Contacts of the helix formed by residues 447 - 455 (chain A) in PDB entry 4ZZH
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 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A CYS* 4.0 19.3 - - + -
363A HIS* 3.7 20.4 - - + +
418A LEU* 4.3 24.9 - - + -
422A PHE* 3.5 37.5 - - + -
426A MET* 5.7 0.2 - - - +
446A ARG* 1.3 84.9 - - + +
448A VAL* 1.3 67.9 + - + +
449A ALA 3.2 2.7 - - - -
450A LEU* 3.4 19.8 + - + +
451A ILE* 3.5 11.3 - - - +
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Residues in contact with VAL 448 (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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259A LEU* 3.6 29.1 - - + +
260A THR 5.2 1.3 - - - +
343A TYR* 4.8 9.6 - - + +
344A THR 4.4 0.9 - - - +
345A GLN* 3.5 42.4 - - + +
362A CYS* 3.8 32.8 - - + -
363A HIS* 4.6 2.5 - - + -
441A SER* 5.3 0.9 - - - +
443A LEU* 3.5 13.1 - - + +
445A VAL 4.5 1.1 - - - +
446A ARG 3.4 0.8 - - - -
447A PRO* 1.3 84.9 - - + +
449A ALA* 1.3 61.9 + - - +
450A LEU 3.2 1.0 + - - -
451A ILE* 3.3 26.8 + - + +
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Residues in contact with ALA 449 (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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345A GLN* 4.8 0.2 - - - +
443A LEU* 3.2 45.0 - - - +
444A LYS* 3.9 2.9 - - - -
445A VAL 3.2 25.5 + - - +
446A ARG* 4.2 4.7 - - + +
447A PRO 3.2 0.6 - - - -
448A VAL* 1.3 78.2 - - - +
450A LEU* 1.3 68.5 + - + +
451A ILE 3.4 0.4 + - - -
452A PRO* 3.7 11.1 - - - +
453A SER* 4.4 6.2 + - - -
471A HIS* 5.4 1.4 + - - -
472A LEU* 5.0 3.5 - - - +
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Residues in contact with LEU 450 (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 MET* 5.2 1.5 - - - +
446A ARG* 3.7 51.4 - - + +
447A PRO* 3.4 10.0 + - + +
448A VAL 3.1 1.2 - - - -
449A ALA* 1.3 84.9 - - + +
451A ILE* 1.3 62.2 + - - +
452A PRO* 3.6 0.9 - - - -
453A SER* 3.7 13.0 + - - +
454A SER* 3.1 25.5 + - - -
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Residues in contact with ILE 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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257A ILE* 5.0 7.0 - - + -
259A LEU* 3.6 27.6 - - + -
343A TYR* 4.1 25.6 - - + -
422A PHE* 4.4 5.4 - - + -
426A MET* 4.0 28.7 - - + -
436A LEU* 4.3 7.9 - - + -
447A PRO 3.5 11.7 - - - +
448A VAL* 3.3 30.1 - - + +
450A LEU* 1.3 77.2 - - - +
452A PRO* 1.4 73.2 - - + +
454A SER* 2.7 20.2 + - - +
455A ILE* 3.7 15.3 + - + +
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Residues in contact with PRO 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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234A ARG* 4.9 4.1 - - - +
259A LEU* 3.9 9.2 - - + -
436A LEU* 4.5 13.9 - - + -
438A VAL* 4.7 0.7 - - + -
443A LEU* 3.6 28.3 - - + -
448A VAL 3.8 6.3 - - - +
449A ALA 3.7 12.1 - - - +
451A ILE* 1.4 93.4 - - + +
453A SER* 1.3 57.5 + - - +
454A SER 3.1 4.4 + - - -
455A ILE* 3.5 8.8 + - - +
461A GLN* 3.2 40.7 + - - +
472A LEU* 4.1 20.9 - - + -
474A PHE* 4.9 1.3 - - + -
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Residues in contact with SER 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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232A PRO 5.4 2.6 - - - +
233A LYS* 3.2 32.3 + - - +
234A ARG* 6.2 3.4 - - - +
449A ALA 4.4 7.8 + - - -
450A LEU* 3.7 13.0 + - - +
451A ILE 3.2 0.8 - - - -
452A PRO* 1.3 76.6 - - - +
454A SER* 1.3 58.0 + - - +
455A ILE 3.6 3.8 - - - +
457A HIS* 5.0 8.0 + - - -
472A LEU* 3.5 19.4 - - - +
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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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426A MET* 3.6 17.1 - - - +
430A LYS* 4.2 21.1 + - - +
450A LEU* 3.1 15.5 + - - -
451A ILE* 2.7 23.9 + - - -
452A PRO 3.1 0.4 - - - -
453A SER* 1.3 78.9 - - - +
455A ILE* 1.3 63.2 + - - +
456A PRO* 4.5 0.9 - - - +
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Residues in contact with ILE 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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234A ARG* 5.4 0.3 - - - +
257A ILE* 5.0 6.1 - - + -
426A MET* 5.8 2.2 - - + -
430A LYS* 4.2 23.1 - - + +
433A VAL* 4.3 12.1 - - + -
436A LEU* 4.1 20.0 - - + -
451A ILE* 3.8 20.4 - - + +
452A PRO* 3.5 18.3 - - + +
453A SER 4.6 1.2 - - - +
454A SER* 1.3 84.5 + - - +
456A PRO* 1.3 75.7 - - + +
457A HIS* 3.3 14.7 + - - -
459A VAL* 3.9 32.3 - - + -
461A GLN* 3.5 19.1 + - - +
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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