Contacts of the helix formed by residues 349 - 365 (chain A) in PDB entry 5I94
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 ASN 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A VAL* 1.3 79.0 - - - +
350A ASN* 1.3 66.6 + - - +
351A ALA* 3.1 11.6 + - - +
352A GLU* 3.1 34.9 + - - +
353A LYS* 3.0 19.9 + - - +
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASN* 1.3 75.4 - - - +
351A ALA* 1.3 61.6 + - - +
353A LYS* 3.7 27.8 + - - +
354A PHE* 3.1 24.4 + - - +
408A GLY* 3.1 34.9 + - - +
409A ILE* 5.4 0.5 - - - +
411A ASP* 4.6 5.1 - - - +
412A PHE* 3.9 23.5 - - + +
415A GLN* 4.5 15.1 - - - +
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Residues in contact with ALA 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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349A ASN* 3.1 13.2 + - - +
350A ASN* 1.3 76.8 - - - +
352A GLU* 1.3 66.0 + - + +
354A PHE* 3.4 4.9 + - - +
355A ASP* 3.2 30.2 + - - +
415A GLN* 5.8 0.7 - - - -
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Residues in contact with GLU 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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348A VAL* 3.7 35.0 - - + +
349A ASN* 3.1 28.8 + - - +
351A ALA* 1.3 74.4 - - + +
353A LYS* 1.3 66.0 + - - +
355A ASP* 3.1 13.0 + - - +
356A TYR* 2.9 23.2 + - - +
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Residues in contact with LYS 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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341A THR 5.5 0.4 + - - -
342A SER* 5.7 2.0 + - - +
344A ILE* 3.8 16.5 + - - +
345A LYS* 3.3 31.4 - - + +
346A GLN* 4.5 7.5 - - - +
347A GLY 5.1 1.0 - - - +
348A VAL* 3.1 32.0 + - + +
349A ASN 3.0 9.5 + - - +
350A ASN* 3.7 27.5 + - - +
351A ALA 3.4 0.2 - - - -
352A GLU* 1.3 75.8 - - - +
354A PHE* 1.3 61.8 + - - +
356A TYR* 3.3 9.5 - - - +
357A VAL* 3.2 18.4 + - - +
409A ILE* 4.0 22.0 - - - +
412A PHE* 3.7 30.7 - - + -
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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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350A ASN 3.1 15.8 + - - +
351A ALA* 3.7 5.4 - - - +
352A GLU 3.1 0.2 - - - -
353A LYS* 1.3 78.3 - - - +
355A ASP* 1.3 69.6 + - - +
357A VAL* 3.2 2.9 + - + -
358A MET* 2.9 37.8 + - + +
372A PHE* 3.7 42.2 - + + -
412A PHE* 3.8 20.4 - + + -
415A GLN* 3.6 34.8 - - + +
416A LEU* 3.7 21.5 - - + -
419A ILE* 4.0 15.9 - - + -
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Residues in contact with ASP 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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351A ALA* 3.2 18.7 + - - +
352A GLU* 3.1 12.0 + - - +
354A PHE* 1.3 79.4 - - - +
356A TYR* 1.3 57.9 + - - +
358A MET* 3.3 9.5 + - - +
359A GLN* 2.8 31.2 + - - +
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Residues in contact with TYR 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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294A ILE* 3.9 8.7 - - + -
298A ASP* 2.4 38.1 + - - -
344A ILE* 4.6 8.5 - - + -
345A LYS* 3.5 39.9 - - + -
352A GLU 2.9 11.0 + - - +
353A LYS* 3.3 13.5 - - - +
354A PHE 3.2 0.2 - - - -
355A ASP* 1.3 78.0 - - - +
357A VAL* 1.3 70.3 + - + +
359A GLN* 3.0 48.6 - - - +
360A PHE* 3.1 29.3 + + - +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 5.7 2.7 - - + -
291A LYS* 5.5 3.8 - - + -
294A ILE* 4.1 18.6 - - + -
344A ILE* 4.4 21.1 - - + -
353A LYS 3.2 12.0 + - - +
354A PHE* 3.2 6.3 + - + +
356A TYR* 1.3 77.1 - - + +
358A MET* 1.3 62.5 + - - +
360A PHE* 2.9 8.4 + - - +
361A LEU* 2.8 37.0 + - + +
412A PHE* 4.2 15.3 - - + -
416A LEU* 3.7 29.8 - - + -
419A ILE* 4.1 12.3 - - + -
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Residues in contact with MET 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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354A PHE* 2.9 36.0 + - + +
