Contacts of the helix formed by residues 341 - 361 (chain A) in PDB entry 1ZDT
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 GLY 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLN 3.7 1.6 + - - -
340A ALA* 1.3 77.6 - - - +
342A SER* 1.3 66.1 + - - +
343A LEU 3.3 2.9 - - - -
344A LEU 4.1 1.3 - - - -
345A HIS* 3.1 20.0 + - - +
1001A PEF 2.8 27.2 + - - -
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Residues in contact with SER 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY* 1.3 71.7 - - - +
343A LEU* 1.3 62.4 + - - +
345A HIS* 3.9 3.6 - - - +
346A SER* 2.7 34.2 + - - -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY* 3.3 0.6 - - - -
342A SER* 1.3 83.2 - - - +
344A LEU* 1.3 65.2 + - - +
346A SER* 3.4 8.3 + - - +
347A LEU* 3.2 25.1 + - - +
435A GLU* 4.6 4.9 - - + +
436A TYR* 4.2 25.8 - - + +
439A HIS* 4.0 39.9 - - + +
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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
----------------------------------------------------------
340A ALA* 3.7 16.8 - - + -
341A GLY 3.6 2.0 + - - -
342A SER 3.5 0.2 - - - -
343A LEU* 1.3 80.1 - - - +
345A HIS* 1.3 62.1 + - - +
347A LEU* 3.2 4.7 + - + +
348A VAL* 3.1 39.5 + - + +
436A TYR* 3.7 23.2 - - + +
1001A PEF 3.2 108.5 + - + +
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Residues in contact with HIS 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU 4.7 1.6 + - - -
336A VAL* 3.5 27.9 - - + +
337A ALA* 3.5 35.4 + - + +
340A ALA* 4.0 10.1 + - + +
341A GLY 3.1 19.2 + - - +
342A SER* 3.9 3.6 - - - +
344A LEU* 1.3 78.6 - - - +
346A SER* 1.3 62.2 + - - +
348A VAL* 3.4 2.2 + - - +
349A LEU* 3.1 51.5 + - + +
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER* 2.7 24.8 + - - -
343A LEU* 3.7 9.3 + - - +
344A LEU 3.3 0.2 - - - -
345A HIS* 1.3 74.6 - - - +
347A LEU* 1.3 58.1 + - - +
349A LEU* 3.3 8.1 + - - +
350A ARG* 2.9 32.0 + - - +
432A GLN* 5.0 8.7 - - - -
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU 3.2 9.3 + - - +
344A LEU* 3.2 11.0 + - + +
346A SER* 1.3 81.4 - - - +
348A VAL* 1.3 58.1 + - - +
350A ARG* 3.4 1.8 + - - +
351A ALA* 3.0 29.7 + - - +
429A LEU* 3.6 32.5 - - + +
432A GLN* 3.8 27.1 - - + +
433A ALA* 3.6 23.3 - - + -
436A TYR* 4.2 15.0 - - + -
1001A PEF 3.7 41.5 - - + -
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Residues in contact with VAL 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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310A HIS* 5.7 2.6 + - - +
323A ILE* 4.7 13.9 - - + -
333A LEU* 3.6 32.1 - - + -
336A VAL* 4.0 18.8 - - + -
344A LEU* 3.1 34.9 + - + +
345A HIS 3.8 3.8 - - - +
347A LEU* 1.3 80.0 - - - +
349A LEU* 1.3 61.6 + - + +
351A ALA* 3.4 7.9 + - - +
352A GLN* 3.0 27.5 + - + +
1001A PEF 4.1 25.6 - - + -
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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
----------------------------------------------------------
333A LEU* 4.3 24.0 - - + -
345A HIS* 3.1 52.9 + - + +
346A SER* 3.7 5.6 - - - +
348A VAL* 1.3 78.8 - - + +
350A ARG* 1.3 64.9 + - - +
352A GLN* 3.1 17.0 + - + +
353A GLU* 3.1 20.0 + - - +
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Residues in contact with ARG 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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346A SER 2.9 17.8 + - - +
347A LEU* 3.8 1.6 - - - +
349A LEU* 1.3 76.2 - - - +
351A ALA* 1.3 61.6 + - - +
353A GLU* 3.2 34.4 + - - +
354A LEU* 3.3 7.8 + - - +
425A GLU* 3.0 35.1 + - - +
428A ALA* 3.8 23.1 + - - +
429A LEU* 3.5 21.2 - - + +
432A GLN* 3.3 41.1 - - - +
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Residues in contact with ALA 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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310A HIS* 4.5 5.8 - - - +
311A ILE* 3.4 17.3 - - + +
347A LEU 3.0 19.2 + - - +
348A VAL 3.4 6.1 - - - +
349A LEU 3.2 0.2 - - - -
350A ARG* 1.3 76.6 - - - +
352A GLN* 1.3 57.7 + - - +
354A LEU* 3.2 5.9 + - - +
355A VAL* 3.0 29.3 + - - +
429A LEU* 3.8 14.7 - - + +
1001A PEF 4.0 24.7 - - + -
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Residues in contact with GLN 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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310A HIS* 4.6 3.8 + - - -
