Contacts of the helix formed by residues 355 - 369 (chain B) in PDB entry 1EZF
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 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B TYR* 4.7 0.9 + - - -
257B GLN 4.8 1.2 + - - -
260B ASN 4.7 0.4 - - - -
261B GLU* 3.4 31.2 + - - +
264B THR* 4.1 8.7 - - - -
353B ASP* 2.9 11.8 + - - -
354B PRO* 1.3 79.8 - - - +
356B SER* 1.3 53.8 + - - +
357B SER 2.6 4.9 + - - -
358B LYS* 2.6 56.5 + - - +
359B THR* 3.0 17.9 + - - -
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 5.3 0.2 - - - -
349B ILE* 3.6 17.6 - - - +
350B PRO 3.4 22.2 - - - -
351B ASP 3.6 10.0 + - - -
353B ASP* 2.7 29.6 + - - -
354B PRO 4.9 0.2 - - - -
355B SER* 1.3 74.5 - - - +
357B SER* 1.3 58.3 + - - -
359B THR* 3.6 5.5 + - - -
360B ARG* 3.0 48.6 + - - +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PRO 5.2 2.2 + - - -
355B SER 2.6 5.8 + - - -
356B SER* 1.3 76.3 + - - +
358B LYS* 1.3 67.5 + - - -
360B ARG* 3.2 13.7 + - - +
361B GLN* 3.0 23.8 + - - +
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 5.4 0.8 - - - +
261B GLU* 3.7 26.8 + - + +
264B THR* 3.7 15.9 - - + +
268B HIS* 5.1 4.8 - - + -
354B PRO* 4.2 8.9 + - - +
355B SER* 2.6 42.4 + - - +
357B SER* 1.3 74.8 + - - +
359B THR* 1.3 62.7 + - - +
361B GLN* 3.1 12.3 + - - +
362B ILE* 3.0 24.3 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASN 4.7 0.5 + - - -
264B THR* 2.7 31.0 + - - +
267B LEU* 4.4 9.2 - - + -
304B TYR* 4.2 12.5 + - + +
345B ILE* 4.0 21.1 - - + -
349B ILE* 3.8 21.5 - - + -
353B ASP* 4.9 0.7 + - - -
355B SER* 3.0 15.3 + - - -
356B SER* 3.7 10.1 + - - -
358B LYS* 1.3 77.2 - - - +
360B ARG* 1.3 61.7 + - - +
362B ILE* 3.1 16.4 - - - +
363B ILE* 3.2 17.8 + - + +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B TYR* 4.0 30.0 + - + +
349B ILE* 3.7 41.2 + - + +
351B ASP* 3.4 28.9 + - - +
356B SER* 3.0 42.5 + - - +
357B SER* 3.2 11.2 + - - +
359B THR* 1.3 75.7 - - - +
361B GLN* 1.3 57.8 + - - +
363B ILE* 3.9 1.6 - - - +
364B SER* 2.9 35.9 + - - +
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 5.5 7.4 + - - +
357B SER* 3.0 14.1 + - - +
358B LYS* 3.1 12.5 + - - +
360B ARG* 1.3 77.8 - - - +
362B ILE* 1.3 63.1 + - - +
364B SER* 3.4 6.6 + - - -
365B THR* 3.0 32.0 + - - +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 4.1 11.9 - - + -
267B LEU* 3.9 40.4 - - + +
268B HIS* 3.7 44.8 + - + +
271B PRO* 4.8 3.8 - - + -
358B LYS 3.0 15.8 + - - +
359B THR* 3.1 25.1 - - - +
361B GLN* 1.3 75.9 - - - +
363B ILE* 1.3 63.7 + - + +
365B THR* 3.0 25.9 + - + -
366B ILE* 3.0 28.0 + - + +
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.5 1.8 - - + -
342B MET* 3.4 50.9 - - + +
343B GLU* 4.5 1.6 - - - +
345B ILE* 4.0 16.4 - - + -
346B TYR* 3.8 39.7 - - + +
349B ILE* 4.3 0.2 - - + -
359B THR* 3.2 23.2 + - + +
360B ARG 3.9 3.1 - - - +
362B ILE* 1.3 80.2 - - + +
364B SER* 1.3 63.6 + - - +
366B ILE* 3.0 11.8 + - - +
367B ARG* 2.9 37.7 + - + +
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 5.4 14.4 - - - -
45A LYS* 5.9 1.2 - - - +
346B TYR* 4.9 1.7 + - - -
360B ARG* 2.9 25.7 + - - +
361B GLN* 3.7 7.2 - - - -
362B ILE 3.3 0.2 - - - -
363B ILE* 1.3 75.8 - - - +
365B THR* 1.3 61.5 + - - +
367B ARG* 3.2 28.9 + - - +
368B THR* 3.1 31.3 + - - +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.3 16.9 + - - +
271B PRO* 4.9 1.8 - - + -
361B GLN* 3.0 21.2 + - - +
362B ILE* 3.0 26.4 + - + +
364B SER* 1.3 75.3 - - - +
366B ILE* 1.3 59.5 + - + +
368B THR* 4.0 5.5 + - - -
369B GLN* 2.9 48.2 + - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.4 2.2 - - + +
270B ILE* 3.8 25.4 - - + -
271B PRO* 3.6 37.5 - - + -
274B ILE* 4.3 6.1 - - + -
338B ILE* 5.1 0.9 - - + -
339B TYR* 3.7 34.8 + - + -
342B MET* 4.3 22.2 - - + -
362B ILE* 3.2 27.6 - - + +
363B ILE* 3.0 10.2 + - - +
365B THR* 1.3 74.8 - - - +
367B ARG* 1.3 65.5 + - - +
369B GLN* 3.1 20.7 - - - +
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Residues in contact with ARG 367 (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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44A TYR* 4.0 12.5 - - + -
45A LYS* 4.7 14.4 - - - +
48A ASN* 3.3 27.4 - - - +
59A GLN* 3.7 25.7 - - - +
66A ARG* 2.6 32.7 + - - -
339B TYR* 5.0 1.5 - - + -
342B MET* 6.2 1.1 - - + -
343B GLU* 2.9 42.6 + - - +
346B TYR* 3.1 50.6 + - - -
363B ILE* 2.9 21.4 + - + +
364B SER* 3.2 35.5 + - - +
366B ILE* 1.3 77.1 - - - +
368B THR* 1.3 57.0 + - + +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.7 12.7 - - - +
41A LYS* 3.2 56.9 - - + +
44A TYR* 3.4 31.1 - - + -
66A ARG* 2.8 15.0 + - - +
67A ASN* 5.5 0.3 - - - +
364B SER* 3.1 17.1 + - - +
365B THR* 4.0 3.6 + - - -
367B ARG* 1.3 71.2 - - + +
369B GLN* 1.3 64.8 + - - +
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Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 3.5 5.6 + - - -
271B PRO* 3.3 50.5 - - - +
274B ILE* 4.3 14.6 - - - +
339B TYR* 5.4 0.2 - - - +
365B THR* 2.9 37.9 + - + +
366B ILE* 3.1 16.3 - - - +
367B ARG 3.2 2.6 - - - -
368B THR* 1.3 84.0 - - - +
370B ASN* 1.3 71.4 + - + +
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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