5.1 1.1 - - - -
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA 3.1 6.1 + - - +
288A CYS* 3.3 26.9 - - - +
289A ALA 3.4 2.4 + - - -
295A LYS* 3.7 12.1 - - - +
399A ASP* 5.4 0.4 - - - -
400A GLU* 4.0 6.5 + - - +
401A ALA 4.1 4.0 - - - -
402A ASP* 2.5 27.6 + - - -
431A PHE* 1.3 79.8 - - - +
433A ALA* 1.3 67.5 + - - +
434A THR 2.7 23.8 + - - +
435A PHE* 4.2 8.1 - - - -
551A ARG* 3.4 7.6 + - - -
575A HIS* 4.0 0.7 - - - -
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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