Contacts of the helix formed by residues 347 - 361 (chain A) in PDB entry 2CXQ
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 ARG 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LEU* 4.8 9.4 - - + +
165A LEU* 3.6 24.5 - - + +
166A MET* 3.4 29.8 + - + +
169A GLU* 4.6 2.0 - - + -
344A TYR 4.7 0.8 + - - -
345A MET 3.1 0.8 - - - -
346A HIS* 1.3 122.0 + - + +
348A PHE* 1.3 59.1 + - - +
349A ALA 3.4 2.2 - - - -
350A ALA* 3.4 23.6 + - - +
351A TYR* 3.0 24.1 + - - +
382A GLU* 4.9 6.9 + - - -
347B ARG* 4.0 19.3 - - - +
382B GLU* 2.9 38.4 + - - -
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Residues in contact with PHE 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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166A MET* 3.6 26.9 - - + +
338A LEU* 4.6 9.6 - - + -
340A PRO* 4.4 9.9 - - + -
345A MET* 3.0 48.6 + - + +
347A ARG* 1.3 74.1 - - - +
349A ALA* 1.3 68.3 + - - +
351A TYR* 3.2 3.8 + - - +
352A PHE* 3.2 53.9 + + - -
407A LEU* 4.3 17.9 - - + -
487A LEU* 4.5 7.2 - - + -
490A LEU* 4.8 9.2 - - + -
491A ILE* 4.3 15.5 - - + -
494A TYR* 3.9 26.5 - + - -
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Residues in contact with ALA 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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338A LEU* 3.7 37.2 - - + +
340A PRO* 5.0 5.2 - - + +
345A MET 4.5 1.2 + - - -
346A HIS 5.1 2.8 + - - +
347A ARG 3.4 0.4 - - - -
348A PHE* 1.3 79.0 - - - +
350A ALA* 1.3 56.6 + - - +
352A PHE* 3.3 2.6 + - - +
353A GLN* 2.8 29.4 + - - +
379A VAL* 4.3 4.3 - - - +
380A TRP* 4.3 2.7 - - - -
381A GLY* 3.7 31.6 - - - +
382A GLU* 5.2 0.7 - - - -
383A PRO* 6.3 0.7 - - + -
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Residues in contact with ALA 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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162A LEU* 3.4 19.4 - - + +
346A HIS 5.4 0.6 + - - +
347A ARG* 3.4 45.4 + - - +
348A PHE 3.3 0.4 - - - -
349A ALA* 1.3 78.8 - - - +
351A TYR* 1.3 63.9 + - - +
353A GLN* 3.2 15.5 - - - +
354A GLN* 3.2 16.6 + - - +
381A GLY 5.4 0.2 + - - -
382B GLU* 3.9 10.5 - - + +
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Residues in contact with TYR 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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162A LEU* 3.7 15.7 - - + +
163A GLY* 3.3 39.0 - - - -
166A MET* 3.7 25.4 - - + -
273A ARG* 3.3 28.3 + - + -
274A TYR* 4.7 1.6 - - - -
275A SER 5.2 0.3 + - - -
276A LEU* 3.4 20.6 + - + +
347A ARG 3.0 14.5 + - - +
348A PHE 3.2 8.0 + - - +
350A ALA* 1.3 77.2 - - - +
352A PHE* 1.3 93.8 + + - +
354A GLN* 3.2 10.9 + - + +
355A GLY* 2.9 22.1 + - - -
491A ILE* 4.0 9.2 - - + -
495A GLU* 4.2 10.0 + - - -
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Residues in contact with PHE 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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338A LEU* 3.7 21.8 - - + -
348A PHE* 3.2 48.6 + + - +
351A TYR* 1.3 97.2 - + - +
353A GLN* 1.3 61.5 + - - +
354A GLN 3.2 0.4 - - - -
355A GLY* 3.6 5.8 - - - +
356A ASP* 2.8 36.9 + - + +
379A VAL* 4.0 4.5 - - + +
491A ILE* 3.4 31.4 - - + -
494A TYR* 3.3 33.2 - + + -
495A GLU* 4.0 14.8 - - + -
498A ILE* 3.8 22.4 - - + -
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Residues in contact with GLN 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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349A ALA 2.8 15.3 + - - +
350A ALA* 3.2 17.6 - - - +
352A PHE* 1.3 76.9 - - - +
354A GLN* 1.3 58.8 + - - +
357A MET* 3.1 43.4 + - - +
379A VAL* 2.9 36.4 + - - +
380A TRP* 4.1 9.5 - - - +
380B TRP* 3.5 23.5 - - - +
381B GLY 5.0 2.6 + - - +
382B GLU* 3.6 26.6 - - - +
390B ALA 4.0 1.1 - - - +
391B PHE* 3.6 21.3 - - + +
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Residues in contact with GLN 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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158A GLY* 3.5 18.3 - - - +
