Contacts of the helix formed by residues 341 - 361 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ALA* 1.3 73.0 - - - +
342B SER* 1.3 59.8 + - - -
343B LEU 3.4 2.0 - - - -
344B LEU 3.5 2.1 + - - -
345B HIS* 2.9 32.7 + - - +
1002B PEF 2.8 29.4 + - - -
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY* 1.3 70.0 - - - +
343B LEU* 1.3 75.4 + - - +
345B HIS* 3.8 3.8 - - - +
346B SER* 3.0 26.3 + - - -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY 3.4 0.6 - - - -
342B SER* 1.3 90.1 - - - +
344B LEU* 1.3 58.6 + - - +
346B SER* 3.3 4.6 + - - -
347B LEU* 3.0 30.7 + - - +
432B GLN* 5.2 1.6 + - - -
435B GLU* 5.7 3.1 - - + +
436B TYR* 4.3 25.6 - - + +
439B HIS* 4.8 28.3 - - + +
1002B PEF 6.0 0.2 - - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL* 6.2 0.2 - - + -
340B ALA* 3.9 11.7 - - + -
341B GLY 3.5 3.1 + - - +
342B SER 3.4 0.4 - - - -
343B LEU* 1.3 76.2 - - - +
345B HIS* 1.3 66.3 - - - +
347B LEU* 3.3 5.1 + - + +
348B VAL* 3.0 41.3 + - + +
436B TYR* 3.8 24.0 - - + +
1002B PEF 3.2 107.2 + - + +
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU 5.0 1.0 + - - -
336B VAL* 3.6 30.2 - - + +
337B ALA* 3.6 35.5 + - + +
340B ALA* 4.1 7.5 - - + +
341B GLY 2.9 21.1 + - - +
342B SER* 3.8 5.4 - - - +
344B LEU* 1.3 77.4 - - - +
346B SER* 1.3 61.7 + - - +
348B VAL* 3.3 2.1 + - - +
349B LEU* 3.1 49.0 + - + +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER 3.0 20.1 + - - -
343B LEU* 3.6 4.2 + - - -
345B HIS* 1.3 73.5 - - - +
347B LEU* 1.3 66.2 + - - +
349B LEU* 3.5 8.9 + - - +
350B ARG* 3.1 26.9 + - - +
432B GLN* 3.6 15.2 + - - -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU 3.0 17.3 + - - +
344B LEU* 3.5 7.0 - - + +
346B SER* 1.3 74.8 + - - +
348B VAL* 1.3 66.3 + - - +
350B ARG* 3.3 2.8 + - - +
351B ALA* 3.0 24.9 + - - +
429B LEU* 3.5 29.8 - - + +
432B GLN* 3.4 41.9 - - + +
433B ALA* 3.6 24.2 - - + +
436B TYR* 4.1 15.5 - - + -
1002B PEF 3.6 33.9 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 5.6 2.4 + - - +
323B ILE* 4.3 23.1 - - + -
333B LEU* 3.8 28.3 - - + -
336B VAL* 4.3 16.8 - - + -
344B LEU* 3.0 33.2 + - + +
345B HIS 3.7 4.0 - - - +
347B LEU* 1.3 75.9 - - - +
349B LEU* 1.3 58.0 + - + +
351B ALA* 3.3 2.9 + - - +
352B GLN* 3.0 27.6 + - + +
1002B PEF 4.0 35.7 - - + -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.1 28.7 - - + +
345B HIS* 3.1 55.1 + - + +
346B SER* 3.9 7.0 - - - +
348B VAL* 1.3 75.0 - - + +
350B ARG* 1.3 63.4 + - - +
352B GLN* 3.3 9.1 + - + +
353B GLU* 3.1 27.1 + - - +
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B SER* 3.1 18.4 + - - +
347B LEU* 3.7 4.9 - - - +
349B LEU* 1.3 75.8 - - - +
351B ALA* 1.3 63.6 + - - +
353B GLU* 3.2 29.9 + - - +
354B LEU* 3.3 12.0 + - - +
425B GLU* 2.8 44.7 + - - +
428B ALA* 3.9 11.5 - - - +
429B LEU* 3.8 29.3 - - + +
432B GLN* 3.1 31.7 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B HIS* 4.4 6.7 - - + +
311B ILE* 3.4 18.4 - - + +
347B LEU 3.0 12.4 + - - +
348B VAL 3.5 9.0 - - - +
350B ARG* 1.3 77.7 - - - +
352B GLN* 1.3 57.5 + - - +
354B LEU 3.1 2.6 + - - -
355B VAL* 3.0 29.8 + - - +
429B LEU* 3.9 14.5 - - + +
1002B PEF 3.8 28.0 - - + -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 4.4 4.9 + - - -
