Contacts of the helix formed by residues 339 - 346 (chain A) in PDB entry 3RCY
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 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.9 28.9 + - + +
337A ILE* 3.6 17.2 + - + -
338A GLU* 1.3 81.8 - - - +
340A PRO* 1.4 77.5 - - - +
341A PHE* 3.5 6.9 + - - +
342A HIS* 2.8 39.4 + - + +
343A ASP* 3.1 21.5 + - - +
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Residues in contact with PRO 340 (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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339A THR* 1.4 87.4 - - - +
341A PHE* 1.3 56.3 + - - +
343A ASP* 3.4 5.9 + - + +
344A ALA* 2.9 31.6 + - - +
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Residues in contact with PHE 341 (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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11A THR* 3.5 24.9 - - + -
12A ALA 4.2 1.6 - - - -
13A PRO* 3.8 20.4 - - + -
14A PRO* 3.5 25.6 - - + -
23A TRP* 3.5 41.3 - + + -
339A THR* 3.2 6.5 + - - +
340A PRO* 1.3 77.7 - - - +
342A HIS* 1.3 64.6 + - - +
344A ALA* 4.5 2.9 - - + +
345A LEU* 2.9 39.6 + - + +
373A LEU* 3.9 27.1 - - + -
377A ASN* 3.8 27.8 - - + -
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Residues in contact with HIS 342 (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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18A TRP 3.3 25.8 + - - -
23A TRP* 3.3 15.1 - + - -
311A LEU* 4.7 4.2 - - + +
313A ALA 2.8 26.5 + - - -
314A GLY 4.0 0.7 - - - -
315A PRO* 3.4 54.9 - - + +
318A TRP* 6.5 0.4 - + - -
337A ILE* 3.4 42.3 - - + +
339A THR* 2.8 34.8 + - - +
341A PHE* 1.3 76.9 - - - +
343A ASP* 1.3 64.1 + - - +
345A LEU 3.5 3.1 + - - -
346A ILE* 3.7 2.9 + - - +
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Residues in contact with ASP 343 (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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339A THR 3.1 14.0 + - - +
340A PRO* 3.8 6.1 - - + +
342A HIS* 1.3 79.8 - - - +
344A ALA* 1.3 58.6 + - - +
346A ILE* 3.4 6.5 + - - +
347A LYS 3.0 7.3 + - - -
348A GLY* 2.8 31.6 + - - -
350A ILE 4.6 1.9 - - - +
351A ARG* 2.8 55.6 + - - +
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Residues in contact with ALA 344 (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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340A PRO 2.9 17.8 + - - +
341A PHE* 4.0 2.2 - - - +
343A ASP* 1.3 78.8 + - - +
345A LEU* 1.3 63.7 + - - +
347A LYS* 3.0 15.7 + - - +
370A ASP* 3.7 15.1 - - - +
373A LEU* 3.7 19.9 - - + +
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Residues in contact with LEU 345 (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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11A THR* 4.5 1.8 - - + -
23A TRP* 3.8 32.5 - - + -
25A LEU* 4.2 19.3 - - + -
315A PRO* 3.8 15.5 - - + -
316A VAL* 5.4 1.3 - - + -
341A PHE* 2.9 26.2 + - + +
342A HIS 3.8 5.4 - - - +
343A ASP 3.3 0.2 - - - -
344A ALA* 1.3 76.4 - - - +
346A ILE* 1.3 60.7 + - + +
369A VAL* 3.3 14.9 - - + +
370A ASP* 2.8 45.4 + - - +
373A LEU* 3.9 9.8 - - + +
374A ALA* 3.8 23.6 - - + +
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Residues in contact with ILE 346 (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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315A PRO* 3.8 36.3 - - + +
316A VAL* 4.4 7.0 - - + -
318A TRP* 4.7 6.1 - - + -
342A HIS 3.7 13.7 + - - +
343A ASP* 3.4 6.5 + - - +
344A ALA 3.2 0.2 - - - -
345A LEU* 1.3 81.2 - - + +
347A LYS* 1.3 62.3 + - - +
348A GLY 4.5 0.2 - - - +
349A SER* 2.6 33.7 + - - +
350A ILE* 3.9 37.5 - - + +
367A ILE* 4.1 41.7 - - + -
368A GLU 3.2 8.7 - - - +
369A VAL* 4.4 3.1 - - + -
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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