Contacts of the helix formed by residues 2375 - 2383 (chain B) in PDB entry 2ASS
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 THR2375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2350B PRO* 5.8 1.0 - - - +
2371B VAL* 3.2 8.8 - - - +
2372B PRO* 2.6 45.3 + - + +
2373B ASP 4.1 4.3 - - - +
2374B GLY* 1.3 85.0 - - - +
2376B LEU* 1.3 60.2 + - - +
2377B GLN* 3.1 3.6 - - - +
2378B LEU* 2.6 52.4 + - + +
2379B LEU* 3.1 5.9 + - - +
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Residues in contact with LEU2376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2371B VAL* 3.4 32.3 - - + +
2372B PRO 4.2 0.6 + - - -
2374B GLY 5.8 1.3 - - - +
2375B THR* 1.3 78.8 + - - +
2377B GLN* 1.3 58.3 + - - +
2378B LEU 3.1 0.2 + - - -
2379B LEU* 3.2 6.4 + - + -
2380B LYS* 2.9 61.2 + - + +
2388B ILE* 4.4 18.6 - - + -
2389B ASN* 4.6 19.3 - - + +
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Residues in contact with GLN2377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2374B GLY 6.2 1.1 - - - -
2375B THR* 3.1 2.1 - - - +
2376B LEU* 1.3 79.9 - - - +
2378B LEU* 1.3 59.0 + - + +
2380B LYS* 3.2 34.1 - - - +
2381B GLU* 3.0 62.1 + - + +
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Residues in contact with LEU2378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2374B GLY 4.7 3.6 - - - +
2375B THR* 2.6 44.1 + - + +
2377B GLN* 1.3 71.2 - - + +
2379B LEU* 1.3 57.6 + - - +
2381B GLU* 3.2 7.4 + - + +
2382B ALA* 2.8 30.9 + - - +
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Residues in contact with LEU2379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2350B PRO* 5.0 5.4 - - + +
2353B LEU* 3.6 38.4 - - + -
2354B LEU* 4.7 9.4 - - + -
2365B LEU* 5.4 1.1 - - + -
2367B VAL* 4.2 8.3 - - + -
2371B VAL* 4.0 21.1 - - + -
2375B THR 3.1 5.7 + - - +
2376B LEU* 3.5 12.1 - - + +
2378B LEU* 1.3 78.4 - - - +
2380B LYS* 1.3 63.4 + - - +
2382B ALA* 3.0 7.0 + - - +
2383B LEU* 3.0 50.7 + - + +
2388B ILE* 3.5 20.6 - - + -
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Residues in contact with LYS2380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2376B LEU* 2.9 50.5 + - + +
2377B GLN* 3.2 38.6 - - - +
2379B LEU* 1.3 78.5 - - - +
2381B GLU* 1.3 63.6 + - - +
2383B LEU 3.2 20.6 + - - +
2384B PRO* 3.4 4.5 - - - +
2386B LEU 5.4 0.3 - - - +
2388B ILE* 3.2 43.9 + - + +
2389B ASN 4.8 2.8 + - - -
2390B CYS* 4.6 9.7 - - - -
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Residues in contact with GLU2381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377B GLN* 3.0 50.3 + - + +
2378B LEU* 3.2 7.8 + - + +
2380B LYS* 1.3 78.0 - - - +
2382B ALA* 1.3 61.2 + - - +
2384B PRO* 3.4 19.0 - - - +
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Residues in contact with ALA2382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2354B LEU* 3.8 25.2 - - + +
2378B LEU 2.8 16.4 + - - +
2379B LEU* 3.0 8.0 + - - +
2381B GLU* 1.3 78.0 - - - +
2383B LEU* 1.3 66.1 + - - +
2384B PRO* 3.1 8.4 - - - +
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Residues in contact with LEU2383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2353B LEU 4.1 16.2 - - - +
2354B LEU* 3.8 23.6 - - + +
2357B GLY* 3.7 24.0 - - - -
2365B LEU* 5.2 3.6 - - + -
2379B LEU* 3.0 36.1 + - + +
2380B LYS* 3.2 8.5 - - - +
2382B ALA* 1.3 85.7 - - - +
2384B PRO* 1.3 65.2 - - - +
2385B HIS* 3.2 14.8 - - + +
2386B LEU* 3.0 34.6 + - + +
2388B ILE* 4.1 15.5 - - + +
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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