314B GLN* 3.5 30.2 + - - +
319B LYS 4.5 5.1 + - - -
320B GLU* 4.3 15.3 + - - +
322B SER 4.3 9.3 + - - -
323B ILE* 3.5 27.3 - - + +
333B LEU* 4.5 14.1 - - + +
348B VAL 3.0 18.1 + - - +
349B LEU* 3.5 13.5 - - + +
350B ARG 3.3 0.2 - - - -
351B ALA* 1.3 78.5 - - - +
353B GLU* 1.3 60.6 + - + +
355B VAL* 3.4 14.4 + - - +
356B LEU* 3.2 24.0 + - - +
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 3.1 15.4 + - + +
350B ARG* 3.2 26.0 + - - +
352B GLN* 1.3 76.5 - - + +
354B LEU* 1.3 62.1 + - - +
356B LEU* 3.3 15.2 + - + +
357B GLN* 3.2 28.0 + - - +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ILE* 3.9 12.6 - - + -
350B ARG 3.3 7.4 + - - +
351B ALA 3.1 9.1 + - - +
353B GLU* 1.3 75.5 - - - +
355B VAL* 1.3 64.6 + - - +
356B LEU 3.2 0.4 - - - -
357B GLN* 3.5 26.5 + - - +
358B LEU* 3.0 33.5 + - + +
422B CYS* 4.0 27.1 - - + +
425B GLU* 4.0 19.7 - - + -
426B VAL* 3.7 25.8 - - + -
429B LEU* 3.7 24.9 - - + -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ILE* 3.7 22.2 - - + +
314B GLN* 3.5 49.1 - - + +
315B VAL* 3.9 10.7 - - - +
351B ALA* 3.0 14.2 + - + +
352B GLN* 3.4 24.2 - - - +
354B LEU* 1.3 75.2 - - - +
356B LEU* 1.3 58.6 + - + +
358B LEU* 3.4 2.3 + - - +
359B LEU* 3.0 40.6 + - + +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLU* 3.8 40.8 - - + +
352B GLN 3.2 13.3 + - - +
353B GLU* 3.4 16.2 - - + +
354B LEU 3.2 0.6 - - - -
355B VAL* 1.3 77.2 - - + +
357B GLN* 1.3 58.0 + - - +
359B LEU* 3.3 18.9 + - + +
360B ALA* 2.9 29.7 + - - +
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Residues in contact with GLN 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B GLU* 3.2 13.1 + - - +
354B LEU* 3.5 33.3 - - + +
356B LEU* 1.3 77.2 - - - +
358B LEU* 1.3 57.6 + - - +
360B ALA* 3.1 8.6 + - - +
361B LEU* 2.9 36.8 + - + +
421B LEU* 5.8 5.2 - - - +
422B CYS* 3.7 21.7 - - - -
425B GLU* 4.7 10.4 - - - +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PHE* 4.5 13.9 - - + -
311B ILE* 3.4 33.2 - - + -
315B VAL* 4.0 13.0 - - + +
354B LEU* 3.0 25.0 + - + +
355B VAL 3.4 3.6 + - - +
357B GLN* 1.3 79.1 - - - +
359B LEU* 1.3 57.0 + - - +
361B LEU* 3.4 4.0 + - + +
362B GLN 3.1 6.9 + - - -
363B LEU* 3.0 52.4 + - + +
371B LEU* 5.6 1.1 - - + -
419B LEU* 4.0 22.0 - - + -
422B CYS* 3.7 30.1 - - + -
426B VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B VAL* 3.6 38.1 - - + +
318B GLY* 4.9 14.4 - - - -
320B GLU* 6.3 1.3 - - + -
355B VAL* 3.0 34.2 + - + +
356B LEU* 3.6 20.9 - - + +
358B LEU* 1.3 72.3 - - - +
360B ALA* 1.3 65.1 + - - +
362B GLN* 3.2 17.9 + - - +
363B LEU 5.1 0.2 - - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU 2.9 17.3 + - - +
357B GLN* 3.1 8.3 + - - +
359B LEU* 1.3 78.4 - - - +
361B LEU* 1.3 60.8 + - + +
362B GLN* 3.2 11.7 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLN* 2.9 23.2 + - + +
358B LEU* 3.9 6.5 - - + +
360B ALA* 1.3 75.5 - - + +
362B GLN* 1.3 63.9 + - - +
363B LEU 4.7 1.3 - - - +
415B LYS* 2.9 37.3 + - + +
418B GLN* 3.8 36.1 - - + +
419B LEU* 4.2 18.2 - - + -
422B CYS* 3.7 29.8 - - - -
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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