159A GLY* 3.3 13.4 - - - +
162A LEU* 3.8 19.7 - - + +
273A ARG* 4.0 14.5 - - + +
350A ALA 3.2 8.5 + - - +
351A TYR* 3.4 10.2 - - + +
352A PHE 3.2 0.4 - - - -
353A GLN* 1.3 78.7 - - - +
355A GLY* 1.3 67.1 + - - +
358A GLU* 2.8 56.0 + - - +
1601A S6P 3.2 20.4 + - - -
389B HIS 3.2 3.8 + - - -
390B ALA* 3.2 29.6 - - + +
391B PHE* 5.5 0.2 - - - -
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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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273A ARG* 4.0 19.7 - - - -
274A TYR* 4.2 2.8 + - - -
351A TYR* 2.9 20.6 + - - -
352A PHE* 3.4 11.4 + - - -
354A GLN* 1.3 75.1 - - - +
356A ASP* 1.3 56.6 + - - +
359A SER* 2.6 31.9 + - - -
498A ILE* 3.9 10.0 - - - +
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Residues in contact with ASP 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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336A HIS* 5.5 1.6 - - - -
352A PHE* 2.8 24.7 + - + +
355A GLY* 1.3 71.3 - - - +
357A MET* 1.3 59.2 + - - +
359A SER* 3.1 2.9 + - - -
360A ASN* 2.9 37.9 + - - +
376A GLY* 4.7 0.2 - - - -
377A PRO* 3.8 23.7 - - - +
379A VAL* 3.6 25.6 - - + +
497A LYS* 4.7 11.8 + - - +
498A ILE* 3.7 28.3 - - + +
501A GLN* 4.5 7.1 - - - +
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Residues in contact with MET 357 (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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353A GLN* 3.1 38.0 + - - +
356A ASP* 1.3 76.6 - - - +
358A GLU* 1.3 57.8 + - - +
360A ASN 5.3 0.2 - - - -
361A GLY* 2.9 28.5 + - - +
376A GLY* 6.1 0.4 - - - -
377A PRO 3.4 17.7 - - - +
378A ILE* 3.8 16.6 - - + -
379A VAL* 3.5 24.9 - - + +
380B TRP* 3.7 26.2 - - + -
390B ALA 4.6 0.2 - - - -
391B PHE* 3.8 18.6 - - + +
393B GLN* 4.1 0.2 - - - +
394B LEU* 3.6 41.9 + - + +
395B ILE* 5.5 0.2 - - + -
402B ILE* 5.2 0.2 - - + -
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Residues in contact with GLU 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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273A ARG* 2.7 35.8 + - - +
354A GLN* 2.8 48.4 + - - +
357A MET* 1.3 76.8 - - - +
359A SER* 1.3 61.4 + - - +
362A LYS* 3.4 9.0 + - - -
511A ASP 3.8 0.7 - - - +
512A GLN* 3.4 10.0 - - + +
515A VAL* 3.9 7.7 - - + +
1601A S6P 2.9 20.6 - - - -
389B HIS 3.0 12.5 - - - +
390B ALA 3.3 10.2 + - - +
393B GLN* 3.4 34.3 - - + +
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Residues in contact with SER 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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273A ARG* 2.8 17.1 + - - +
274A TYR* 2.8 15.1 + - - -
355A GLY 2.6 25.0 + - - -
356A ASP 3.1 1.4 + - - -
358A GLU* 1.3 79.9 - - - +
360A ASN* 1.3 65.6 + - - +
362A LYS* 2.8 25.5 + - - +
498A ILE* 3.5 20.4 - - - -
509A SER* 3.2 24.1 + - - -
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Residues in contact with ASN 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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356A ASP* 2.9 17.6 + - - +
359A SER* 1.3 76.8 - - - +
361A GLY* 1.3 59.7 + - - +
362A LYS* 2.9 9.5 + - - -
375A THR* 3.3 6.4 + - - -
376A GLY* 3.0 27.1 + - - -
498A ILE* 3.0 39.3 + - - +
501A GLN* 4.0 6.3 + - - +
502A GLY* 3.8 6.4 - - - +
505A TRP* 3.8 22.9 - - + -
507A ILE* 3.6 15.4 - - + +
509A SER* 2.7 25.5 + - - -
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Residues in contact with GLY 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 MET 2.9 20.8 + - - -
359A SER 3.6 1.0 - - - -
360A ASN* 1.3 72.2 - - - +
362A LYS* 1.3 59.3 + - - +
375A THR* 4.7 1.1 - - - -
376A GLY 4.9 0.2 - - - -
393B GLN* 3.0 32.4 - - - +
394B LEU* 3.7 25.7 - - - +
397B GLN 3.5 9.1 - - - +
398B GLY* 3.9 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