Contacts of the helix formed by residues 339 - 354 (chain A) in PDB entry 1DNC
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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30A SER* 3.2 20.4 - - - +
58A CYS* 3.8 7.9 - - - -
63A CSD 2.7 29.7 + - - +
338A LEU* 1.3 70.5 - - - +
340A PRO* 1.3 72.6 - - + +
341A VAL 3.1 0.3 + - - -
342A ALA* 3.1 5.1 + - - +
343A ILE* 3.1 25.4 + - + +
499A FAD 3.0 37.1 + - - -
1029A GSH 3.5 23.6 - - - +
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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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63A CSD 5.0 0.2 - - - +
338A LEU* 3.8 6.7 - - + -
339A THR* 1.3 95.5 - - + +
341A VAL* 1.3 57.0 + - + +
343A ILE* 3.8 9.8 - - + +
344A ALA* 3.0 30.3 + - - +
499A FAD 3.2 14.6 - - - +
1029A GSH 5.7 1.1 - - - +
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Residues in contact with VAL 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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335A LYS 4.6 1.3 - - - +
336A ALA* 3.5 27.6 - - + +
338A LEU* 3.6 15.7 - - + +
339A THR 3.1 1.2 - - - -
340A PRO* 1.3 77.4 - - + +
342A ALA* 1.3 65.4 + - - +
344A ALA* 4.8 0.4 - - - -
345A ALA* 2.9 24.9 + - - +
362A LEU* 3.7 12.1 - - + +
364A TYR* 3.6 33.4 - - + +
367A ILE* 3.6 36.3 - - + -
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Residues in contact with ALA 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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30A SER* 4.3 1.3 - - - -
31A GLY* 3.7 28.1 - - - +
329A VAL* 4.2 2.1 - - - +
330A GLY* 3.8 31.4 - - - +
331A ASP* 5.7 0.2 - - - +
338A LEU 3.3 8.4 + - - +
339A THR 3.1 9.0 + - - +
341A VAL* 1.3 78.6 - - - +
343A ILE* 1.3 57.7 + - - +
345A ALA* 4.0 1.9 - - - +
346A GLY* 2.9 27.0 + - - -
499A FAD 4.2 12.6 - - - +
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Residues in contact with ILE 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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30A SER* 3.7 20.9 - - - +
34A ALA* 3.8 14.9 - - + +
339A THR* 3.1 24.2 + - + +
340A PRO* 3.8 8.5 - - + +
342A ALA* 1.3 72.4 - - - +
344A ALA* 1.3 61.0 + - - +
346A GLY* 3.2 1.7 + - - -
347A ARG* 2.9 66.2 + - - +
1029A GSH 3.4 52.5 - - + +
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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 3.0 19.1 + - - +
341A VAL* 4.2 2.0 - - - +
343A ILE* 1.3 78.8 - - + +
345A ALA* 1.3 61.9 + - - +
347A ARG* 3.3 7.0 + - - +
348A LYS* 2.9 33.4 + - + +
362A LEU* 3.8 24.5 - - + -
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Residues in contact with ALA 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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319A GLN* 3.9 19.5 - - - +
329A VAL* 4.2 11.8 - - + +
330A GLY 5.5 0.9 - - - +
341A VAL 2.9 19.0 + - - +
342A ALA* 4.0 3.4 - - - +
344A ALA* 1.3 77.0 - - - +
346A GLY* 1.3 62.4 + - - +
348A LYS* 3.5 2.9 + - - +
349A LEU* 3.1 24.8 + - - +
362A LEU* 4.0 14.7 - - + +
364A TYR* 3.8 21.5 - - - +
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Residues in contact with GLY 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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31A GLY 4.4 4.5 - - - -
35A SER* 2.8 40.0 + - - -
329A VAL* 4.3 11.6 - - - +
342A ALA 2.9 17.1 + - - -
343A ILE 3.2 3.6 + - - -
345A ALA* 1.3 76.3 - - - +
347A ARG* 1.3 59.4 + - - +
349A LEU* 3.5 3.0 + - - +
350A ALA 3.2 11.8 + - - -
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Residues in contact with ARG 347 (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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34A ALA* 3.8 20.1 + - + +
