Contacts of the helix formed by residues 344 - 356 (chain A) in PDB entry 4OWT
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY* 3.5 7.4 - - - -
214A ARG* 2.9 30.9 + - - -
217A VAL* 4.3 13.7 - - - -
218A ASP* 2.6 31.0 + - - -
341A ASP 3.7 3.0 + - - -
343A GLN* 1.3 77.6 - - - +
345A LEU* 1.3 63.6 + - - +
346A ARG 3.2 0.9 + - - -
347A CYS* 3.5 18.3 + - - +
348A ASP* 3.7 4.2 - - - +
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Residues in contact with LEU 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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173A GLY* 3.5 27.4 - - - +
174A GLY* 4.6 0.9 - - - +
214A ARG* 3.6 4.5 - - - +
304A ARG 4.3 6.5 - - - +
309A MSE 3.9 38.1 - - + -
336A TYR* 4.1 26.7 - - + +
337A LEU* 4.2 3.1 - - + -
342A SER 3.0 15.5 + - - +
344A SER* 1.3 81.9 + - - +
346A ARG* 1.3 63.3 + - - +
348A ASP* 3.1 30.2 + - + +
349A LEU* 3.1 33.5 + - + +
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Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 4.1 22.4 + - + +
342A SER 4.2 0.6 + - - -
343A GLN* 2.9 49.7 + - - +
344A SER 3.2 0.4 - - - -
345A LEU* 1.3 78.7 - - - +
347A CYS* 1.3 58.5 + - - +
349A LEU* 3.2 12.8 + - - +
350A ILE* 2.9 47.8 + - + +
378A LEU* 2.9 39.8 + - + +
381A THR* 2.7 32.8 + - - -
382A CYS* 3.3 27.7 - - - -
387A ALA* 4.1 4.5 - - - +
391A ALA* 4.2 8.7 - - + -
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Residues in contact with CYS 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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214A ARG* 6.2 0.2 - - - +
256A ARG* 4.1 18.2 - - - +
260A ASN* 5.8 4.0 - - - +
343A GLN 5.6 1.3 - - - -
344A SER* 3.5 12.2 + - - +
345A LEU 3.2 0.4 - - - -
346A ARG* 1.3 76.2 - - - +
348A ASP* 1.3 66.9 + - - +
350A ILE* 3.8 3.5 - - - +
351A ARG* 3.0 30.9 + - - +
387A ALA 4.9 1.1 - - - -
390A ASN* 3.5 47.6 - - - -
391A ALA* 3.6 8.1 - - - -
394A ALA* 4.2 9.9 - - + -
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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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173A GLY* 4.9 0.9 - - - -
210A TYR* 5.4 2.1 + - - -
214A ARG* 2.6 51.4 + - - +
256A ARG* 4.8 12.3 + - - +
257A LEU* 5.5 0.9 - - - +
301A LEU 4.9 3.0 - - - +
304A ARG* 3.9 37.2 + - + +
305A LEU* 3.9 8.3 - - + +
344A SER 3.7 2.6 - - - +
345A LEU* 3.1 13.3 + - + +
347A CYS* 1.3 78.1 - - - +
349A LEU* 1.3 58.4 + - - +
351A ARG* 3.5 5.9 + - - +
352A TYR* 3.0 29.6 + - - +
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Residues in contact with LEU 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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305A LEU* 3.7 23.3 - - + -
309A MSE 4.5 4.3 - - + -
313A LEU* 3.8 23.3 - - + -
332A PHE* 3.7 33.0 - - + -
337A LEU* 4.3 8.1 - - + -
345A LEU* 3.1 33.0 + - + +
346A ARG* 3.2 6.9 + - - +
348A ASP* 1.3 75.0 - - - +
350A ILE* 1.3 59.8 + - - +
352A TYR* 3.3 5.0 + - - +
353A ILE* 2.8 36.2 + - - +
378A LEU* 4.0 28.7 - - + -
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Residues in contact with ILE 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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346A ARG* 2.9 28.6 + - + +
347A CYS* 3.8 5.6 - - - +
348A ASP 3.3 0.2 - - - -
349A LEU* 1.3 75.5 - - - +
351A ARG* 1.3 62.9 + - - +
