Contacts of the helix formed by residues 339 - 351 (chain A) in PDB entry 3IQS
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 THR 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ILE 4.1 8.1 - - - +
338A MET* 1.3 73.9 - - - +
340A TYR* 1.3 69.0 + - - +
341A SER* 3.1 9.0 + - - -
342A GLU* 2.5 29.4 + - - -
343A PHE* 2.9 30.5 + - - -
368A SER* 3.1 22.2 - - - +
372A SER* 5.2 6.1 - - - +
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Residues in contact with TYR 340 (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 THR* 1.3 75.9 - - - +
341A SER* 1.3 65.8 + - - +
343A PHE* 3.5 2.9 + - - +
344A LYS* 3.0 62.2 + - + +
358A PHE* 3.6 20.9 + + - -
360A PRO* 3.3 37.8 - - + +
364A LEU* 3.7 14.7 - - + +
365A ASP* 4.0 19.2 + - - +
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Residues in contact with SER 341 (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 THR* 3.1 7.8 + - - -
340A TYR* 1.3 88.7 - - - +
342A GLU* 1.3 70.3 + - - +
344A LYS* 4.0 3.9 - - - +
345A HIS* 3.0 29.6 + - - +
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Residues in contact with GLU 342 (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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282A PHE* 3.9 11.9 - - + -
310A PHE* 3.5 44.0 - - + -
337A ILE 4.1 2.3 - - - +
338A MET* 3.7 24.4 - - + -
339A THR* 2.5 45.1 + - - +
341A SER* 1.3 81.8 - - - +
343A PHE* 1.3 64.7 - - - +
345A HIS* 3.4 6.0 + - - +
346A CYS* 3.0 28.9 + - - -
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Residues in contact with PHE 343 (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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202A PHE* 3.6 10.6 - + + -
206A PHE* 3.2 31.9 - - + -
208A ASN* 3.6 30.7 - - + -
312A ALA* 3.9 15.7 - - + -
338A MET* 3.5 47.1 - - + -
339A THR 2.9 26.4 + - - +
340A TYR 3.8 2.2 - - - +
342A GLU* 1.3 75.7 - - - +
344A LYS* 1.3 56.9 + - - +
346A CYS 3.4 1.0 + - - -
347A TRP* 2.9 28.4 + - - +
358A PHE* 3.8 22.0 - - + -
361A TRP* 4.0 11.9 - + - -
364A LEU* 3.6 22.9 - - + -
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Residues in contact with LYS 344 (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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340A TYR* 3.0 46.7 + - + +
341A SER* 4.0 4.5 - - - +
343A PHE* 1.3 72.8 - - - +
345A HIS* 1.3 65.7 + - - +
347A TRP* 3.2 2.1 + - - +
348A ASP* 2.9 49.5 + - - +
358A PHE* 3.6 34.7 - - + +
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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
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223A GLU* 2.6 38.1 + - - -
282A PHE* 3.7 24.7 - + - -
341A SER 3.0 19.8 + - - +
342A GLU* 3.6 7.9 - - - +
344A LYS* 1.3 75.6 - - - +
346A CYS* 1.3 60.0 + - - +
348A ASP* 3.2 6.7 + - - +
349A THR* 2.9 50.2 + - - -
350A PHE* 4.8 0.7 - + - -
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Residues in contact with CYS 346 (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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202A PHE* 3.9 17.5 - - + -
206A PHE* 5.2 1.1 - - + -
221A CYS* 4.8 7.2 - - - -
282A PHE* 3.2 50.0 - - - -
338A MET* 3.7 7.4 - - + -
342A GLU 3.0 21.1 + - - +
343A PHE 3.8 3.8 - - - +
345A HIS* 1.3 75.0 - - - +
347A TRP* 1.3 56.6 + - - +
350A PHE* 2.7 49.2 + - + +
351A VAL* 3.6 3.6 + - - +
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Residues in contact with TRP 347 (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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199A PRO* 4.0 21.5 - - + -
202A PHE* 3.4 34.2 - + + -
203A THR* 4.2 12.6 - - - -
343A PHE 2.9 13.8 + - - +
344A LYS 3.2 7.6 + - - +
346A CYS* 1.3 78.0 - - - +
348A ASP* 1.3 82.0 - - - +
351A VAL* 3.3 40.7 + - + +
353A HIS* 3.3 36.8 + - + +
356A CYS* 2.8 32.4 + - + -
357A PRO 4.1 6.3 - - - -
358A PHE* 3.6 37.1 - + + +
359A GLN 5.5 1.3 - - - -
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Residues in contact with ASP 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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344A LYS* 2.9 49.4 + - - +
345A HIS* 3.7 5.6 + - - +
347A TRP* 1.3 93.4 - - - +
349A THR* 1.3 61.6 + - - +
351A VAL 5.0 0.4 - - - +
353A HIS* 3.6 23.1 + - + -
357A PRO* 5.3 2.1 - - - +
358A PHE* 4.5 3.8 + - - +
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Residues in contact with THR 349 (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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223A GLU* 3.6 11.4 - - - +
239A ARG* 3.3 39.5 - - - +
345A HIS* 2.9 34.1 + - - -
348A ASP* 1.3 84.0 - - - +
350A PHE* 1.3 77.4 + - + +
351A VAL 3.7 1.6 - - - -
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Residues in contact with PHE 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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197A MET* 3.1 33.1 + - + +
202A PHE* 6.4 0.4 - - + -
221A CYS* 3.6 37.9 - - + -
222A TYR 3.5 17.9 - - - -
223A GLU* 3.6 21.1 - - + -
239A ARG* 4.1 10.1 - - + -
240A GLY* 3.3 40.2 - - - -
241A PHE* 4.4 9.6 - + + -
282A PHE* 4.4 10.1 - + - -
345A HIS* 4.8 0.7 - + - -
346A CYS* 2.7 29.9 + - + +
349A THR* 1.3 92.0 - - + +
351A VAL* 1.3 59.3 + - + +
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Residues in contact with VAL 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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197A MET* 3.4 15.0 - - + +
198A ASP 4.2 0.4 - - - -
199A PRO* 3.8 31.9 - - + -
202A PHE* 3.6 35.9 - - + -
346A CYS 3.8 1.8 - - - +
347A TRP* 3.3 40.7 + - + +
348A ASP 5.1 0.5 - - - +
349A THR 3.7 0.9 - - - -
350A PHE* 1.3 84.6 - - + +
352A ASP* 1.3 60.7 + - - +
353A HIS* 2.9 27.5 + - - +
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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