Contacts of the helix formed by residues 340 - 360 (chain A) in PDB entry 4IX8
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 PRO 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 5.1 7.0 - - + -
338A LYS 3.3 6.6 - - - +
339A CYS* 1.3 87.8 - - + +
341A THR* 1.3 68.6 + - + +
342A GLU* 3.0 12.7 + - + +
343A CYS* 3.1 45.0 + - - +
344A THR* 4.2 3.6 + - - -
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A CYS 3.8 1.6 + - - -
340A PRO* 1.3 72.8 - - + +
342A GLU* 1.3 67.2 + - + +
344A THR* 3.2 17.6 + - - -
345A GLU* 3.2 27.2 + - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PRO* 3.0 11.1 - - + +
341A THR* 1.3 84.1 - - + +
343A CYS* 1.3 62.9 + - - +
345A GLU* 3.2 33.9 - - - +
346A HIS* 3.3 11.6 + - - +
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Residues in contact with CYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 5.4 1.7 - - - +
90A PRO* 4.0 34.8 - - + -
92A ILE* 5.8 0.4 - - - -
339A CYS* 5.6 1.8 - - + -
340A PRO* 3.1 39.9 + - + +
342A GLU* 1.3 79.7 - - - +
344A THR* 1.3 60.6 + - - +
346A HIS* 3.8 10.6 + - - +
347A ILE* 3.7 20.4 - - - +
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Residues in contact with THR 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU* 3.2 40.8 + - + +
259A MET* 5.3 4.0 - - + -
287A TYR* 3.7 26.2 + - + -
340A PRO 4.2 3.3 + - - -
341A THR* 3.2 11.7 + - - -
342A GLU 3.2 0.2 - - - -
343A CYS* 1.3 77.9 - - - +
345A GLU* 1.3 61.2 + - - +
346A HIS 3.0 2.5 - - - -
347A ILE* 2.9 25.9 + - + +
348A VAL* 3.0 18.2 + - + +
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Residues in contact with GLU 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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341A THR* 3.2 24.1 + - - +
342A GLU* 3.2 32.4 - - + +
344A THR* 1.3 79.5 - - - +
346A HIS* 1.3 56.8 + - - +
348A VAL* 3.7 10.3 - - + +
349A THR* 2.9 33.7 + - - +
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Residues in contact with HIS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN 3.3 26.2 + - - -
87A LEU* 4.7 4.7 - - + -
88A LYS* 5.3 5.8 + - + +
342A GLU 3.3 11.9 + - - +
343A CYS* 3.8 11.6 + - - +
345A GLU* 1.3 76.9 - - - +
347A ILE* 1.3 73.8 + - - +
349A THR* 3.4 8.7 + - + -
350A GLN* 3.2 40.7 + - + +
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Residues in contact with ILE 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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87A LEU* 4.0 37.7 - - + -
88A LYS 4.6 8.1 - - - +
259A MET* 4.5 17.3 - - + -
286A LLP 5.8 0.4 - - - +
287A TYR* 3.2 29.4 - - + +
289A VAL* 3.9 17.3 - - + -
343A CYS 3.7 17.7 - - - +
344A THR* 2.9 13.2 + - + +
346A HIS* 1.3 83.2 - - - +
348A VAL* 1.3 64.2 + - + +
350A GLN* 3.1 5.4 + - - +
351A LEU* 3.0 36.3 + - + +
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Residues in contact with VAL 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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258A GLU 4.5 5.8 - - - +
259A MET* 4.7 6.1 - - + -
260A VAL 3.8 21.3 - - - +
261A LEU* 4.0 14.1 - - + -
262A ASN 4.8 0.4 - - - +
344A THR* 3.0 25.0 + - + +
345A GLU* 3.7 12.1 - - - +
347A ILE* 1.3 74.9 - - + +
349A THR* 1.3 59.5 + - - +
351A LEU* 3.1 10.8 + - + +
352A GLU* 2.9 53.0 + - - +
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Residues in contact with THR 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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345A GLU* 2.9 21.9 + - - +
346A HIS* 3.6 9.6 - - + -
347A ILE 3.3 0.2 - - - -
348A VAL* 1.3 76.6 - - - +
350A GLN* 1.3 69.7 + - - +
352A GLU* 3.4 15.8 + - - +
353A ALA* 3.2 22.0 + - + +
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Residues in contact with GLN 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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86A ASN* 3.4 33.2 + - - +
87A LEU* 3.8 20.2 - - + -
346A HIS* 3.2 35.2 + - - +
347A ILE 3.1 7.7 + - - +
349A THR* 1.3 82.9 - - - +
351A LEU* 1.3 57.8 + - + +
353A ALA* 3.4 8.4 + - - +
354A GLY* 3.1 22.3 + - - -
425A VAL 4.2 3.8 - - - +
426A SER* 5.8 2.2 - - - +
427A ARG 5.1 3.1 - - - +
428A PRO* 5.6 2.8 - - - +
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Residues in contact with LEU 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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87A LEU* 5.1 3.1 - - + -
