Contacts of the helix formed by residues 322 - 334 (chain I) in PDB entry 1DFJ
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 ALA 322 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321I THR* 1.3 75.1 - - - +
323I ALA* 1.3 56.7 + - - +
324I CYS 2.8 7.6 + - - -
325I CYS* 2.9 27.7 + - - +
326I GLN* 4.2 2.1 + - - +
347I LYS 3.6 6.6 + - - +
348I LEU 3.8 18.4 + - - +
351I SER* 4.0 16.6 - - - +
352I GLY* 4.5 3.8 - - - +
355I GLU* 4.3 6.5 - - - +
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Residues in contact with ALA 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I ASP* 3.1 24.8 - - + +
321I THR* 3.1 5.1 + - - +
322I ALA* 1.3 77.5 - - - +
324I CYS* 1.3 56.6 + - - +
325I CYS 3.5 0.2 - - - -
326I GLN* 4.6 8.3 + - - +
327I HIS* 4.2 12.3 + - - -
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Residues in contact with CYS 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I ASP* 3.4 19.5 + - - +
296I ALA* 3.6 24.9 - - + -
297I ARG 5.9 0.2 - - - +
320I LEU* 3.6 24.5 - - - -
321I THR 3.0 23.1 + - - -
322I ALA 2.8 4.0 + - - -
323I ALA* 1.3 73.6 - - - +
325I CYS* 1.3 55.2 + - - +
326I GLN 3.2 2.7 - - - -
327I HIS* 2.8 14.4 + - - +
328I VAL* 2.6 45.8 + - + +
343I LEU* 5.4 0.7 - - - -
348I LEU* 4.1 10.3 - - - -
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Residues in contact with CYS 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I ALA* 2.9 14.4 + - - +
324I CYS* 1.3 75.3 - - - +
326I GLN* 1.3 62.0 + - - +
328I VAL* 3.6 10.3 - - - +
329I SER* 2.8 34.1 + - - -
343I LEU* 6.4 0.2 - - - -
348I LEU* 3.9 29.4 - - - -
352I GLY* 3.4 41.7 - - - +
355I GLU* 3.9 13.1 - - + +
356I LEU* 4.5 9.2 - - + -
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Residues in contact with GLN 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I ALA 4.2 1.2 + - - -
323I ALA 4.8 8.4 - - - +
324I CYS 3.2 0.8 - - - -
325I CYS* 1.3 78.4 - - - +
327I HIS* 1.3 68.7 + - + +
329I SER* 3.1 15.3 + - - +
330I LEU* 3.2 25.0 - - + +
355I GLU* 3.6 26.5 + - - +
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Residues in contact with HIS 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I ASP 5.8 0.4 + - - -
296I ALA 5.5 0.2 - - - -
297I ARG* 4.0 42.9 - - + +
300I CYS* 3.9 18.3 - - + +
301I GLU* 5.6 4.9 - - - -
323I ALA 4.2 14.8 + - - -
324I CYS* 2.8 9.1 + - + +
326I GLN* 1.3 89.0 - - - +
328I VAL* 1.3 66.0 - - - +
329I SER 3.1 1.5 + - - -
330I LEU* 3.2 17.4 + - + +
331I MET* 3.1 22.9 + - - +
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Residues in contact with VAL 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I ALA* 5.2 4.5 - - + -
300I CYS* 4.0 15.0 - - - -
320I LEU* 6.1 0.7 - - + -
324I CYS* 2.6 50.2 + - + +
325I CYS* 3.8 11.0 - - - +
327I HIS* 1.3 73.4 - - - +
329I SER* 1.3 60.8 + - - +
331I MET* 3.5 7.2 - - - +
332I LEU* 3.2 28.7 + - + +
341I LEU* 4.3 17.9 - - + -
343I LEU* 4.5 14.8 - - + -
356I LEU* 3.7 18.4 - - + -
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Residues in contact with SER 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I CYS 2.8 15.1 + - - -
326I GLN* 3.1 13.9 + - - +
328I VAL* 1.3 75.7 - - - +
330I LEU* 1.3 70.5 + - - +
332I LEU* 3.1 18.5 + - - +
333I THR* 3.2 19.5 + - - +
355I GLU* 3.7 19.4 + - - +
356I LEU* 4.2 3.6 - - - +
359I ALA* 3.3 24.8 - - - +
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Residues in contact with LEU 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I LEU* 4.8 5.1 - - + +
326I GLN* 3.2 33.8 + - + +
327I HIS* 3.2 18.4 + - + +
329I SER* 1.3 83.4 + - - +
331I MET* 1.3 64.3 + - - +
333I THR* 3.0 22.9 + - - +
334I GLN* 3.6 7.8 + - - +
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Residues in contact with MET 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300I CYS* 4.1 22.9 - - + +
303I LEU* 3.9 29.4 - - + -
304I LEU* 4.1 17.5 - - + +
327I HIS 3.1 8.9 + - - +
328I VAL* 3.5 14.1 - - - +
330I LEU* 1.3 79.9 - - - +
332I LEU* 1.3 74.7 + - + +
334I GLN* 3.1 4.3 + - - +
335I ASN* 2.9 72.2 + - + +
338I LEU* 3.4 30.7 - - + -
341I LEU* 6.2 1.3 - - - -
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Residues in contact with LEU 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328I VAL* 3.2 19.9 + - + +
329I SER* 3.1 11.2 + - - +
331I MET* 1.3 96.6 - - + +
333I THR* 1.3 58.3 + - - +
334I GLN 3.5 0.2 - - - -
335I ASN* 4.3 9.9 + - - +
338I LEU* 4.6 4.5 - - + +
341I LEU* 4.6 9.6 - - + -
356I LEU* 3.8 26.5 - - + -
359I ALA* 4.7 5.4 - - + -
360I LEU* 4.0 29.8 - - + +
365I THR* 4.4 12.9 - - - +
366I THR* 4.8 5.4 + - - -
367I LEU* 4.2 35.9 + - + -
370I LEU* 5.8 0.4 - - + -
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Residues in contact with THR 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329I SER 3.2 15.9 - - - +
330I LEU* 3.0 14.0 + - - +
331I MET 3.1 0.4 + - - -
332I LEU* 1.3 77.3 - - - +
334I GLN* 1.3 67.4 + - - +
335I ASN 5.3 0.2 - - - -
336I LYS* 3.4 18.2 + - - -
359I ALA* 3.4 34.8 - - + +
362I GLN* 4.6 12.8 - - + -
363I PRO 5.4 3.1 - - - +
365I THR* 4.7 11.0 + - - +
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Residues in contact with GLN 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I LEU* 4.0 21.7 - - + +
330I LEU 3.6 4.2 + - - +
331I MET 3.1 2.2 + - - +
333I THR* 1.3 87.3 + - - +
335I ASN* 1.3 61.5 + - - +
336I LYS* 3.3 22.7 + - - +
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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