Contacts of the helix formed by residues 347 - 364 (chain A) in PDB entry 3CQ6
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 VAL 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.7 32.3 - - + +
39A TYR* 3.9 24.7 - - + +
346A GLY* 1.3 74.3 - - - -
348A PRO* 1.4 65.7 - - + +
349A GLU* 3.6 18.2 - - + +
350A GLU* 2.8 51.4 + - + +
351A ASN* 3.0 10.0 + - - -
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Residues in contact with PRO 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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39A TYR* 4.2 13.0 - - + +
287A GLU* 3.7 33.7 - - + +
290A ARG* 3.6 4.1 + - - +
346A GLY 4.0 1.3 - - - +
347A VAL* 1.4 88.4 - - + +
349A GLU* 1.3 66.1 + - + +
351A ASN* 3.4 0.9 + - - +
352A ASP* 2.9 37.3 + - - +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 5.3 1.7 - - - +
347A VAL* 3.6 17.8 - - + +
348A PRO* 1.3 87.6 - - + +
350A GLU* 1.3 62.0 + - + +
352A ASP* 3.4 10.1 + - - +
353A ALA* 3.1 22.0 + - - +
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Residues in contact with GLU 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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29A ASP 4.8 6.2 - - - +
30A ILE* 4.0 39.0 - - + +
31A ARG 5.2 4.7 + - - -
32A LEU* 3.9 11.4 - - + +
38A PRO* 3.7 10.7 - - - +
346A GLY* 3.3 12.4 - - - -
347A VAL* 2.8 41.4 + - + +
349A GLU* 1.3 74.6 - - + +
351A ASN* 1.3 61.0 + - - +
353A ALA* 3.2 4.5 + - - +
354A PHE* 2.9 27.9 + - - +
62C ARG* 4.2 15.1 + - - -
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Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.7 2.4 - - - +
287A GLU* 2.7 40.7 + - - +
290A ARG* 3.7 3.6 - - - +
291A VAL* 3.7 22.5 - - + +
344A THR 4.2 3.3 - - - +
345A ILE* 3.7 7.9 - - - +
346A GLY 2.9 44.3 + - - -
347A VAL 3.0 4.4 + - - -
348A PRO 3.7 3.4 - - - +
350A GLU* 1.3 76.8 - - - +
352A ASP* 1.3 62.5 + - - +
354A PHE* 3.2 9.0 + - - +
355A LEU* 2.9 29.3 + - - +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 2.8 34.5 + - - -
348A PRO* 2.9 20.3 + - - +
349A GLU* 3.6 10.5 - - - +
350A GLU 3.3 0.2 - - - -
351A ASN* 1.3 75.9 - - - +
353A ALA* 1.3 56.6 + - - +
355A LEU* 3.2 5.8 + - - +
356A ASP* 2.8 39.4 + - - +
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Residues in contact with ALA 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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30A ILE* 4.1 25.1 - - + -
330A VAL* 4.0 7.4 - - + +
349A GLU 3.1 14.4 + - - +
350A GLU 3.5 7.6 - - - +
352A ASP* 1.3 73.5 - - - +
354A PHE* 1.3 66.8 + - - +
356A ASP* 3.4 9.8 + - - +
357A ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 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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32A LEU* 3.9 14.8 - - + -
291A VAL* 3.7 28.5 - - + -
295A LEU* 3.9 15.5 - - + -
312A PHE* 3.7 19.1 - + - -
325A PHE* 3.4 29.6 - + - -
330A VAL* 4.1 19.6 - - + +
332A ILE* 4.2 3.6 - - + -
343A THR* 3.5 38.1 - - + -
350A GLU 2.9 12.9 + - - +
351A ASN* 3.5 9.9 - - - +
353A ALA* 1.3 74.9 - - - +
355A LEU* 1.3 75.0 + - + +
357A ALA* 3.3 3.6 + - - +
358A ALA* 2.8 26.9 + - + +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 3.6 27.6 - - - +
291A VAL* 4.0 31.6 - - + +
294A ARG* 3.5 36.0 + - + +
295A LEU* 4.4 9.2 - - + -
298A LEU* 4.2 3.7 - - + +
351A ASN 2.9 21.1 + - - +
352A ASP* 3.5 6.1 - - - +
354A PHE* 1.3 97.9 - - + +
356A ASP* 1.3 67.4 + - - +
358A ALA* 3.7 3.6 - - + +
359A ALA* 3.0 24.9 + - - +
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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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352A ASP* 2.8 29.7 + - - +
353A ALA* 3.4 9.5 + - - +
355A LEU* 1.3 75.5 - - - +
357A ALA* 1.3 61.8 + - - +
