Contacts of the helix formed by residues 409 - 419 (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 PHE 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A PRO* 3.6 36.3 - - + -
376A PRO* 3.6 25.6 - - + -
403A ARG* 3.7 25.2 + - + -
404A MET* 3.0 31.0 - - + +
406A ASP 3.1 3.0 + - - -
408A GLY* 1.3 79.9 - - - +
410A SER* 1.3 67.0 + - - +
411A GLU 3.4 2.2 - - - -
412A ASP* 3.2 12.1 + - + +
413A MET* 2.8 20.3 + - + +
4E U 3.7 18.4 - - - -
5E U 3.3 47.8 - - - -
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Residues in contact with SER 410 (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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404A MET 3.6 6.9 + - - -
405A LEU* 3.8 15.9 - - - +
406A ASP 2.9 19.7 + - - -
407A MET* 3.7 15.8 + - - -
408A GLY 3.7 1.2 - - - -
409A PHE* 1.3 69.7 - - - +
411A GLU* 1.3 56.0 + - - +
413A MET* 3.6 3.4 - - - +
414A ARG* 2.7 40.1 + - - +
442A MET* 5.8 3.4 - - - -
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Residues in contact with GLU 411 (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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407A MET 5.0 1.2 + - - -
408A GLY 5.3 1.1 + - - +
409A PHE 3.4 0.8 - - - -
410A SER* 1.3 82.7 + - - +
412A ASP* 1.3 69.2 + - - +
414A ARG* 3.2 8.3 + - - +
415A ARG* 3.0 31.1 + - - +
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Residues in contact with ASP 412 (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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376A PRO* 4.3 12.5 - - + +
377A GLY* 4.3 14.6 + - - -
380A LEU* 3.3 26.2 - - + +
409A PHE* 3.2 13.6 + - + +
411A GLU* 1.3 83.9 - - - +
413A MET* 1.3 63.9 + - - +
415A ARG* 3.4 16.3 + - - +
416A ILE* 3.1 29.5 + - - +
5E U 4.8 2.4 + - - -
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Residues in contact with MET 413 (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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324A VAL* 4.0 7.0 - - + -
376A PRO* 3.5 17.0 - - + -
398A LEU* 3.7 34.3 - - + -
404A MET* 3.2 51.4 - - + +
405A LEU* 4.1 6.3 - - + -
409A PHE* 2.8 16.7 + - + +
410A SER* 3.6 4.5 - - - +
412A ASP* 1.3 76.2 - - - +
414A ARG* 1.3 65.2 + - - +
416A ILE* 3.3 16.2 + - + +
417A MET* 3.1 47.9 + - + +
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Residues in contact with ARG 414 (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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410A SER* 2.7 22.2 + - - +
411A GLU* 3.6 8.5 - - - +
413A MET* 1.3 72.0 - - - +
415A ARG* 1.3 54.8 + - + +
417A MET* 4.2 7.3 - - - +
418A THR* 2.7 58.4 + - + -
445A GLU* 3.0 39.2 + - - -
446A PHE* 3.8 24.5 - - + -
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Residues in contact with ARG 415 (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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380A LEU* 3.9 33.2 - - + +
384A ASP* 2.7 42.2 + - - -
411A GLU* 3.0 18.3 + - - +
412A ASP* 3.6 19.5 + - - +
414A ARG* 1.3 78.9 - - + +
416A ILE* 1.3 61.8 + - - +
418A THR* 3.8 8.1 - - + +
419A HIS* 3.1 32.7 + - - +
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Residues in contact with ILE 416 (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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322A VAL* 5.3 3.6 - - + -
324A VAL* 4.6 11.0 - - + -
376A PRO* 4.2 9.9 - - + -
379A LEU* 3.8 31.4 - - + -
380A LEU* 3.4 30.7 - - + -
390A PHE* 4.1 16.6 - - + -
396A VAL* 5.9 3.6 - - + -
398A LEU* 6.5 0.2 - - + -
412A ASP 3.1 16.5 + - - +
413A MET* 3.7 27.1 - - + +
414A ARG 3.3 0.4 - - - -
415A ARG* 1.3 79.6 - - - +
417A MET* 1.3 68.8 + - + +
419A HIS* 3.6 13.8 - - - +
422A MET* 3.6 14.7 - - + +
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Residues in contact with MET 417 (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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396A VAL* 4.4 22.0 - - + -
398A LEU* 3.9 24.0 - - + -
405A LEU* 4.1 5.8 - - + -
413A MET* 3.1 37.9 + - + +
414A ARG 4.2 0.7 - - - +
416A ILE* 1.3 81.9 - - + +
418A THR* 1.3 60.1 + - - +
419A HIS 3.4 0.4 - - - -
422A MET* 3.9 25.3 - - - +
426A HIS* 5.0 7.9 + - + -
428A THR* 5.0 4.9 - - - -
430A MET* 4.9 3.1 - - - -
446A PHE* 3.6 56.3 - - + -
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Residues in contact with THR 418 (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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414A ARG* 2.7 47.6 + - + +
415A ARG* 3.9 8.1 - - - +
417A MET* 1.3 73.3 - - - +
419A HIS* 1.3 69.3 + - - +
420A VAL* 3.5 3.8 + - - +
422A MET* 5.1 0.2 - - - -
446A PHE* 5.5 6.4 - - - -
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Residues in contact with HIS 419 (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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380A LEU* 6.2 1.0 - - - +
383A VAL* 3.6 26.4 + - + +
384A ASP* 5.3 4.5 - - - -
389A THR* 5.1 2.1 + - - -
390A PHE* 4.0 21.8 - + + -
415A ARG* 3.1 20.2 + - - +
416A ILE 3.6 11.4 - - - +
417A MET 3.4 2.2 - - - -
418A THR* 1.3 80.9 - - - +
420A VAL* 1.3 67.7 + - + +
421A THR* 3.0 41.9 + - - +
422A MET* 3.0 19.1 + - + +
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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