Contacts of the helix formed by residues 346 - 364 (chain A) in PDB entry 5I4V
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 GLN 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A HIS* 4.5 3.4 - - - -
344A GLY 5.4 0.2 - - - +
345A LEU* 1.3 77.1 - - - +
347A VAL* 1.3 58.7 + - - +
348A GLU* 3.4 35.5 - - - +
349A PHE* 2.8 24.3 + - - +
350A ILE* 2.9 15.7 + - - +
434A VAL 5.3 0.6 + - - -
437A GLU* 3.7 12.9 + - - +
438A GLN* 2.9 43.9 + - - +
441A ALA* 3.4 21.6 - - + +
445A GLN* 4.9 5.0 - - - +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A HIS* 4.0 23.8 - - + +
346A GLN* 1.3 73.8 - - - +
348A GLU* 1.3 63.7 + - - +
349A PHE 3.0 0.2 - - - -
350A ILE* 4.1 10.5 - - + -
351A ASN* 3.0 61.8 + - - +
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLN* 3.2 32.4 + - + +
347A VAL* 1.3 84.1 + - + +
349A PHE* 1.3 56.5 + - - +
352A PRO* 3.1 22.0 - - - +
434A VAL* 3.4 10.9 - - + +
437A GLU* 6.5 0.9 - - + -
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Residues in contact with PHE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 4.6 9.0 - - + -
313A LEU* 4.9 6.7 - - + -
345A LEU* 4.3 13.7 - - + -
346A GLN* 2.8 6.4 + - + +
348A GLU* 1.3 78.5 - - - +
350A ILE* 1.3 66.7 + - - +
351A ASN 3.4 1.1 - - - -
352A PRO* 3.3 4.4 - - + +
353A ILE* 3.3 48.2 + - + +
431A LEU* 4.7 5.8 - - + -
434A VAL* 3.8 17.5 - - + -
435A HIS* 3.8 40.6 - + + -
438A GLN* 3.3 47.3 - - + +
501A 67S 4.3 19.5 - + + -
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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
----------------------------------------------------------
337A LYS* 3.9 33.4 - - + +
340A PHE* 3.7 14.8 - - + -
341A HIS* 3.5 42.4 - - + +
345A LEU* 3.8 20.6 - - + +
346A GLN 2.9 21.0 + - - +
347A VAL* 4.1 10.1 - - + +
349A PHE* 1.3 75.4 - - - +
351A ASN* 1.3 67.1 + - - +
353A ILE* 3.2 10.0 + - - +
354A PHE* 3.2 34.2 + - + -
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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
----------------------------------------------------------
337A LYS* 3.0 33.6 + - - +
347A VAL* 3.0 40.4 + - - +
348A GLU* 5.5 0.2 - - - -
350A ILE* 1.3 79.6 - - - +
352A PRO* 1.3 65.2 - - + +
354A PHE* 3.3 2.4 + - - +
355A GLU* 2.9 47.8 + - - +
358A ARG* 4.7 0.7 + - - -
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Residues in contact with PRO 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 GLU* 3.1 28.5 - - - +
349A PHE 3.3 7.4 - - - +
351A ASN* 1.3 92.5 - - + +
353A ILE* 1.3 58.7 + - - +
355A GLU* 3.5 14.6 - - + +
356A PHE* 2.8 33.1 + - - +
431A LEU* 3.5 24.1 - - + +
434A VAL* 4.1 14.4 - - + -
452B LYS* 6.3 3.4 - - - -
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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* 3.8 23.1 - - + -
316A THR* 4.0 27.1 - - + -
327A ILE* 4.4 4.9 - - + -
340A PHE* 4.7 9.2 - - + -
345A LEU* 5.1 0.2 - - + -
349A PHE* 3.3 51.5 + - + +
350A ILE* 3.2 11.8 + - - +
352A PRO* 1.3 77.3 - - - +
354A PHE* 1.3 66.1 + - + +
356A PHE* 3.4 7.1 + - - +
357A SER* 2.8 35.3 + - - -
431A LEU* 4.4 2.0 - - + +
501A 67S 4.3 17.7 - - + -
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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
----------------------------------------------------------
320A TYR* 4.1 18.6 - + - -
325A GLU* 3.6 26.9 - - + -
326A CYS* 4.8 0.2 - - - -
327A ILE* 3.7 28.0 - - + -
335A TYR 4.5 1.3 - - - -
336A SER 4.0 4.7 - - - -
337A LYS* 3.6 50.9 - - + +
340A PHE* 4.1 18.6 - + - -
350A ILE* 3.2 27.3 + - + +
351A ASN 3.9 3.1 - - - +
353A ILE* 1.3 82.4 - - + +
355A GLU* 1.3 65.2 + - - +
356A PHE 3.2 0.4 - - - -
357A SER* 3.6 5.6 - - - -
358A ARG* 3.0 42.4 + - - +
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LYS* 5.5 1.4 + - - -
351A ASN* 2.9 37.2 + - - +
352A PRO* 3.3 18.7 + - + +
354A PHE* 1.3 75.6 - - - +
356A PHE* 1.3 56.5 + - - +
358A ARG* 3.3 28.3 + - - +
359A ALA* 3.0 27.6 + - - +
362A ARG* 5.2 0.5 + - - -
