Contacts of the helix formed by residues 413 - 422 (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 THR 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A GLN* 3.8 20.2 - - - +
409A LEU 3.4 0.6 + - - +
410A LYS* 3.6 22.4 - - - +
411A ASP 3.7 1.2 - - - -
412A TYR* 1.3 77.2 - - - +
414A PRO* 1.3 71.2 - - - +
415A GLU* 3.7 12.0 + - - +
416A LYS* 3.0 30.8 + - + +
417A ALA* 2.7 25.6 + - - +
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Residues in contact with PRO 414 (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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309A GLY* 5.0 0.6 - - - +
312A GLN* 3.3 15.9 - - - +
313A VAL* 3.7 26.9 - - + -
412A TYR 4.3 0.2 - - - +
413A THR* 1.3 86.8 - - - +
415A GLU* 1.3 62.0 + - - +
417A ALA* 4.3 2.0 - - + -
418A SER* 2.8 32.6 + - - -
425A VAL* 3.6 24.9 - - + +
428A ILE* 3.6 24.3 - - + +
429A ARG* 3.5 21.1 - - + +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 3.7 10.9 + - - +
414A PRO* 1.3 86.4 - - - +
416A LYS* 1.3 64.8 + - + +
418A SER* 3.5 3.1 - - - -
419A ALA* 3.2 20.1 + - - +
425A VAL* 3.7 20.1 - - + +
429A ARG* 3.2 26.8 + - - -
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LYS* 3.0 30.4 + - - +
411A ASP* 3.3 30.3 + - - +
413A THR* 3.0 20.5 + - - +
415A GLU* 1.3 77.5 - - + +
417A ALA* 1.3 65.1 + - - +
419A ALA* 3.2 15.7 + - - +
420A LYS* 3.2 21.6 + - - +
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Residues in contact with ALA 417 (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 ALA* 3.3 27.3 - - - +
309A GLY* 3.9 16.6 - - - -
412A TYR* 4.0 8.0 - - + +
413A THR 2.7 20.4 + - - +
416A LYS* 1.3 72.2 - - - +
418A SER* 1.3 58.3 + - - +
420A LYS* 2.9 14.0 + - - +
421A CYS* 2.9 30.4 + - - +
428A ILE* 3.9 12.3 - - + -
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Residues in contact with SER 418 (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 ARG* 4.2 1.0 + - - -
414A PRO 2.8 20.3 + - - -
415A GLU 3.5 5.4 - - - -
417A ALA* 1.3 77.3 - - - +
419A ALA* 1.3 56.6 + - - +
421A CYS* 4.4 1.6 - - - -
422A GLY* 2.8 30.5 + - - -
423A VAL 2.7 28.7 + - - -
424A PRO* 4.1 1.9 - - - +
425A VAL* 3.7 19.8 + - - +
428A ILE* 3.5 4.8 - - - +
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Residues in contact with ALA 419 (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 ARG* 2.6 35.2 + - - +
415A GLU 3.2 10.2 + - - +
416A LYS* 3.2 14.1 + - - +
418A SER* 1.3 79.0 - - - +
420A LYS* 1.3 53.2 + - + +
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Residues in contact with LYS 420 (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 ARG* 3.5 13.8 + - - +
302A SER* 3.7 12.3 - - - -
305A ALA* 3.7 10.5 - - + -
411A ASP* 3.5 26.2 - - - -
412A TYR* 3.8 31.2 - - + -
416A LYS* 3.4 15.2 + - - +
417A ALA 2.9 7.4 + - - +
419A ALA* 1.3 81.6 - - + +
421A CYS* 1.3 57.7 + - - +
831A HIS* 4.1 23.3 + - + -
833A ASP* 4.6 4.0 - - - +
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Residues in contact with CYS 421 (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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298A VAL* 3.4 6.5 - - + -
299A ARG* 2.8 30.4 + - - -
302A SER* 3.2 32.5 - - - +
305A ALA* 4.1 2.0 - - + -
306A PHE* 3.9 22.2 - - + +
417A ALA 2.9 22.5 + - - +
420A LYS* 1.3 77.2 - - - +
422A GLY* 1.3 60.8 + - - +
423A VAL* 3.2 36.5 + - + -
428A ILE* 4.3 4.0 - - - -
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Residues in contact with GLY 422 (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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297A PRO* 4.3 12.4 - - - +
299A ARG* 3.8 22.8 - - - +
418A SER* 2.8 15.9 + - - -
420A LYS 3.7 1.0 - - - -
421A CYS* 1.3 78.2 - - - +
423A VAL* 1.3 62.6 + - - +
424A PRO* 3.7 5.4 - - - +
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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