314A GLN* 3.4 21.6 - - - +
319A LYS 4.4 8.3 + - - -
320A GLU* 4.5 9.4 + - + +
322A SER 4.3 8.9 + - - -
323A ILE* 3.0 34.6 - - + +
333A LEU* 4.4 14.4 - - + +
348A VAL* 3.0 23.2 + - + +
349A LEU* 3.1 12.5 + - + +
351A ALA* 1.3 77.2 - - - +
353A GLU* 1.3 62.6 + - - +
355A VAL* 3.2 15.1 + - - +
356A LEU* 3.1 24.3 + - - +
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.1 13.2 + - - +
350A ARG* 3.3 27.3 + - + +
352A GLN* 1.3 76.8 - - - +
354A LEU* 1.3 57.0 + - - +
356A LEU* 3.2 13.4 + - + +
357A GLN* 3.1 30.7 + - - +
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Residues in contact with LEU 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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311A ILE* 4.1 14.1 - - + -
350A ARG 3.3 8.1 + - - +
351A ALA 3.2 10.5 + - - +
353A GLU* 1.3 77.5 - - - +
355A VAL* 1.3 63.9 + - - +
357A GLN* 3.4 12.8 + - + +
358A LEU* 3.2 30.5 + - + +
422A CYS* 4.1 26.5 - - + +
425A GLU* 3.7 36.6 - - + -
426A VAL* 3.7 30.5 - - + +
429A LEU* 3.9 13.5 - - + -
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Residues in contact with VAL 355 (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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311A ILE* 3.9 19.7 - - + +
314A GLN* 3.4 51.4 - - + +
315A VAL* 3.9 10.7 - - + +
351A ALA 3.0 15.9 + - - +
352A GLN* 3.2 23.1 + - - +
354A LEU* 1.3 75.7 - - - +
356A LEU* 1.3 58.8 + - + +
358A LEU* 3.3 2.4 + - - +
359A LEU* 3.0 39.2 + - + +
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Residues in contact with LEU 356 (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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320A GLU* 3.5 33.2 - - + +
352A GLN 3.1 11.9 + - - +
353A GLU* 3.3 15.0 - - + +
355A VAL* 1.3 77.5 - - + +
357A GLN* 1.3 58.4 + - + +
359A LEU* 3.4 17.9 + - + +
360A ALA* 3.1 26.9 + - - +
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Residues in contact with GLN 357 (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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353A GLU 3.1 17.0 + - - +
354A LEU* 3.5 20.3 - - + +
355A VAL 3.2 0.2 - - - -
356A LEU* 1.3 77.4 - - - +
358A LEU* 1.3 61.8 + - - +
360A ALA* 3.2 8.8 + - - +
361A LEU* 3.1 31.6 + - + +
418A GLN 5.7 0.2 + - - -
421A LEU* 6.2 1.8 - - - +
422A CYS* 4.3 19.0 - - - +
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Residues in contact with LEU 358 (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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308A PHE* 4.6 12.6 - - + -
311A ILE* 3.5 32.8 - - + -
315A VAL* 4.1 7.6 - - + -
354A LEU* 3.2 22.0 + - + +
355A VAL 3.9 3.4 - - - +
357A GLN* 1.3 75.3 - - - +
359A LEU* 1.3 61.6 + - - +
361A LEU* 3.4 4.3 + - + -
362A GLN 3.3 3.8 + - - -
363A LEU* 3.0 53.2 + - + +
371A LEU* 5.7 1.3 - - + -
419A LEU* 3.9 22.4 - - + -
422A CYS* 3.5 31.6 - - + -
426A VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 359 (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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314A GLN 4.8 2.5 - - - +
315A VAL* 3.7 37.5 - - + +
318A GLY* 4.9 12.1 - - - -
355A VAL* 3.0 33.9 + - + +
356A LEU* 3.6 18.8 - - + +
357A GLN 3.2 0.2 - - - -
358A LEU* 1.3 77.1 - - - +
360A ALA* 1.3 57.0 + - - +
362A GLN* 3.1 21.0 + - - +
363A LEU* 4.9 2.5 - - - +
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Residues in contact with ALA 360 (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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356A LEU 3.1 14.7 + - - +
357A GLN* 3.2 10.7 + - - +
359A LEU* 1.3 75.9 - - - +
361A LEU* 1.3 61.5 + - + +
362A GLN* 3.2 6.7 + - - +
409A TYR* 3.8 9.9 + - - -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLN* 3.1 19.2 + - + +
358A LEU* 3.7 9.0 - - - +
359A LEU 3.2 0.6 - - - -
360A ALA* 1.3 79.4 - - + +
362A GLN* 1.3 58.8 + - - +
363A LEU 3.3 0.9 - - - +
409A TYR* 3.3 16.6 - - - +
415A LYS* 2.7 45.4 + - + -
418A GLN* 3.0 49.8 - - + +
419A LEU* 3.9 23.8 - - + -
422A CYS* 4.2 17.0 - - - -
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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
------------------------------------------------------------
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