353A ILE* 3.3 2.1 + - - +
354A CYS* 2.9 27.5 + - - +
375A ILE* 4.2 23.3 - - + -
378A LEU* 4.0 19.3 - - + -
379A LEU* 4.3 12.3 - - + -
391A ALA* 3.7 36.3 - - + +
394A ALA* 4.1 3.6 - - + -
395A LEU* 3.8 33.7 - - + +
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Residues in contact with ARG 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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253A ASP* 2.9 35.7 + - - -
256A ARG* 3.6 28.7 - - - +
296A THR* 5.5 1.0 - - - +
301A LEU* 4.0 30.2 - - + +
347A CYS 3.0 22.3 + - - +
348A ASP* 3.9 5.2 - - - +
350A ILE* 1.3 75.3 - - - +
352A TYR* 1.3 54.0 + - - +
354A CYS* 3.9 12.4 - - - +
355A GLY* 2.7 34.7 + - - -
394A ALA* 3.4 33.4 + - + +
395A LEU 5.2 1.4 + - - -
397A TYR* 4.1 10.2 - - - +
398A ASP* 3.2 41.9 + - - +
411A ASN* 5.2 1.2 + - - +
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Residues in contact with TYR 352 (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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301A LEU* 4.1 5.5 - - - +
302A ALA* 4.0 16.2 - - + -
305A LEU* 3.5 29.6 - - + -
310A GLU* 2.6 45.1 + - + +
313A LEU* 4.1 17.7 - - + -
314A LEU* 3.7 23.4 - - + +
348A ASP 3.0 17.8 + - - +
349A LEU 3.4 4.3 - - - +
351A ARG* 1.3 74.6 - - - +
353A ILE* 1.3 61.4 + - - +
356A VAL* 2.8 64.2 + - + +
357A VAL* 3.2 28.4 + - + -
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Residues in contact with ILE 353 (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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313A LEU* 4.0 33.2 - - + -
317A THR* 4.5 11.9 - - + -
349A LEU 2.8 26.4 + - - +
350A ILE 3.7 4.0 - - - +
352A TYR* 1.3 74.2 - - + +
354A CYS* 1.3 61.2 + - - +
357A VAL* 3.3 26.8 - - + +
371A ARG* 3.0 50.5 + - + +
374A ILE* 4.2 17.3 - - + -
375A ILE* 3.7 24.7 - - + -
378A LEU* 4.8 2.9 - - + -
414A PRO* 5.3 0.2 - - + -
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Residues in contact with CYS 354 (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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350A ILE* 2.9 26.7 + - - +
351A ARG* 3.9 15.3 - - - +
353A ILE* 1.3 79.1 - - - +
355A GLY* 1.3 57.5 + - - +
358A HIS* 3.0 20.3 - - - -
371A ARG* 3.3 10.6 + - - +
375A ILE* 4.4 4.9 - - - -
395A LEU* 4.1 28.9 - - - -
398A ASP* 5.1 0.7 - - - +
411A ASN* 3.5 29.0 - - - +
414A PRO* 4.0 21.5 - - - -
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Residues in contact with GLY 355 (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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298A ARG* 3.1 25.6 + - - +
301A LEU* 4.1 11.6 - - - +
351A ARG* 2.7 20.8 + - - -
354A CYS* 1.3 74.3 - - - +
356A VAL* 1.3 62.2 + - - +
358A HIS* 3.8 8.5 + - - -
398A ASP* 5.2 1.1 - - - -
411A ASN* 3.5 18.9 + - - -
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Residues in contact with VAL 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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298A ARG* 4.0 39.2 + - + +
301A LEU* 3.7 30.1 - - + -
302A ALA* 4.5 5.4 - - + +
310A GLU* 5.4 0.9 - - - +
314A LEU* 6.0 1.1 - - + -
352A TYR* 2.8 50.6 + - + +
355A GLY* 1.3 83.7 - - - +
357A VAL* 1.3 62.5 + - + +
358A HIS* 3.3 4.7 + - - +
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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