Contacts of the helix formed by residues 326 - 347 (chain A) in PDB entry 1DGD
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.5 31.9 - - + -
320A VAL* 4.3 8.1 - - + -
321A VAL* 3.0 25.9 + - + +
324A ASP* 3.7 26.0 - - + +
325A GLY* 1.3 78.0 - - - +
327A VAL* 1.3 62.8 + - - +
329A ARG* 3.4 23.8 - - - +
330A ALA* 3.0 22.0 + - - +
411A LEU* 4.0 33.8 - - + +
412A THR* 4.2 16.4 - - + -
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY* 3.7 25.4 - - - +
253A GLY* 3.2 31.4 - - - +
254A THR* 3.4 13.2 - - - +
255A MET* 4.0 15.0 - - + +
321A VAL* 4.1 19.9 + - + +
322A GLN* 6.4 0.2 - - - -
325A GLY* 3.2 2.0 - - - -
326A LEU* 1.3 77.6 - - - +
328A ALA* 1.3 62.0 + - - +
330A ALA* 3.4 12.1 - - - +
331A ASN* 3.2 12.5 + - - +
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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
----------------------------------------------------------
325A GLY* 3.4 12.8 - - - +
327A VAL* 1.3 76.6 - - - +
329A ARG* 1.3 59.7 + - - +
331A ASN* 2.6 35.2 + - - +
332A VAL* 3.1 14.5 + - + +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ASP 5.1 2.9 - - - -
325A GLY 3.1 10.2 + - - +
326A LEU* 3.4 28.9 - - - +
328A ALA* 1.3 79.8 - - - +
330A ALA* 1.3 62.4 + - - +
332A VAL* 3.1 7.1 + - + -
333A MET* 2.8 59.4 + - + +
359A LEU* 5.6 0.2 - - - -
411A LEU 3.1 20.6 + - - +
412A THR* 3.5 9.6 + - - +
413A VAL 2.7 28.9 + - - -
414A SER* 4.1 10.1 - - - +
415A GLU* 4.8 2.4 - - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY 3.4 21.8 - - - +
251A ARG 4.1 9.2 - - - +
253A GLY 4.2 3.4 - - - +
326A LEU 3.0 13.2 + - - +
327A VAL 3.4 11.9 - - - +
328A ALA 3.0 0.2 - - - -
329A ARG* 1.3 77.8 - - - +
331A ASN* 1.3 57.6 + - - +
334A GLY* 3.1 24.1 + - - -
358A GLY* 3.8 6.1 - - - -
359A LEU* 3.8 16.5 - - + +
411A LEU* 3.9 15.0 - - + -
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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
----------------------------------------------------------
252A THR 4.2 0.3 - - - +
253A GLY* 3.2 35.9 + - - -
260A ARG* 3.8 15.5 + - - +
327A VAL* 3.2 14.3 + - - +
328A ALA* 2.6 21.8 + - - +
330A ALA* 1.3 70.9 - - - +
332A VAL* 1.3 60.8 + - + +
334A GLY* 3.8 0.6 - - - -
335A ASP* 2.9 29.3 + - - +
358A GLY* 4.8 6.0 - - - -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA 3.1 8.9 + - - +
329A ARG* 3.1 10.0 + - - +
331A ASN* 1.3 83.8 - - + +
333A MET* 1.3 82.5 + - + +
335A ASP* 3.2 8.5 + - - +
336A ARG* 3.1 24.8 + - - +
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Residues in contact with MET 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG* 2.8 61.2 + - + +
332A VAL* 1.3 91.7 - - + +
334A GLY* 1.3 57.0 + - - +
335A ASP 3.1 1.6 - - - -
336A ARG* 3.0 10.8 + - - +
337A LEU* 2.8 35.7 + - - +
359A LEU* 3.9 16.6 - - + -
413A VAL* 4.0 22.4 - - + +
414A SER 4.4 1.6 - - - +
415A GLU* 3.9 41.1 - - + +
418A ILE* 4.2 9.6 - - + +
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Residues in contact with GLY 334 (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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330A ALA 3.1 17.3 + - - -
331A ASN 4.0 0.4 - - - -
333A MET* 1.3 75.7 - - - +
335A ASP* 1.3 57.2 + - - +
337A LEU* 3.9 2.3 - - - +
338A ARG* 2.9 30.8 + - - +
358A GLY* 3.3 28.2 - - - +
359A LEU* 3.5 9.3 - - - +
361A LEU* 4.3 0.9 - - - +
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Residues in contact with ASP 335 (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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331A ASN 2.9 19.9 + - - +
332A VAL* 3.4 8.2 - - - +
333A MET 3.1 0.2 - - - -
334A GLY* 1.3 75.6 - - - +
336A ARG* 1.3 67.1 + - - +
338A ARG* 4.0 6.7 - - - +
339A ARG* 2.6 66.5 + - - +
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Residues in contact with ARG 336 (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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332A VAL 3.1 12.8 + - - +
333A MET* 3.0 15.2 + - - +
335A ASP* 1.3 82.1 + - - +
337A LEU* 1.3 65.4 + - - +
339A ARG* 3.2 10.3 + - - +
340A GLY* 3.2 15.1 + - - -
415A GLU* 2.7 45.5 + - - +
418A ILE* 3.6 21.8 - - + -
419A ASP* 2.6 49.6 + - - -