259A MET* 4.2 18.2 - - + -
261A LEU* 4.0 22.8 - - + +
347A ILE* 3.0 37.0 + - + +
348A VAL* 3.1 6.5 + - - +
350A GLN* 1.3 75.9 - - + +
352A GLU* 1.3 65.6 + - - +
354A GLY 3.2 0.2 + - - -
355A ALA* 2.9 20.4 + - - +
376A SER 3.7 18.6 - - - +
377A MET* 3.9 16.4 - - + -
425A VAL* 3.0 18.6 - - + +
426A SER* 3.7 36.3 - - - +
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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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261A LEU* 4.0 14.1 - - + -
262A ASN* 2.8 44.8 + - - +
263A ASN 4.8 0.2 + - - -
348A VAL* 2.9 34.2 + - - +
349A THR* 3.7 14.0 + - - +
351A LEU* 1.3 75.5 - - - +
353A ALA* 1.3 63.6 + - - +
355A ALA* 3.1 8.8 + - - +
356A LYS* 3.0 21.1 + - - +
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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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349A THR* 3.2 13.8 + - + +
350A GLN* 3.7 11.2 - - - +
351A LEU 3.2 0.2 - - - -
352A GLU* 1.3 76.2 - - - +
354A GLY* 1.3 62.9 + - - +
356A LYS* 3.3 16.4 + - - +
357A VAL* 3.3 17.8 + - - +
429A SER* 4.1 15.7 - - - +
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Residues in contact with GLY 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 GLN 3.1 12.4 + - - -
351A LEU 3.2 3.9 + - - -
353A ALA* 1.3 76.9 - - - +
355A ALA* 1.3 61.1 + - - +
357A VAL* 3.2 12.9 + - - +
358A TYR* 3.4 18.9 + - - -
425A VAL* 3.7 15.3 - - - -
427A ARG 5.1 0.9 - - - -
429A SER* 4.9 2.2 + - - -
432A LEU* 3.5 25.6 - - - +
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Residues in contact with ALA 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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261A LEU* 5.1 3.6 - - + -
351A LEU 2.9 12.2 + - - +
352A GLU* 3.1 13.4 + - - +
354A GLY* 1.3 78.2 - - - +
356A LYS* 1.3 62.1 + - - +
358A TYR* 3.0 16.1 + - - +
359A ALA* 3.2 11.3 + - - +
370A MET* 5.0 2.6 - - - +
372A ALA* 5.8 2.5 - - + +
373A PRO* 3.8 31.6 - - + +
425A VAL* 3.6 8.2 - - + +
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Residues in contact with LYS 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 GLU 3.0 11.8 + - - +
353A ALA* 3.3 11.6 + - - +
355A ALA* 1.3 76.5 - - - +
357A VAL* 1.3 63.4 + - + +
359A ALA* 3.2 22.7 + - - +
360A ARG* 3.6 8.8 + - - +
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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
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353A ALA 3.4 14.4 - - - +
354A GLY* 3.2 8.5 + - - +
355A ALA 3.1 0.8 - - - -
356A LYS* 1.3 78.3 - - + +
358A TYR* 1.3 62.5 + - + +
360A ARG* 3.2 26.8 + - - +
429A SER* 4.4 12.1 - - - +
432A LEU* 3.7 18.8 - - + -
433A ASN* 3.4 57.0 - - - +
436A VAL* 3.9 13.7 - - + +
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Residues in contact with TYR 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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76A LEU* 3.4 28.9 - - + +
354A GLY 3.4 20.4 + - - -
355A ALA* 3.0 8.9 + - - +
357A VAL* 1.3 73.9 - - + +
359A ALA* 1.3 59.6 + - - +
360A ARG 3.0 2.5 - - - -
361A LEU* 2.8 49.5 + - + +
362A LEU 4.2 0.2 + - - -
370A MET* 3.8 25.4 - - + +
379A VAL* 4.0 12.1 - - + -
381A LEU* 4.7 3.8 - - + -
423A ALA* 3.4 22.6 - - + +
424A THR 2.6 30.2 + - - -
425A VAL* 3.7 23.6 - - + -
432A LEU* 3.6 16.8 - - + +
436A VAL* 4.2 15.0 - - + -
439A ILE* 5.5 2.2 - - + -
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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 ALA 3.2 10.2 + - - +
356A LYS* 3.3 17.7 - - - +
357A VAL 3.2 0.2 - - - -
358A TYR* 1.3 77.6 - - - +
360A ARG* 1.3 62.6 + - - +
362A LEU* 2.9 36.1 + - + +
363A GLU* 4.0 6.5 + - - +
370A MET* 4.5 4.7 - - + +
372A ALA* 6.3 2.9 - - + -
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Residues in contact with ARG 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 LYS 3.6 7.8 + - - +
357A VAL* 3.2 18.8 + - - +
358A TYR 3.0 0.8 - - - -
359A ALA* 1.3 78.3 - - - +
361A LEU* 1.3 59.8 + - - +
363A GLU* 3.1 41.7 + - - +
364A HIS* 3.7 14.8 + - + -
433A ASN* 2.6 48.3 + - - +
436A VAL* 3.8 21.1 - - + +
437A ASP* 2.6 30.7 + - - -
440A ILE* 3.9 13.8 - - + +
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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
------------------------------------------------------------
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