355A ASP* 3.4 12.3 - - - +
357A VAL* 1.3 75.6 - - - +
359A GLN* 1.3 64.1 + - - +
360A PHE 2.9 0.9 + - - -
361A LEU* 2.9 5.6 + - - +
362A ASN* 2.9 46.5 + - - +
370A VAL* 3.5 45.1 - - + +
371A GLY* 4.2 13.7 - - - +
372A PHE* 5.6 1.6 - - - -
419A ILE* 4.7 13.5 - - + -
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Residues in contact with GLN 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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355A ASP 2.8 17.2 + - - +
356A TYR* 3.0 43.1 - - - +
358A MET* 1.3 71.7 - - - +
360A PHE* 1.3 68.3 + - - +
362A ASN* 3.4 12.9 + - - +
363A LYS* 3.3 50.0 + - - +
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Residues in contact with PHE 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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294A ILE* 3.6 35.9 - - + -
297A ASN* 3.7 19.5 - - - -
298A ASP* 4.1 0.2 - - - -
356A TYR* 3.4 35.4 - + - +
357A VAL 2.9 9.9 + - - +
359A GLN* 1.3 83.1 - - + +
361A LEU* 1.3 66.0 - - - +
363A LYS* 3.3 14.7 + - + +
364A MET* 3.2 30.1 + - + +
446A VAL* 3.4 36.3 - - + -
447A LEU* 3.4 26.0 - - + -
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Residues in contact with LEU 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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283A LEU* 4.7 6.5 - - + -
287A VAL* 5.1 2.5 - - + -
290A LEU* 3.9 28.3 - - + -
294A ILE* 4.8 3.1 - - + -
357A VAL* 2.8 25.8 + - + +
358A MET* 2.9 7.2 + - - +
360A PHE* 1.3 75.6 - - - +
362A ASN* 1.3 59.0 + - - +
364A MET* 3.2 24.3 + - + +
365A ALA* 2.9 31.2 + - - +
370A VAL* 4.2 11.7 - - + -
419A ILE* 3.6 44.9 - - + -
429A MET* 3.7 18.1 - - + +
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Residues in contact with ASN 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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358A MET* 2.9 37.5 + - - +
359A GLN* 3.6 12.5 - - - +
360A PHE 3.2 0.2 - - - -
361A LEU* 1.3 74.0 - - - +
363A LYS* 1.3 64.6 + - - +
365A ALA* 3.4 1.2 + - - -
366A GLY 3.3 2.1 + - - -
367A ASN* 2.9 45.8 + - - +
368A GLU 4.1 7.4 - - - +
370A VAL* 3.7 22.5 + - - +
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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 GLN* 3.3 49.7 + - - +
360A PHE* 3.3 18.5 + - + +
362A ASN* 1.3 77.0 - - - +
364A MET* 1.3 63.1 + - - +
366A GLY* 3.3 11.9 + - - -
367A ASN* 4.9 3.6 - - - +
439A CYS* 3.8 16.1 - - - +
442A THR* 5.0 1.2 + - - +
444A GLU* 2.9 32.9 - - - +
445A ARG 5.4 0.7 - - - +
446A VAL* 3.9 27.1 - - + +
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Residues in contact with MET 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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290A LEU* 4.2 26.9 - - + +
294A ILE* 4.1 11.4 - - + -
360A PHE* 3.2 36.4 + - + +
361A LEU* 3.2 29.3 + - + +
363A LYS* 1.3 77.8 - - - +
365A ALA* 1.3 56.7 + - - +
366A GLY 3.4 0.7 - - - -
428A VAL* 3.5 4.7 - - - +
429A MET* 3.2 30.5 + - + +
432A THR* 2.8 33.8 + - + +
433A LEU* 5.4 1.1 - - - -
439A CYS* 4.2 0.2 - - - -
446A VAL* 3.5 20.6 - - + -
447A LEU* 3.9 17.9 - - + -
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Residues in contact with ALA 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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361A LEU 2.9 15.6 + - - +
362A ASN 4.2 1.6 - - - +
363A LYS 3.2 0.2 - - - -
364A MET* 1.3 75.8 - - - +
366A GLY* 1.3 52.2 + - - +
367A ASN 2.9 4.0 - - - -
368A GLU* 2.8 43.5 + - - +
370A VAL* 4.2 11.4 - - + -
425A SER* 3.7 19.3 - - - +
428A VAL* 3.8 14.1 - - - +
429A MET* 3.7 17.9 - - + -
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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
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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