422A LEU* 4.6 2.9 - - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 4.7 11.7 - - + -
333A MET 2.8 18.1 + - - +
334A GLY* 3.9 5.2 - - - +
336A ARG* 1.3 71.8 - - - +
338A ARG* 1.3 64.0 + - - +
340A GLY* 3.0 3.6 + - - -
341A LEU* 2.9 37.5 + - + +
359A LEU* 4.4 4.9 - - + -
361A LEU* 3.5 23.1 - - + -
407A ILE* 3.9 24.0 - - + -
409A PRO* 4.3 12.1 - - + -
418A ILE* 3.4 30.7 - - + +
422A LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 5.3 1.0 + - - -
334A GLY 2.9 22.5 + - - +
335A ASP* 4.0 7.9 - - - +
337A LEU* 1.3 73.2 - - - +
339A ARG* 1.3 58.8 + - + +
341A LEU* 3.3 7.5 + - - +
342A LEU* 2.9 46.2 + - + +
354A VAL* 3.5 29.2 + - + +
355A ARG* 3.9 6.6 - - - +
356A GLY 3.0 36.4 + - - +
357A ARG* 5.9 0.8 - - - +
361A LEU* 4.3 17.2 - - + +
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Residues in contact with ARG 339 (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 ASP* 2.6 53.0 + - - +
336A ARG* 3.9 9.7 - - - +
338A ARG* 1.3 74.6 - - + +
340A GLY* 1.3 60.7 + - - +
342A LEU* 3.2 14.1 + - + +
343A ASP* 3.0 33.8 + - - +
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Residues in contact with GLY 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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336A ARG 3.2 6.4 + - - -
337A LEU 3.0 7.1 + - - -
339A ARG* 1.3 74.5 - - - +
341A LEU* 1.3 65.4 + - - +
343A ASP* 3.0 11.6 + - - +
344A LEU* 2.9 24.1 + - - +
422A LEU* 3.4 27.0 - - - +
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Residues in contact with LEU 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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337A LEU* 2.9 27.1 + - + +
338A ARG 3.6 7.2 - - - +
340A GLY* 1.3 77.4 - - - +
342A LEU* 1.3 63.2 + - - +
344A LEU* 3.3 7.7 + - + +
345A MET* 3.0 21.0 + - - +
351A ILE* 4.8 2.7 - - + +
354A VAL* 4.0 27.3 - - + +
361A LEU* 4.3 16.2 - - + -
363A VAL* 4.0 17.5 - - + -
407A ILE* 3.9 23.6 - - + -
422A LEU* 3.9 13.5 - - + -
425A LEU* 4.0 25.1 - - + -
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Residues in contact with LEU 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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338A ARG* 2.9 49.6 + - + +
339A ARG* 3.7 13.0 - - + +
340A GLY 3.0 0.4 - - - -
341A LEU* 1.3 78.8 - - - +
343A ASP* 1.3 65.7 + - - +
345A MET* 3.0 23.0 + - - +
346A GLU* 3.0 20.0 + - - +
354A VAL* 4.3 19.7 - - + +
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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
----------------------------------------------------------
339A ARG* 3.0 19.9 + - - +
340A GLY* 3.0 10.6 + - - +
342A LEU* 1.3 78.0 - - - +
344A LEU* 1.4 55.5 + - - +
346A GLU* 2.7 36.9 + - - +
347A ARG* 3.1 37.4 + - - +
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Residues in contact with LEU 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 GLY 2.9 15.8 + - - +
341A LEU* 3.7 17.0 - - + +
342A LEU 3.2 0.2 - - - -
343A ASP* 1.4 72.3 - - + +
345A MET* 1.3 59.7 + - - +
347A ARG* 2.7 28.9 + - + +
348A PHE* 2.9 28.6 + - + -
351A ILE* 3.7 17.0 - - + -
422A LEU* 4.1 20.9 - - + +
425A LEU* 3.4 35.0 - - + -
426A GLY* 3.9 23.1 - - - +
429A ILE* 4.7 2.7 - - + -
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Residues in contact with MET 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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341A LEU 3.0 10.2 + - - +
342A LEU* 3.0 25.9 + - - +
344A LEU* 1.3 76.5 - - - +
346A GLU* 1.3 55.2 + - - +
351A ILE* 3.4 44.4 - - + +
352A GLY 3.3 30.1 - - - +
353A ASP* 3.8 4.9 - - - +
354A VAL* 4.3 13.7 - - + -
369A ARG* 2.3 54.2 + - - +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU 3.0 9.3 + - - +
343A ASP* 2.7 23.7 + - - +
345A MET* 1.3 74.8 - - - +
347A ARG* 1.4 108.1 + - - +
349A ASP* 4.9 2.1 - - - +
369A ARG* 4.3 5.2 + - - +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASP* 3.2 46.1 + - - +
344A LEU* 2.7 19.0 + - + +
346A GLU* 1.4 125.4 + - - +
348A PHE* 1.3 77.5 + - + +
349A ASP* 4.0 5.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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