Contacts of the helix formed by residues 355 - 368 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A TYR* 4.7 0.2 + - - -
257A GLN 4.9 0.2 + - - -
260A ASN 4.7 0.2 - - - -
261A GLU* 3.4 27.5 + - - +
264A THR* 4.2 8.7 - - - -
353A ASP* 3.0 14.7 + - - -
354A PRO* 1.3 79.6 - - - +
356A SER* 1.3 64.7 + - - +
357A SER* 3.3 2.7 - - - -
358A LYS* 2.8 47.5 + - - +
359A THR* 2.9 22.7 + - - -
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Residues in contact with SER 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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304A TYR* 5.7 0.2 - - - -
349A ILE* 3.8 14.7 - - - +
350A PRO 2.4 30.7 + - - -
351A ASP 3.5 10.9 - - - -
353A ASP* 2.7 27.6 + - - +
354A PRO 3.5 0.6 - - - -
355A SER* 1.3 76.0 - - - +
357A SER* 1.3 63.9 + - - +
359A THR* 3.6 1.6 + - - -
360A ARG* 3.1 44.9 + - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PRO 5.2 1.3 + - - -
355A SER 3.1 1.0 + - - -
356A SER* 1.3 77.5 - - - +
358A LYS* 1.3 60.2 + - - +
360A ARG* 3.4 16.0 + - - +
361A GLN* 3.0 31.7 + - - +
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Residues in contact with LYS 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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261A GLU* 3.9 22.8 + - + +
264A THR* 3.8 17.4 - - + +
268A HIS* 5.2 2.6 - - + -
354A PRO* 4.5 8.2 + - - +
355A SER* 2.8 43.0 + - - +
357A SER* 1.3 71.5 - - - +
359A THR* 1.3 65.9 + - - +
361A GLN* 3.1 7.2 + - - +
362A ILE* 3.1 23.4 + - - +
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Residues in contact with THR 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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260A ASN 4.7 0.3 + - - -
263A ILE* 5.9 0.4 - - + -
264A THR* 2.7 30.8 + - - +
267A LEU* 4.1 18.6 - - + -
304A TYR* 4.4 12.9 + - + -
345A ILE* 4.2 12.6 - - + -
349A ILE* 3.7 26.9 - - + -
353A ASP* 4.9 0.7 + - - -
355A SER* 2.9 19.7 + - - -
356A SER* 3.9 2.9 + - - -
358A LYS* 1.3 75.7 - - - +
360A ARG* 1.3 62.5 + - - +
362A ILE* 3.1 6.0 - - - +
363A ILE* 3.1 26.5 + - + +
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Residues in contact with ARG 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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346A TYR* 4.1 28.7 + - + -
349A ILE* 3.7 35.2 + - + +
351A ASP* 3.0 52.2 + - - +
356A SER* 3.1 39.6 + - - +
357A SER* 3.7 13.0 + - - +
358A LYS 3.2 0.2 - - - -
359A THR* 1.3 75.8 - - - +
361A GLN* 1.3 58.6 + - + +
363A ILE* 3.3 4.0 + - - +
364A SER* 2.9 33.3 + - - +
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Residues in contact with GLN 361 (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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357A SER 3.0 18.1 + - - +
358A LYS* 3.1 6.2 + - - +
360A ARG* 1.3 74.9 - - + +
362A ILE* 1.3 65.6 + - - +
364A SER* 3.3 12.0 + - - -
365A THR* 3.0 27.9 + - - -
38C ASN* 5.9 4.0 + - - +
41C LYS* 2.8 35.9 + - - +
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Residues in contact with ILE 362 (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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264A THR* 4.3 2.2 - - + -
267A LEU* 3.8 39.7 - - + +
