Contacts of the helix formed by residues 333 - 347 (chain D) in PDB entry 5ZR1
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 SER 333 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A PHE* 3.7 22.1 - - - -
104D ARG 6.1 1.1 - - - -
105D GLN* 5.5 4.7 - - - -
278D ILE* 4.9 2.0 - - - -
284D MET* 4.6 1.3 - - - +
327D ASN* 2.9 21.8 + - - +
331D PHE* 3.3 4.1 - - - +
332D ARG* 1.3 78.9 - - - +
334D LEU* 1.3 62.6 + - - +
335D PRO* 4.4 8.7 - - - -
336D THR* 2.6 36.4 + - - -
183E CYS* 4.8 3.6 - - - -
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 3.5 36.3 - - + -
74D TYR* 4.8 7.0 - - + +
107D TYR* 4.1 4.5 - - - +
278D ILE* 4.5 15.4 - - + +
284D MET* 4.0 22.9 - - + +
287D ALA* 3.7 20.0 - - + -
288D VAL* 3.7 27.8 - - + -
291D LEU* 4.0 14.1 - - + -
327D ASN* 4.5 2.2 - - - +
332D ARG 4.3 0.2 - - - -
333D SER* 1.3 69.3 - - - +
335D PRO* 1.3 68.7 - - + +
336D THR 3.2 0.7 - - - -
337D LEU* 3.3 8.4 + - + -
338D LYS* 2.9 27.3 + - - +
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Residues in contact with PRO 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLN* 3.9 47.8 - - + +
107D TYR* 4.0 18.2 - - + +
333D SER* 3.8 6.7 - - - -
334D LEU* 1.3 92.0 - - + +
336D THR* 1.3 58.6 + - - +
338D LYS* 3.6 12.1 - - + +
339D ASN* 3.2 29.6 + - - -
2001D AGS 4.3 17.7 - - - +
183E CYS* 4.1 11.2 - - + +
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Residues in contact with THR 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A PHE* 4.2 5.2 - - + -
327D ASN* 4.5 4.9 - - - +
331D PHE* 4.1 32.8 - - + -
333D SER* 2.6 29.6 + - - -
334D LEU 3.2 1.2 - - - -
335D PRO* 1.3 74.3 - - - +
337D LEU* 1.3 65.2 + - - +
338D LYS 3.5 0.3 + - - -
339D ASN* 3.5 15.8 + - - +
340D SER* 3.4 14.8 + - - +
367D TYR* 5.2 2.3 - - + -
183E CYS* 3.2 18.7 - - - -
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Residues in contact with LEU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D MET* 4.5 4.7 - - + -
288D VAL* 3.8 30.7 - - + -
320D LEU* 6.0 1.3 - - + -
323D HIS* 4.3 24.9 - - + +
324D ILE* 3.9 19.7 - - + -
327D ASN* 3.3 24.5 - - + +
333D SER 3.7 2.2 + - - -
334D LEU* 3.3 13.8 + - + +
336D THR* 1.3 76.6 - - - +
338D LYS* 1.3 64.0 + - - +
340D SER* 3.1 23.7 + - - +
341D ILE* 3.1 35.9 + - + +
364D LEU* 5.0 2.9 - - + -
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Residues in contact with LYS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.2 43.0 - - + +
61D TYR* 5.5 2.1 - - - -
72D PHE* 4.9 2.0 - - - -
107D TYR* 2.9 34.2 + - - -
291D LEU* 4.1 30.0 - - + +
334D LEU* 2.9 17.4 + - - +
335D PRO* 3.6 10.4 - - + +
336D THR 3.2 0.4 - - - -
337D LEU* 1.3 78.3 - - - +
339D ASN* 1.3 62.4 + - - +
340D SER 3.4 0.5 + - - -
341D ILE* 3.6 4.2 + - - +
342D ILE* 3.2 31.5 + - + +
2001D AGS 3.8 26.0 + - - +
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Residues in contact with ASN 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TYR* 6.0 0.5 - - - -
335D PRO 3.2 15.9 + - - -
336D THR* 3.9 8.6 - - - +
337D LEU 3.3 0.6 - - - -
338D LYS* 1.3 79.0 - - - +
340D SER* 1.3 57.5 - - - +
342D ILE* 4.2 12.6 - - - +
343D PRO* 3.3 19.2 - - - +
367D TYR* 3.8 19.9 + - - +
21E TYR* 3.3 14.2 + - - +
183E CYS* 2.6 36.4 + - - +
184E ILE 4.3 0.6 + - - -
185E PRO* 4.0 25.6 - - + +
