Contacts of the helix formed by residues 450 - 458 (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 PRO 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A THR* 3.1 36.1 - - + -
276A ILE* 3.7 24.7 - - + -
448A LYS 4.6 1.1 - - - +
449A LEU* 1.3 91.0 - - + +
451A PRO* 1.3 78.7 - - + +
452A LEU 3.3 2.9 - - - +
453A LEU* 3.1 14.2 + - + +
454A SER* 3.1 17.5 + - - -
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Residues in contact with PRO 451 (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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448A LYS* 6.5 0.7 - - - -
449A LEU 3.8 1.3 - - - +
450A PRO* 1.3 85.8 - - + +
452A LEU* 1.3 64.2 + - - +
454A SER* 2.9 9.0 + - - -
455A GLU* 2.7 24.4 + - - +
463A SER* 4.2 9.6 - - - +
468A HIS* 4.5 14.8 - - + +
470A ILE* 3.4 21.9 - - + +
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Residues in contact with LEU 452 (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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276A ILE* 4.4 31.4 - - + +
279A VAL* 3.8 39.5 - - + -
280A GLN* 5.0 4.3 - - + +
450A PRO* 3.2 1.0 + - - +
451A PRO* 1.3 80.8 - - - +
453A LEU* 1.3 59.2 + - + +
455A GLU* 3.4 3.4 + - - +
456A ILE* 3.1 29.1 + - + +
470A ILE* 3.6 34.7 - - + +
471A LEU* 4.6 12.6 - - + +
474A LEU* 4.1 20.0 - - + -
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Residues in contact with LEU 453 (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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272A THR* 3.9 25.4 - - + +
275A ALA* 4.0 18.6 - - + -
276A ILE* 4.3 9.9 - - + +
279A VAL* 3.8 28.7 - - + -
449A LEU* 4.2 8.5 - - + -
450A PRO* 3.1 27.1 + - + +
452A LEU* 1.3 74.8 - - + +
454A SER* 1.3 59.1 + - - +
456A ILE* 3.2 6.9 - - + +
457A TRP* 3.0 66.4 + - + +
459A VAL* 4.1 1.9 - - - +
501A 67S 4.2 7.9 - - - -
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Residues in contact with SER 454 (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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449A LEU* 4.5 3.4 - - - +
450A PRO 3.1 12.9 + - - -
451A PRO* 2.9 7.7 + - - -
453A LEU* 1.3 74.4 - - - +
455A GLU* 1.3 60.5 + - - +
458A ASP* 2.8 26.9 + - - -
459A VAL* 3.1 20.4 + - - +
460A HIS* 3.0 37.3 + - - +
463A SER* 2.8 26.6 + - - -
464A GLY* 3.4 4.9 + - - -
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Residues in contact with GLU 455 (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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305A LYS* 3.4 11.6 + - + +
451A PRO 2.7 15.2 + - - +
452A LEU* 3.4 10.9 - - - +
454A SER* 1.3 77.0 - - - +
456A ILE* 1.3 64.4 + - + +
458A ASP* 3.3 15.2 - - - +
463A SER 3.3 19.2 + - - +
464A GLY 4.1 2.8 - - - +
466A GLY* 4.3 11.6 - - - -
468A HIS* 3.7 5.0 + - - +
469A LYS* 3.1 15.5 + - - -
470A ILE* 2.9 36.2 + - + +
471A LEU* 2.9 39.3 + - + +
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Residues in contact with ILE 456 (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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279A VAL* 4.3 16.6 - - + -
304A LEU* 4.2 3.6 - - + +
305A LYS* 3.8 47.2 - - + +
308A THR* 3.1 42.6 - - + +
452A LEU* 3.1 16.6 + - + +
453A LEU* 3.2 23.1 - - + +
455A GLU* 1.3 81.6 - - + +
457A TRP* 1.3 82.2 + - + +
458A ASP* 3.6 0.9 - - - +
471A LEU* 4.9 12.8 - - + -
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Residues in contact with TRP 457 (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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275A ALA* 5.0 0.9 - - + -
305A LYS 4.6 6.9 + - - -
308A THR* 4.4 11.7 - - + +
309A ILE* 4.2 15.9 - - + +
312A MET* 3.7 38.4 - - + -
435A HIS* 3.5 35.5 - + + -
439A VAL* 4.8 10.7 - - + +
449A LEU* 4.2 10.5 - - + -
453A LEU* 3.0 53.1 + - + +
454A SER 3.7 0.2 - - - -
456A ILE* 1.3 95.6 - - + +
458A ASP* 1.3 74.5 + - - +
459A VAL* 3.6 10.3 - - + +
501A 67S 3.9 24.9 - + - -
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Residues in contact with ASP 458 (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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305A LYS* 3.0 32.4 + - - -
439A VAL* 5.5 1.0 - - - +
443A ARG* 4.7 3.1 + - - -
454A SER 2.8 11.7 + - - -
455A GLU 3.3 3.6 - - - +
456A ILE 4.9 0.2 - - - -
457A TRP* 1.3 82.4 - - - +
459A VAL* 1.3 60.4 + - - +
464A GLY 3.3 18.7 - - - +
232E VAL* 5.3 1.2 - - - +
233E ALA* 6.2 2.5 - - + -
236E LEU* 3.4 26.0 - - + +
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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
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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