268A HIS* 3.7 54.3 - - + +
271A PRO* 5.2 1.6 - - + -
358A LYS 3.1 10.2 + - - +
359A THR* 3.1 15.9 - - - +
361A GLN* 1.3 75.3 - - - +
363A ILE* 1.3 61.3 + - - +
365A THR* 3.2 13.7 + - + +
366A ILE* 3.0 49.2 + - + +
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Residues in contact with ILE 363 (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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267A LEU* 4.2 6.1 - - + -
342A MET* 3.4 45.1 - - + +
343A GLU* 4.0 17.5 - - - +
345A ILE* 3.9 15.3 - - + -
346A TYR* 3.8 40.6 - - + +
349A ILE* 4.3 3.8 - - + -
359A THR* 3.1 20.2 + - + +
360A ARG 3.6 4.0 - - - +
361A GLN 3.2 0.2 - - - -
362A ILE* 1.3 76.3 - - - +
364A SER* 1.3 58.5 + - - +
366A ILE* 3.2 8.2 + - - +
367A ARG* 2.9 34.6 + - + +
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Residues in contact with SER 364 (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 TYR* 5.2 2.4 - - - -
360A ARG* 2.9 19.9 + - - +
361A GLN* 3.7 13.6 + - - -
363A ILE* 1.3 77.1 - - - +
365A THR* 1.3 62.8 + - - +
367A ARG* 3.4 25.3 + - - +
368A THR* 3.0 29.3 + - - +
41C LYS* 4.0 29.3 + - - +
45C LYS* 5.9 0.2 - - - +
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Residues in contact with THR 365 (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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271A PRO* 5.0 1.3 - - + -
361A GLN* 3.0 17.1 + - - -
362A ILE* 3.3 20.5 - - + +
363A ILE 3.2 0.2 - - - -
364A SER* 1.3 78.6 - - - +
366A ILE* 1.3 69.7 + - + +
368A THR* 3.3 4.9 + - - -
369A GLN* 3.1 56.5 + - - +
41C LYS* 3.8 16.7 + - - +
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Residues in contact with ILE 366 (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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267A LEU 4.4 0.4 - - - +
270A ILE* 3.7 25.1 - - + -
271A PRO* 3.4 39.0 - - + -
274A ILE* 4.7 3.3 - - + +
338A ILE* 5.0 0.2 - - + -
339A TYR* 3.6 34.4 + - + -
342A MET* 4.0 31.0 - - + -
362A ILE* 3.0 31.7 + - + +
363A ILE* 3.6 5.6 - - - +
365A THR* 1.3 76.4 - - + +
367A ARG* 1.3 62.6 + - - +
368A THR 3.5 0.2 + - - -
369A GLN* 3.5 12.1 + - - +
370A ASN 4.6 0.5 + - - -
66C ARG* 3.6 2.4 + - - -
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Residues in contact with ARG 367 (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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339A TYR* 4.9 1.6 - - + -
342A MET* 6.2 1.6 - - + -
343A GLU* 2.8 41.0 + - - +
346A TYR* 3.5 42.4 - - - -
363A ILE* 2.9 22.2 + - + +
364A SER* 3.4 21.7 + - - +
365A THR 3.2 0.2 - - - -
366A ILE* 1.3 79.3 - - + +
368A THR* 1.3 61.1 + - + +
41C LYS 5.0 1.4 + - - -
44C TYR* 3.5 23.5 - - + -
45C LYS* 3.5 30.9 - - - +
48C ASN* 3.2 22.7 - - - +
59C GLN* 3.8 19.8 - - - +
66C ARG* 2.5 23.5 + - - -
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A SER* 3.0 18.2 + - - +
365A THR* 3.8 2.8 + - - -
367A ARG* 1.3 78.1 - - + +
369A GLN* 1.3 60.5 + - - +
40C LEU* 4.0 16.2 - - - +
41C LYS* 3.5 41.6 - - + +
44C TYR* 3.3 39.0 - - + -
66C ARG* 3.5 6.0 + - - +
67C ASN* 5.7 0.5 - - - +
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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