359A ALA* 3.3 13.0 + - - +
360A GLU* 3.3 19.9 + - - +
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Residues in contact with ALA 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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325A PHE* 3.9 19.1 - - + -
328A ARG* 3.9 33.0 - - + +
330A VAL* 4.3 6.1 - - + -
353A ALA 3.0 17.8 + - - +
354A PHE 3.6 3.8 - - - +
356A ASP* 1.3 76.4 - - - +
358A ALA* 1.3 63.0 + - - +
360A GLU* 3.1 5.9 + - - +
361A ILE* 2.9 29.4 + - - +
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Residues in contact with ALA 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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295A LEU* 3.7 29.8 - - + -
298A LEU* 4.3 2.9 - - + -
300A TYR* 2.6 35.8 + - + -
325A PHE* 3.7 19.7 - - + -
354A PHE* 2.8 19.8 + - + +
355A LEU* 3.3 8.7 + - - +
357A ALA* 1.3 76.3 - - - +
359A ALA* 1.3 60.8 + - - +
361A ILE* 4.5 0.2 - - - -
362A ILE* 3.3 6.9 + - - +
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Residues in contact with ALA 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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294A ARG* 4.7 8.3 - - - +
298A LEU* 4.1 26.0 - - + +
355A LEU 3.0 16.9 + - - +
356A ASP* 3.6 7.4 - - - +
357A ALA 3.1 0.2 - - - -
358A ALA* 1.3 75.7 - - - +
360A GLU* 1.3 63.6 + - + +
362A ILE* 3.4 14.8 - - - +
363A LYS* 3.7 13.0 - - - +
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Residues in contact with GLU 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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328A ARG* 2.9 37.1 + - - +
356A ASP* 3.3 13.1 + - - +
357A ALA* 3.1 8.4 + - - +
359A ALA* 1.3 77.1 - - + +
361A ILE* 1.3 64.3 + - - +
363A LYS* 3.3 27.9 + - - +
364A LEU* 3.7 11.8 + - - +
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Residues in contact with ILE 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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300A TYR* 3.8 12.1 - - - +
315A PHE* 4.2 19.0 - - + -
321A ALA* 4.8 1.8 - - + -
324A ALA* 3.9 13.2 - - + +
325A PHE* 3.3 59.2 - - + +
328A ARG* 4.1 13.9 - - - +
357A ALA 2.9 21.6 + - - +
358A ALA 3.6 0.2 + - - -
359A ALA 3.3 0.4 - - - -
360A GLU* 1.3 78.1 - - - +
362A ILE* 1.3 61.4 + - - +
364A LEU* 3.1 22.7 + - + +
365A ASN 3.7 2.9 + - - -
366A LEU* 4.4 21.8 + - + -
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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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298A LEU* 3.6 31.0 - - + +
299A GLY* 3.6 24.0 - - - +
300A TYR* 3.4 38.3 + - + +
315A PHE* 5.9 0.7 - - - -
358A ALA 3.3 10.1 + - - +
359A ALA* 3.4 19.5 - - - +
361A ILE* 1.3 75.9 - - - +
363A LYS* 1.3 68.0 + - + +
365A ASN* 3.4 14.5 + - - +
405A PO4 4.3 22.1 + - - +
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Residues in contact with LYS 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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359A ALA 3.7 18.4 - - - +
360A GLU* 3.5 13.9 - - - +
361A ILE 3.2 0.6 - - - -
362A ILE* 1.3 83.4 - - + +
364A LEU* 1.3 62.2 + - + +
365A ASN* 3.3 3.7 + - - +
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Residues in contact with LEU 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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324A ALA* 4.7 2.7 - - + -
328A ARG* 3.8 29.6 - - - +
360A GLU 3.7 14.6 - - - +
361A ILE* 3.1 14.2 + - - +
363A LYS* 1.3 77.6 - - + +
365A ASN* 1.3 71.0 + - - +
366A LEU* 3.4 33.9 + - + +
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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
------------------------------------------------------------
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