Contacts of the helix formed by residues 424 - 438 (chain A) in PDB entry 2IVF
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A PRO* 4.6 5.8 - - + -
418A SER* 4.1 2.7 - - - +
422A GLY 3.7 6.3 - - - +
423A VAL* 1.3 94.0 - - + +
425A VAL* 1.3 64.7 + - - +
426A SER* 3.8 7.2 - - - +
427A LEU* 3.1 16.3 + - + +
428A ILE* 3.1 11.1 + - - +
281B PHE* 3.6 27.4 - - + -
285B GLY 3.0 28.3 - - - +
286B GLU* 3.4 17.0 - - - +
287B ILE 4.7 0.7 - - - +
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Residues in contact with VAL 425 (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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414A PRO* 3.6 29.8 - - + +
415A GLU* 3.7 26.0 - - + +
418A SER* 3.7 11.1 + - - +
423A VAL 3.5 1.4 + - - -
424A PRO* 1.3 71.1 - - - +
426A SER* 1.3 58.4 + - - +
428A ILE* 3.2 8.2 + - - +
429A ARG* 2.8 55.9 + - - +
286B GLU* 3.7 12.2 + - - +
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PRO* 3.8 1.7 - - - +
425A VAL* 1.3 78.3 - - - +
427A LEU* 1.3 59.9 + - - +
429A ARG* 4.0 4.2 - - - +
430A GLU* 2.9 30.3 + - - +
286B GLU* 2.5 32.7 + - - -
287B ILE* 2.9 35.4 + - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.8 27.6 - - + -
295A HIS 3.7 23.8 - - - +
296A VAL* 4.1 7.4 - - + -
423A VAL* 4.0 20.6 - - + -
424A PRO* 3.1 12.4 + - + +
426A SER* 1.3 78.8 + - - +
428A ILE* 1.3 64.5 + - - +
430A GLU* 4.3 5.8 - - - +
431A LEU* 3.0 54.0 + - + +
281B PHE* 3.9 20.4 - - + -
287B ILE* 4.2 20.4 - - + -
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Residues in contact with ILE 428 (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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306A PHE* 4.2 10.1 - - + +
309A GLY* 3.9 27.8 - - - +
310A LEU* 3.3 13.1 - - + +
313A VAL* 4.3 1.1 - - + +
414A PRO* 3.6 28.5 - - + +
417A ALA* 3.9 10.1 - - + -
418A SER* 3.5 36.8 - - - +
421A CYS* 4.3 7.9 - - - -
423A VAL* 3.7 19.1 - - + +
424A PRO 3.1 11.2 + - - +
425A VAL 3.6 6.7 - - - +
427A LEU* 1.3 75.6 - - - +
429A ARG* 1.3 57.3 + - - +
432A GLY* 2.8 26.9 + - - -
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 4.1 14.8 - - + +
317A GLU* 4.0 8.9 + - - +
414A PRO* 3.5 28.7 - - + +
415A GLU* 3.2 24.9 + - - -
425A VAL* 2.8 36.6 + - - +
426A SER* 4.0 4.7 - - - +
428A ILE* 1.3 76.4 - - - +
430A GLU* 1.3 64.0 + - - +
432A GLY* 3.4 1.4 + - - -
433A ARG* 3.1 65.3 + - - +
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Residues in contact with GLU 430 (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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277A GLU* 3.9 1.4 - - - +
294A LEU* 4.1 4.0 - - - +
426A SER 2.9 18.3 + - - +
427A LEU* 3.9 11.4 - - + +
429A ARG* 1.3 76.6 - - - +
431A LEU* 1.3 58.8 + - + +
433A ARG* 3.4 8.3 + - - +
434A LYS* 2.7 69.0 + - + +
279B ARG* 2.7 37.3 + - - -
287B ILE* 3.7 11.3 - - - +
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Residues in contact with LEU 431 (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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249A LEU* 4.5 5.4 - - + -
251A PHE* 4.3 11.9 - - + -
279A VAL* 4.0 20.4 - - + -
294A LEU* 3.8 20.6 - - + -
296A VAL* 3.4 32.8 - - + -
306A PHE* 3.8 11.2 - - + -
310A LEU* 3.9 17.9 - - + -
427A LEU* 3.0 33.6 + - + +
430A GLU* 1.3 75.6 - - + +
432A GLY* 1.3 59.3 + - - +
