Contacts of the strand formed by residues 411 - 415 (chain H) in PDB entry 4ZZ7
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 GLY 411 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250H LYS 4.8 0.5 - - - +
251H ASN* 3.0 44.2 + - - +
252H HIS 3.9 1.0 + - - -
281H MET* 3.6 10.1 - - - -
409H GLY 3.8 0.2 - - - -
410H ASN* 1.3 82.7 + - - +
412H THR* 1.3 63.7 + - - -
431H VAL* 3.9 4.4 - - - +
433H MET 3.3 8.7 - - - -
441H PRO* 5.0 1.1 - - - -
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Residues in contact with THR 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H ASN* 5.1 0.9 - - - -
252H HIS 2.9 17.0 + - - -
283H LEU* 5.8 0.9 - - - -
403H ILE* 3.7 14.6 - - - +
411H GLY* 1.3 75.9 - - - -
413H CYS* 1.3 67.4 + - - +
425H PHE* 3.4 32.3 - - + -
429H ILE* 4.1 4.0 - - + -
431H VAL* 3.4 32.8 - - + -
433H MET 2.9 6.5 + - - -
434H VAL* 3.4 11.3 - - + -
435H GLY 2.9 22.9 + - - -
439H PRO 5.4 0.4 - - - -
441H PRO* 3.4 9.9 - - - +
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Residues in contact with CYS 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H HIS 3.1 3.9 + - - +
253H ALA* 3.2 12.9 - - + -
254H ILE 3.0 22.3 + - - -
283H LEU* 4.2 3.1 - - + -
412H THR* 1.3 79.0 + - - +
414H ILE* 1.3 75.4 + - - +
415H PHE* 3.9 19.7 - - - -
425H PHE* 3.6 9.6 - - - -
435H GLY 3.2 7.2 - - - -
438H ILE 3.1 46.4 - - - +
439H PRO* 3.5 15.5 - - + +
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Residues in contact with ILE 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H ILE* 3.6 16.2 - - + +
256H MET* 4.0 16.4 - - + -
396H MET* 3.8 29.4 - - + -
413H CYS* 1.3 74.5 - - - +
415H PHE* 1.3 60.4 + - - +
416H THR* 3.8 23.9 + - + -
421H ALA* 4.2 3.4 - - + +
422H ALA* 4.8 1.1 - - - -
425H PHE* 3.2 38.8 - - + -
435H GLY 2.9 13.6 + - - +
436H ILE* 3.6 19.8 - - + +
437H ASN* 2.6 31.5 + - - -
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Residues in contact with PHE 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H ALA* 3.8 24.2 - - + -
254H ILE 3.1 11.0 + - - +
255H VAL* 4.0 21.3 - - + -
256H MET* 3.3 23.2 + - - +
259H ALA* 3.3 19.6 - - + +
260H ASP 5.8 0.4 - - - +
263H ASN* 4.8 2.2 - - - -
264H ALA* 3.8 29.8 - - + -
267H GLN* 3.9 21.1 - - - -
268H LEU* 4.1 24.0 - - + -
413H CYS* 3.9 16.6 - - - -
414H ILE* 1.3 70.3 - - - +
416H THR* 1.3 64.5 + - - +
437H ASN* 3.1 23.6 - - + +
439H PRO* 4.0 17.7 - - + -
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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
------------------------------------------------------------
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