Contacts of the helix formed by residues 412 - 420 (chain A) in PDB entry 2IZV
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A ILE* 1.3 93.3 - - + +
413A SER* 1.3 61.4 + - - +
414A SER* 3.9 17.5 - - - +
415A MET* 3.1 18.4 + - + +
416A LYS* 3.2 9.9 + - - +
105C MET* 3.5 31.2 - - + -
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Residues in contact with SER 413 (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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411A ILE 3.8 0.2 + - - -
412A PRO* 1.3 70.5 - - - +
414A SER* 1.3 61.9 + - - +
415A MET 3.0 1.1 - - - -
416A LYS* 3.6 20.4 - - - +
417A LEU* 2.7 30.8 + - - +
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Residues in contact with SER 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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412A PRO* 3.9 14.5 - - - +
413A SER* 1.3 79.5 + - - +
415A MET* 1.3 69.6 + - - +
417A LEU* 3.3 23.1 - - - +
418A TYR* 3.3 9.0 + - - +
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Residues in contact with MET 415 (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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390A GLN* 3.2 24.9 - - - +
411A ILE* 3.7 20.4 - - + -
412A PRO* 3.1 12.1 + - + +
413A SER 3.0 0.8 - - - -
414A SER* 1.3 83.3 + - - +
416A LYS* 1.3 66.9 + - - +
417A LEU 3.2 1.1 - - - -
418A TYR* 3.1 12.2 + - + +
419A LEU* 2.9 27.0 + - - +
104C LEU* 4.0 22.2 - - - -
105C MET* 3.6 25.4 - - + +
108C ASN* 3.1 44.4 - - + +
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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
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406A ILE* 3.6 29.2 - - + +
407A ASP* 2.9 37.5 + - - +
409A LEU 3.3 21.6 + - - -
411A ILE* 3.7 21.5 + - + -
412A PRO 3.2 6.0 + - - +
413A SER* 3.1 27.1 + - - +
415A MET* 1.3 76.9 - - - +
417A LEU* 1.3 62.1 + - - +
419A LEU* 3.2 3.1 + - - +
420A LYS* 3.1 37.2 + - - +
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Residues in contact with LEU 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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413A SER 2.7 12.9 + - - +
414A SER* 3.3 15.9 - - - +
416A LYS* 1.3 76.1 - - - +
418A TYR* 1.3 66.8 - - + +
420A LYS* 3.4 17.3 + - - +
421A GLU* 3.6 10.6 + - - +
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Residues in contact with TYR 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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388A SER* 4.5 1.7 + - - -
390A GLN* 3.5 39.9 - - + +
391A HIS* 3.2 29.3 + - - +
394A ARG* 3.1 74.3 + - + +
414A SER 3.3 9.3 + - - +
415A MET* 3.1 21.9 + - + +
417A LEU* 1.3 82.0 - - + +
419A LEU* 1.3 69.6 + - + +
420A LYS 3.2 0.9 + - - -
421A GLU* 3.3 10.1 + - - +
104C LEU* 4.2 5.4 - - + -
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Residues in contact with LEU 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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274A LEU* 3.8 3.3 - - - +
394A ARG* 3.8 38.3 + - + +
397A ILE* 4.1 18.4 - - + -
398A CYS* 3.2 23.4 - - - -
406A ILE* 3.8 19.8 - - + +
409A LEU* 3.6 21.1 - - + -
411A ILE* 3.4 31.9 - - + -
415A MET 2.9 14.4 + - - +
416A LYS 3.8 3.8 - - - +
418A TYR* 1.3 77.7 - - + +
420A LYS* 1.3 60.1 + - - +
421A GLU 3.5 1.0 + - - -
422A TYR* 4.6 2.4 + - - -
104C LEU* 3.8 22.0 - - + -
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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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274A LEU* 4.6 1.6 - - - -
403A TYR* 3.5 52.0 + - + +
406A ILE* 3.8 26.7 - - + -
407A ASP* 3.2 35.9 + - - -
416A LYS* 3.1 25.4 + - - +
417A LEU* 3.8 8.7 - - - +
418A TYR 3.1 1.0 - - - -
419A LEU* 1.3 76.6 - - - +
421A GLU* 1.3 54.3 + - - +
422A TYR 3.3 2.6 + - - -
423A HIS* 2.7 38.7 + - + +
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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