434A LYS* 4.3 16.2 - - + +
435A VAL* 2.9 36.4 + - - +
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Residues in contact with GLY 432 (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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310A LEU* 3.6 23.4 - - - +
313A VAL* 4.0 17.0 - - - -
314A MET* 3.4 15.1 - - - +
428A ILE 2.8 18.8 + - - -
429A ARG 3.8 1.8 - - - -
431A LEU* 1.3 76.0 - - - +
433A ARG* 1.3 61.2 + - - +
435A VAL* 3.6 1.3 + - - +
436A ALA* 3.4 15.2 + - - +
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Residues in contact with ARG 433 (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 VAL* 4.1 2.9 - - + -
317A GLU* 2.7 44.2 + - - +
319A LEU* 4.0 15.7 - - + +
429A ARG* 3.1 39.4 + - - +
430A GLU* 3.7 7.0 - - - +
432A GLY* 1.3 76.5 - - - +
434A LYS* 1.3 63.1 + - + +
436A ALA* 3.5 5.2 + - - +
437A LYS* 3.5 33.7 + - - +
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Residues in contact with LYS 434 (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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249A LEU* 3.8 13.9 - - + -
277A GLU* 2.6 44.0 + - - +
430A GLU* 2.7 50.7 + - + +
431A LEU* 3.9 11.2 - - + +
433A ARG* 1.3 75.3 - - + +
435A VAL* 1.3 65.9 + - - +
437A LYS* 3.1 16.6 + - - +
438A LYS* 2.9 44.3 + - - +
279B ARG* 4.0 3.6 - - - +
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Residues in contact with VAL 435 (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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249A LEU* 3.7 7.9 - - + -
251A PHE* 3.5 37.2 - - + -
307A TRP* 4.6 0.9 - - + -
310A LEU* 3.8 11.9 - - + -
314A MET* 4.2 9.9 - - + -
431A LEU 2.9 21.9 + - - +
432A GLY 4.0 3.8 - - - +
434A LYS* 1.3 76.4 - - - +
436A ALA* 1.3 62.2 + - - +
437A LYS 3.3 0.5 + - - -
438A LYS 3.3 5.4 - - - +
440A THR* 4.1 4.0 - - - +
464A ALA* 4.0 13.0 - - + +
465A MET* 4.7 9.9 - - + -
468A SER* 3.2 22.1 - - - +
470A ASN* 3.2 21.0 - - - +
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Residues in contact with ALA 436 (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 MET* 3.7 14.1 - - - -
319A LEU* 3.6 43.7 - - + +
432A GLY 3.4 7.0 + - - +
433A ARG 3.7 9.2 - - - +
434A LYS 3.2 0.8 - - - -
435A VAL* 1.3 79.0 - - - +
437A LYS* 1.3 57.8 + - + +
438A LYS 3.7 0.2 - - - -
468A SER* 3.8 20.6 - - - +
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Residues in contact with LYS 437 (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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248A GLU* 4.2 4.5 - - - +
433A ARG* 3.5 24.1 + - - +
434A LYS* 3.1 25.0 + - - +
436A ALA* 1.3 77.8 - - - +
438A LYS* 1.3 79.5 + - + +
439A ARG 4.3 0.2 + - - -
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Residues in contact with LYS 438 (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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248A GLU* 3.5 25.5 - - + +
249A LEU* 3.8 28.9 - - + -
277A GLU* 3.8 22.0 - - - +
434A LYS* 2.9 38.6 + - + +
435A VAL 3.3 1.7 - - - +
436A ALA 3.7 0.2 - - - -
437A LYS* 1.3 100.0 - - + +
439A ARG* 1.3 59.2 + - - +
440A THR* 2.8 16.8 + - - +
470A ASN* 3.0 15.0 + - - +
321B ARG* 6.0 4.4 - - - +
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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