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Residues in contact with PHE 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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313A LEU* 3.8 31.2 - - + -
314A LEU* 4.1 10.3 - - + -
317A ALA* 4.2 7.2 - - + -
352A PRO 2.8 17.3 + - - +
353A ILE* 3.6 6.5 - - - +
355A GLU* 1.3 75.6 - - - +
357A SER* 1.3 59.3 + - - +
359A ALA* 3.4 9.8 + - + +
360A MET* 3.0 55.7 + - + +
424A LYS* 4.5 11.0 - - + -
427A SER* 4.2 20.0 - - - -
428A LEU* 3.5 32.1 - - + -
431A LEU* 3.6 24.9 - - + -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 4.5 1.4 - - - +
317A ALA* 3.5 28.9 + - - +
320A TYR* 3.7 35.2 - - - +
327A ILE* 4.5 3.8 - - - +
353A ILE* 2.8 28.4 + - - +
354A PHE* 3.6 7.0 - - - -
356A PHE* 1.3 75.1 - - - +
358A ARG* 1.3 65.8 + - - +
360A MET* 3.1 2.8 + - - +
361A ARG* 2.9 23.9 + - - +
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Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.7 26.5 + - + +
322A HIS* 3.8 29.7 - - - +
325A GLU* 5.4 4.8 + - - +
337A LYS* 4.5 15.5 - - - +
354A PHE* 3.0 34.0 + - - +
355A GLU* 3.3 44.1 + - - +
357A SER* 1.3 76.0 - - - +
359A ALA* 1.3 61.3 + - - +
361A ARG* 3.1 16.2 + - - +
362A ARG* 3.2 29.9 + - - +
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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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355A GLU 3.0 14.3 + - - +
356A PHE* 3.5 14.4 - - + +
358A ARG* 1.3 77.0 - - - +
360A MET* 1.3 62.9 + - - +
362A ARG* 3.5 36.7 + - - +
363A LEU* 3.5 10.9 + - - +
424A LYS* 3.6 27.7 + - - +
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Residues in contact with MET 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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314A LEU* 4.2 15.9 - - + -
317A ALA* 3.8 16.8 - - + -
356A PHE* 3.0 41.3 + - - +
357A SER 3.1 5.6 + - - +
359A ALA* 1.3 74.3 - - - +
361A ARG* 1.3 67.2 + - - +
363A LEU* 3.1 26.6 + - + +
364A GLY 3.5 4.0 + - - -
365A LEU* 3.7 29.6 + - + +
370A TYR* 3.3 29.1 + - + +
373A LEU* 4.3 4.9 - - + -
424A LYS* 3.6 34.3 - - + -
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Residues in contact with ARG 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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317A ALA 5.9 1.3 + - - +
320A TYR* 4.7 10.8 - - + +
322A HIS* 3.3 51.4 - - + +
357A SER 2.9 13.0 + - - +
358A ARG* 3.1 9.8 + - - +
360A MET* 1.3 77.0 - - - +
362A ARG* 1.3 73.1 + - - +
364A GLY* 3.1 16.0 + - - +
370A TYR* 5.7 0.7 - - - -
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Residues in contact with ARG 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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322A HIS* 6.3 1.8 - - - -
355A GLU 5.2 0.6 + - - -
358A ARG* 3.2 22.7 + - - +
359A ALA* 3.6 43.3 + - - +
361A ARG* 1.3 89.7 - - - +
363A LEU* 1.3 60.6 + - - +
364A GLY* 3.5 0.7 + - - -
424A LYS* 5.7 0.8 - - - +
461B GLU* 4.4 19.8 + - - -
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Residues in contact with LEU 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 3.5 4.4 + - - +
360A MET* 3.1 28.7 + - + +
362A ARG* 1.3 80.1 - - - +
364A GLY* 1.3 59.7 + - - +
365A LEU* 3.5 19.5 - - + -
417A ARG* 3.0 42.7 + - + +
420A ARG* 4.0 38.1 - - + +
421A MET* 4.2 10.5 - - + -
424A LYS* 3.8 30.7 - - + -
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Residues in contact with GLY 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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360A MET 3.5 2.0 + - - -
361A ARG* 3.1 16.1 + - - -
362A ARG 3.3 1.1 - - - -
363A LEU* 1.3 78.6 - - - +
365A LEU* 1.3 64.1 + - - +
366A ASP 3.8 0.2 + - - -
410A LYS* 4.7 2.4 - - - -
411A ARG* 4.6 9.3 + - - -
417A ARG* 2.9 16.0 + - - -
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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
------------------------------------------------------------
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