Contacts of the helix formed by residues 324 - 329 (chain A) in PDB entry 3UGM
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 THR 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A LEU* 3.9 0.3 - - - +
318A CYS* 3.9 3.6 - - - -
323A LEU* 1.3 84.5 - - - +
325A PRO* 1.4 75.3 - - + +
326A ALA* 3.1 14.8 + - + +
327A GLN* 2.6 39.4 + - - +
328A VAL* 3.1 26.9 + - - +
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Residues in contact with PRO 325 (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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288A ASN 5.5 6.7 - - - +
289A LEU* 5.4 6.3 - - + -
293A GLN* 4.4 10.3 + - - +
314A LEU* 4.0 22.7 - - + -
318A CYS* 3.8 14.6 - - + -
323A LEU 4.6 0.7 - - - +
324A THR* 1.4 89.1 - - + +
326A ALA* 1.3 57.4 + - - +
329A VAL* 2.9 34.2 + - + +
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Residues in contact with ALA 326 (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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293A GLN* 5.1 4.7 - - - +
324A THR* 2.8 14.5 - - + +
325A PRO* 1.3 79.1 - - - +
327A GLN* 1.3 64.9 + - - +
329A VAL* 3.3 7.2 - - - +
330A ALA* 3.3 21.3 + - - +
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Residues in contact with GLN 327 (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 GLY 4.4 0.9 - - - +
323A LEU* 2.8 44.4 - - + +
324A THR* 2.6 37.0 + - - +
326A ALA* 1.3 70.2 - - - +
328A VAL* 1.3 64.4 + - - +
330A ALA* 2.7 29.9 + - - +
331A ILE* 3.2 10.9 + - - +
360A ASP* 4.7 12.5 + - - +
363A VAL* 3.5 40.0 - - + +
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Residues in contact with VAL 328 (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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310A VAL* 3.9 17.0 - - + -
313A LEU 5.4 0.2 - - - -
314A LEU* 3.5 24.2 - - + -
317A LEU* 3.4 39.9 - - + -
318A CYS* 5.1 0.2 - - - -
323A LEU* 3.8 17.3 - - + -
324A THR 3.1 16.9 + - - +
327A GLN* 1.3 75.3 - - - +
329A VAL* 1.3 53.4 + - + +
330A ALA 2.6 11.8 + - - -
331A ILE* 2.7 23.9 + - + +
332A ALA* 3.3 8.7 + - - +
341A LEU* 3.9 18.5 - - + +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.6 30.7 - - + -
293A GLN* 3.7 33.2 - - + +
296A ALA* 5.1 2.0 - - + +
297A ILE* 3.5 25.5 - - + +
310A VAL* 5.0 4.9 - - + -
314A LEU* 5.1 1.1 - - + -
325A PRO* 2.9 27.7 + - + +
326A ALA* 3.3 9.0 - - - +
328A VAL* 1.3 77.8 - - + +
330A ALA* 1.3 56.8 + - + +
331A ILE 3.3 0.7 - - - -
332A ALA* 4.4 3.4 - - - -
333A SER* 3.1 22.2 - - - -
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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