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Residues in contact with SER 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D THR* 3.4 10.8 + - - +
337D LEU* 3.1 21.2 + - - +
339D ASN* 1.3 78.6 - - - +
341D ILE* 1.3 63.7 + - - +
342D ILE 3.3 0.4 - - - -
343D PRO* 3.6 11.0 - - - +
344D LEU* 3.7 5.9 + - - +
363D PHE* 4.1 2.9 - - - -
364D LEU* 3.4 31.0 - - - +
367D TYR* 3.2 30.5 - - - -
368D ASN* 4.6 5.0 + - - -
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.9 23.3 - - + -
288D VAL* 5.9 4.0 - - + -
292D LEU* 4.0 28.5 - - + -
320D LEU* 4.3 17.5 - - + -
337D LEU* 3.1 30.4 + - + +
338D LYS* 3.6 5.1 + - - +
340D SER* 1.3 74.8 - - - +
342D ILE* 1.3 64.4 + - - +
344D LEU* 3.0 24.7 + - + +
345D VAL* 3.1 20.8 + - + +
358D ILE* 5.6 2.9 - - + -
364D LEU* 4.2 25.1 - - + -
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 3.6 18.8 - - + +
60D LEU* 3.7 37.0 - - + +
61D TYR* 3.4 43.1 - - + +
338D LYS* 3.2 23.0 + - + +
339D ASN* 4.4 10.5 - - - +
340D SER 3.3 1.2 - - - -
341D ILE* 1.3 78.6 - - - +
343D PRO* 1.3 66.7 - - + +
345D VAL 3.4 0.3 + - - -
346D ALA* 3.0 26.0 + - - +
20E SER* 4.3 9.2 - - - +
21E TYR* 4.0 13.0 - - + -
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Residues in contact with PRO 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ASN 3.3 21.5 - - - +
340D SER 3.6 3.6 - - - +
342D ILE* 1.3 87.1 - - + +
344D LEU* 1.3 55.8 + - - -
345D VAL 3.2 0.9 - - - -
346D ALA 4.1 2.0 - - - +
347D THR* 2.3 35.8 + - + -
363D PHE* 3.5 32.0 - - + -
367D TYR* 4.6 6.3 - - + -
17E CYS* 4.5 8.7 - - - -
20E SER* 3.3 26.0 - - - +
21E TYR* 3.7 17.5 - - + +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D TRP* 6.3 0.2 - - + -
340D SER 3.7 9.4 + - - +
341D ILE* 3.0 19.6 + - + +
343D PRO* 1.3 80.2 - - - +
345D VAL* 1.3 69.8 + - + +
347D THR* 4.4 2.1 + - - -
348D SER* 3.9 15.1 + - - -
354D LEU* 4.0 6.2 - - + +
357D ALA* 3.6 44.0 - - + +
358D ILE* 4.2 19.3 - - + +
361D CYS* 4.6 6.5 - - - -
363D PHE* 3.9 21.3 - - + -
364D LEU* 3.8 33.4 - - + -
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Residues in contact with VAL 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 6.5 0.2 - - + -
53D GLN* 3.1 34.7 + - + +
56D LEU* 3.7 35.4 - - + -
57D LEU* 4.7 11.0 - - + -
60D LEU* 4.6 1.6 - - + -
292D LEU* 5.3 0.7 - - + -
305D TRP* 5.6 2.9 - - + -
341D ILE* 3.1 27.4 + - + +
342D ILE 4.0 3.1 - - - +
344D LEU* 1.3 85.7 - - + +
346D ALA* 1.3 60.9 + - - +
347D THR 3.3 0.2 - - - -
348D SER* 2.6 22.2 + - - -
354D LEU* 3.9 20.4 - - + -
358D ILE* 6.2 0.4 - - + -
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLN* 4.0 15.7 + - - +
57D LEU* 4.0 23.3 - - + +
342D ILE 3.0 11.7 + - - +
345D VAL* 1.3 78.6 - - - +
347D THR* 1.3 58.3 + - - +
348D SER 3.2 3.3 + - - +
1E MET* 4.1 23.3 + - + +
20E SER* 3.3 29.5 - - - +
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Residues in contact with THR 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D PRO* 2.3 34.0 + - + +
344D LEU* 4.4 2.9 + - - -
345D VAL 3.3 0.4 - - - -
346D ALA* 1.3 77.5 - - - +
348D SER* 1.3 57.7 + - - +
349D LYS* 4.0 20.1 + - - +
363D PHE* 4.4 13.2 - - + -
16E ASN* 3.3 42.2 - - + +
17E CYS 4.8 0.2 - - - +
19E ALA 5.9 0.2 - - - -
20E SER* 3.9 11.9 - - - -
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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