37A ARG* 5.9 0.8 - - - +
38A ARG* 3.6 47.8 - - + +
343A ILE* 2.9 39.4 + - - +
344A ALA* 3.9 6.3 - - - +
346A GLY* 1.3 75.1 - - - +
348A LYS* 1.3 65.0 + - + +
350A ALA* 3.2 3.6 + - - +
351A HIS* 3.1 30.0 + - + -
1029A GSH 2.9 57.2 + - - -
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Residues in contact with LYS 348 (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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344A ALA* 2.9 24.4 + - - +
345A ALA 3.8 3.6 - - - +
347A ARG* 1.3 75.7 - - + +
349A LEU* 1.3 58.0 + - - +
351A HIS* 3.4 5.0 + - + -
352A ARG* 3.0 17.3 + - - +
360A SER* 2.7 39.3 + - - +
361A LYS* 3.8 37.8 + - - +
362A LEU* 4.0 11.2 - - + +
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Residues in contact with LEU 349 (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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23A TYR* 3.8 17.3 - - - +
35A SER* 4.5 1.1 - - - +
153A LEU* 3.8 13.9 - - + -
318A PHE 3.7 10.8 - - - +
319A GLN* 4.6 3.8 - - + -
327A TYR* 3.7 31.9 - - + -
329A VAL* 4.4 9.2 - - + -
345A ALA 3.1 17.9 + - - +
346A GLY 3.5 5.4 - - - +
347A ARG 3.1 0.2 - - - -
348A LYS* 1.3 74.4 - - - +
350A ALA* 1.3 66.0 + - - +
352A ARG* 2.9 50.3 + - - +
353A LEU* 2.9 31.0 + - + +
360A SER 5.2 0.9 - - - -
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Residues in contact with ALA 350 (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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23A TYR* 5.0 2.0 - - - -
35A SER* 3.8 13.4 + - - +
38A ARG* 3.8 12.6 - - + +
39A ALA* 3.8 30.7 - - + +
42A LEU* 3.6 2.4 - - - +
346A GLY 3.2 8.3 + - - +
347A ARG 3.6 7.9 - - - +
349A LEU* 1.3 79.5 - - - +
351A HIS* 1.3 57.1 + - - +
354A PHE* 2.7 44.1 + - - +
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Residues in contact with HIS 351 (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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38A ARG* 2.9 46.1 + - + -
42A LEU* 4.0 16.3 - - + +
347A ARG* 3.1 29.8 + - + -
348A LYS* 3.7 3.8 - - + +
350A ALA* 1.3 75.5 - - - +
352A ARG* 1.3 58.5 + - - +
355A GLU* 2.8 53.9 + - - +
356A TYR 3.3 3.5 + - - -
357A LYS* 3.4 16.0 + - + +
360A SER* 3.7 17.0 - - - +
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Residues in contact with ARG 352 (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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318A PHE* 3.0 47.0 + - - +
320A ASN* 2.9 32.5 + - - +
327A TYR* 3.8 6.5 - - - -
348A LYS 3.0 13.1 + - - +
349A LEU* 2.9 28.2 + - - +
351A HIS* 1.3 77.8 - - - +
353A LEU* 1.3 71.5 + - + +
356A TYR* 3.4 20.3 - - - -
357A LYS 3.3 20.7 + - - +
358A GLU* 4.0 15.6 + - + +
360A SER* 3.7 17.0 + - - +
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Residues in contact with LEU 353 (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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23A TYR* 4.0 19.5 - - + +
151A HIS* 3.9 25.8 + - + +
327A TYR* 3.8 43.3 - - + +
349A LEU* 2.9 28.1 + - + +
352A ARG* 1.3 106.4 - - - +
354A PHE* 1.3 80.0 + - + +
355A GLU 3.7 0.2 - - - -
356A TYR* 3.7 21.1 - - - -
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Residues in contact with PHE 354 (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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22A ASP* 3.8 25.1 - - + -
23A TYR* 3.8 37.5 - + + -
39A ALA* 3.8 20.0 - - + -
42A LEU* 3.8 33.9 - - + +
44A ALA* 3.8 20.9 - - + -
151A HIS* 3.9 22.7 - + - -
350A ALA* 2.7 24.9 + - - +
353A LEU* 1.3 86.0 - - + +
355A GLU* 1.3 58.6 + - - +
356A TYR* 3.5 19.2 - - - -
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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