Contacts of the helix formed by residues 2398 - 2407 (chain A) in PDB entry 5DZZ
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 ASN2398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2351A PHE* 3.5 26.4 - - + -
2392A TYR* 3.4 6.5 - - - -
2397A PHE* 1.3 83.2 - - - +
2399A GLU* 1.3 77.1 + - - +
2400A GLU* 3.0 29.8 + - - +
2401A LEU* 3.0 26.3 + - + +
2402A SER* 3.1 15.1 + - - -
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Residues in contact with GLU2399 (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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2392A TYR* 3.3 42.5 - - + +
2398A ASN* 1.3 72.3 + - - +
2400A GLU* 1.3 68.0 + - - +
2401A LEU 3.0 10.1 + - - -
2402A SER* 3.5 8.3 + - - -
2403A GLU* 4.0 20.2 + - + +
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Residues in contact with GLU2400 (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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2398A ASN* 3.0 23.0 + - - +
2399A GLU* 1.3 85.8 - - - +
2401A LEU* 1.3 57.7 + - - +
2403A GLU* 5.0 2.7 - - - -
2404A ILE* 3.2 25.0 - - - +
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Residues in contact with LEU2401 (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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2351A PHE* 4.0 20.6 - - + -
2354A MET* 4.1 9.6 - - + -
2365A ILE* 5.9 8.1 - - + -
2368A LEU* 4.0 16.2 - - + -
2397A PHE* 3.6 25.4 - - + -
2398A ASN* 3.5 15.5 - - + +
2399A GLU 3.0 0.4 - - - -
2400A GLU* 1.3 80.9 - - - +
2402A SER* 1.3 64.5 + - - +
2403A GLU 3.3 1.8 - - - -
2404A ILE* 3.4 26.7 + - + +
2405A LEU* 3.1 34.6 + - + +
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Residues in contact with SER2402 (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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2372A ILE* 5.8 0.4 - - - -
2388A VAL* 3.8 6.5 - - - +
2392A TYR* 2.6 29.2 + - - -
2397A PHE* 3.2 27.9 - - - -
2398A ASN 3.1 6.0 + - - -
2399A GLU* 3.5 5.1 + - - -
2401A LEU* 1.3 80.5 - - - +
2403A GLU* 1.3 60.0 + - - +
2405A LEU* 3.7 2.6 + - - +
2406A SER* 3.1 26.7 + - - -
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Residues in contact with GLU2403 (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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2399A GLU* 4.0 17.8 + - + +
2400A GLU* 5.8 0.9 - - - -
2401A LEU 5.7 0.4 - - - +
2402A SER* 1.3 76.9 - - - +
2404A ILE* 1.3 65.5 + - + +
2406A SER* 2.4 27.0 + - - +
2407A ASP* 3.6 7.1 + - - +
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Residues in contact with ILE2404 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2400A GLU 3.2 26.0 - - - +
2401A LEU* 3.4 23.3 + - + +
2402A SER 3.3 0.4 - - - -
2403A GLU* 1.3 81.4 - - + +
2405A LEU* 1.3 57.8 + - + +
2407A ASP 3.1 21.5 - - - +
2409A SER* 4.1 9.3 + - - +
2411A ASP* 6.5 0.4 - - + -
2412A THR* 3.7 21.0 - - + +
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Residues in contact with LEU2405 (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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2365A ILE* 3.7 30.1 - - + -
2368A LEU* 4.1 19.7 - - + -
2369A GLU* 4.1 21.8 - - + +
2372A ILE* 3.9 18.2 - - + -
2397A PHE* 3.7 28.7 - - + -
2401A LEU* 3.1 26.7 + - + +
2402A SER 3.9 2.9 - - - +
2404A ILE* 1.3 75.5 - - + +
2406A SER* 1.3 66.2 + - - +
2407A ASP 4.5 2.5 - - - +
2412A THR* 3.8 17.8 - - + -
2425A THR* 5.5 7.1 - - - +
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Residues in contact with SER2406 (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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2402A SER 3.1 17.4 + - - -
2403A GLU* 2.4 31.2 + - - +
2405A LEU* 1.3 81.3 - - - +
2407A ASP* 1.3 65.4 + - - +
2408A PRO* 3.6 8.0 - - - +
2427A LEU* 5.6 6.4 - - - +
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Residues in contact with ASP2407 (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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2403A GLU 3.6 5.2 + - - +
2404A ILE 3.1 16.9 - - - +
2405A LEU 4.7 1.3 - - - -
2406A SER* 1.3 84.6 + - - +
2408A PRO* 1.3 85.2 - - - +
2409A SER* 3.1 14.2 + - - +
2412A THR* 4.2 0.5 + - - -
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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