Contacts of the helix formed by residues 326 - 331 (chain A) in PDB entry 3THY
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 LEU 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A LEU 4.3 2.7 - - - +
311A ASN 2.7 21.4 + - - +
312A LEU* 3.6 26.7 - - + -
325A SER* 1.3 73.2 - - - +
327A ALA* 1.3 57.1 + - - +
329A LEU* 3.2 13.0 + - + +
330A LEU* 3.1 33.7 + - + +
346A ILE* 4.3 10.3 - - + +
640A ALA* 4.1 16.2 - - + -
641A CYS* 3.8 8.8 - - - -
684A VAL* 3.9 29.6 - - + -
687A LEU* 3.6 23.6 - - + -
688A MET* 4.3 12.1 - - + -
691A ILE* 5.2 1.6 - - + -
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Residues in contact with ALA 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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141A MET* 4.3 8.7 - - + -
312A LEU 2.9 20.7 + - - +
313A PHE* 3.7 18.2 - - + -
325A SER* 3.9 2.9 - - - +
326A LEU* 1.3 74.8 - - - +
328A ALA* 1.3 55.8 + - - +
329A LEU 2.9 5.3 + - - -
330A LEU 4.5 0.2 - - - +
331A ASN* 2.8 37.6 + - + +
343A ASN* 4.0 13.7 - - - +
346A ILE* 3.5 19.5 - - + +
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Residues in contact with ALA 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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141A MET* 5.9 3.3 - - + +
324A GLN* 2.9 30.9 + - + +
325A SER* 2.7 29.9 + - - +
327A ALA* 1.3 71.5 - - - +
329A LEU* 1.3 56.3 + - - +
331A ASN* 5.1 2.0 - - - -
332A LYS* 3.4 21.9 + - - -
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Residues in contact with LEU 329 (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 GLN* 3.0 23.8 - - - +
325A SER 3.1 10.9 + - - +
326A LEU* 3.3 13.5 - - + +
327A ALA 2.9 0.4 - - - -
328A ALA* 1.3 81.0 - - - +
330A LEU* 1.3 78.7 + - + +
331A ASN 3.6 0.2 - - - -
332A LYS* 3.3 17.9 - - - +
611A VAL* 3.5 16.5 - - + +
619A TYR* 4.0 11.0 - - - +
640A ALA* 3.7 44.0 - - + +
641A CYS* 4.3 4.7 - - - -
644A VAL* 4.4 13.7 - - + -
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Residues in contact with LEU 330 (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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326A LEU* 3.1 21.9 + - + +
327A ALA 4.7 0.2 - - - +
329A LEU* 1.3 106.9 - - + +
331A ASN* 1.3 59.5 - - - +
332A LYS* 3.3 2.2 - - - -
342A VAL* 4.4 6.3 - - + +
346A ILE* 5.1 5.2 - - + -
607A SER* 2.8 23.4 + - - -
608A PHE* 3.9 30.1 - - + -
611A VAL* 3.9 18.5 - - + +
619A TYR* 5.0 0.9 - - + -
688A MET* 3.9 23.6 - - + -
691A ILE* 5.0 8.5 - - + -
693A CYS* 3.7 31.6 - - + -
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Residues in contact with ASN 331 (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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138A ASN* 5.8 1.2 + - - -
141A MET* 4.9 4.6 - - - +
327A ALA 2.8 21.2 + - - +
328A ALA* 5.1 1.6 - - - -
329A LEU 3.6 0.8 - - - -
330A LEU* 1.3 73.9 - - - +
332A LYS* 1.3 71.8 + - - +
333A CYS* 3.4 5.3 + - - +
339A GLN* 3.4 35.8 + - - +
342A VAL* 3.3 32.6 - - + +
343A ASN* 3.2 25.0 + - - +
607A SER* 4.1 0.4 - - - -
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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