Contacts of the helix formed by residues 425 - 436 (chain A) in PDB entry 4BTF
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 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.7 52.7 - - + +
156A GLN* 6.2 1.1 - - + -
157A ILE* 4.7 9.2 - - + -
292A MET* 3.7 17.0 - - + -
296A SER* 4.3 11.0 - - - +
423A ASP 3.4 6.5 - - - +
424A CYS* 1.3 90.7 - - - +
426A GLU* 1.3 60.4 - - - +
427A LEU 4.5 0.4 - - - +
428A LEU* 2.8 25.0 + - + +
429A ARG* 3.0 9.4 + - - +
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Residues in contact with GLU 426 (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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422A GLN 5.1 4.9 - - - +
424A CYS 3.3 9.9 + - - +
425A PRO* 1.3 70.5 - - - +
427A LEU* 1.3 63.6 + - - +
429A ARG* 2.7 48.2 + - - +
430A GLU* 3.0 38.1 + - - +
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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
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154A GLN* 3.9 39.3 - - + +
155A LEU* 3.5 26.2 - - + -
425A PRO* 3.2 0.8 - - + +
426A GLU* 1.3 78.7 - - - +
428A LEU* 1.3 61.1 + - - +
430A GLU* 3.5 12.5 + - + +
431A ILE* 3.3 33.0 + - + +
452A ARG* 3.9 29.2 - - + +
453A LEU* 4.6 10.5 - - + +
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Residues in contact with LEU 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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155A LEU* 4.3 6.0 - - + +
292A MET* 4.1 10.3 - - + -
295A ARG 5.4 0.2 - - - -
296A SER* 3.9 22.9 - - - +
299A VAL* 4.1 35.9 - - + -
389A LEU* 5.3 0.7 - - + -
393A ALA* 4.3 7.9 - - + -
424A CYS* 3.6 18.8 - - - -
425A PRO* 2.8 22.6 + - + +
427A LEU* 1.3 80.1 - - - +
429A ARG* 1.3 62.5 + - - +
431A ILE* 3.6 11.1 + - + +
432A ILE* 3.2 50.3 + - + +
453A LEU* 5.6 4.5 - - + -
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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
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420A VAL* 3.5 31.4 - - + -
421A GLY 5.9 0.2 - - - -
424A CYS* 3.8 9.3 - - + +
425A PRO 3.0 10.4 + - - +
426A GLU* 2.7 38.4 + - - +
428A LEU* 1.3 75.8 - - - +
430A GLU* 1.3 88.2 + - - +
432A ILE* 3.9 3.0 - - - +
433A ASN* 2.9 66.6 + - - +
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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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426A GLU* 3.0 35.9 + - - +
427A LEU* 3.6 15.9 + - + +
429A ARG* 1.3 90.5 + - - +
431A ILE* 1.3 59.2 + - - +
433A ASN* 3.5 8.6 + - - +
434A GLU* 2.9 48.4 + - + +
452A ARG* 4.3 7.4 - - - +
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Residues in contact with ILE 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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299A VAL* 6.2 0.2 - - + -
389A LEU* 4.2 10.1 - - + -
427A LEU* 3.3 21.8 + - + +
428A LEU* 4.0 8.5 - - + +
429A ARG 3.4 0.2 - - - -
430A GLU* 1.3 74.4 - - - +
432A ILE* 1.3 59.3 + - + +
434A GLU* 3.2 3.9 + - - +
435A CYS* 2.9 34.6 + - - -
444A PRO* 4.7 1.4 - - + +
449A ILE* 3.9 39.0 - - + +
452A ARG* 3.7 41.1 - - + +
453A LEU* 3.4 33.4 - - + -
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Residues in contact with ILE 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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386A GLY 3.9 14.6 - - - +
389A LEU* 3.3 40.8 - - + +
390A TRP* 4.0 8.5 - - + +
393A ALA* 3.7 15.5 - - + -
420A VAL* 4.1 14.1 - - + -
428A LEU* 3.2 38.5 + - + +
429A ARG* 4.0 4.0 - - - +
431A ILE* 1.3 72.5 - - - +
433A ASN* 1.3 66.6 + - - +
434A GLU 3.3 0.5 + - - -
435A CYS* 3.4 6.5 + - - +
436A ARG* 3.3 46.2 + - - +
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Residues in contact with ASN 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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417A GLN* 3.7 22.3 + - - +
419A PRO* 6.1 0.3 - - - +
420A VAL* 5.4 2.3 + - - +
429A ARG* 2.9 58.5 + - - +
430A GLU* 3.5 7.1 - - - +
432A ILE* 1.3 76.3 - - - +
434A GLU* 1.3 62.9 + - + +
436A ARG* 3.2 21.7 + - - +
437A ALA* 3.5 14.4 + - - +
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Residues in contact with GLU 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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430A GLU* 2.9 27.3 + - - +
431A ILE 3.2 3.3 + - - +
433A ASN* 1.3 76.6 - - + +
435A CYS* 1.3 64.8 + - - +
436A ARG 3.0 2.2 - - - -
437A ALA* 3.2 21.5 + - - +
442A GLN 4.4 9.5 - - - +
443A ARG* 3.4 13.0 - - - +
444A PRO* 3.7 12.4 - - + +
452A ARG* 2.2 45.6 + - - -
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Residues in contact with CYS 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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382A ILE* 3.7 16.6 - - - +
383A TYR* 3.3 22.6 - - - -
385A PHE* 4.8 0.9 - - - -
386A GLY* 3.5 27.1 - - - -
389A LEU* 4.5 5.8 - - - -
431A ILE* 2.9 27.2 + - - +
432A ILE* 3.4 3.6 + - - +
434A GLU* 1.3 75.3 - - - +
436A ARG* 1.3 57.5 + - - +
437A ALA 3.4 0.2 - - - -
443A ARG* 3.4 12.5 - - - -
444A PRO* 3.9 10.3 - - - -
449A ILE* 3.5 33.7 - - - -
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Residues in contact with ARG 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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366A PRO* 5.6 0.2 - - - +
383A TYR* 3.6 24.5 - - + -
386A GLY* 4.1 18.2 - - - -
387A ILE* 3.8 30.2 - - + +
390A TRP* 3.4 15.5 - - - +
417A GLN* 3.0 38.1 + - + +
418A GLU* 2.6 44.1 + - - +
419A PRO* 5.1 0.6 - - - +
420A VAL* 5.0 3.8 - - - +
432A ILE* 3.3 32.1 + - - +
433A ASN* 3.2 30.9 + - - +
434A GLU 3.0 0.6 - - - -
435A CYS* 1.3 79.4 - - - +
437A ALA* 1.3 65.5 + - - +
438A HIS* 3.3 2.3 + - - -
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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