Contacts of the strand formed by residues 411 - 415 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LYS 4.7 0.7 - - - +
251A ASN* 2.9 43.9 + - - +
252A HIS 3.9 0.7 + - - -
281A MET* 3.7 9.6 - - - -
409A GLY 3.7 0.4 - - - -
410A ASN* 1.3 81.9 + - - +
412A THR* 1.3 62.4 + - - -
431A VAL* 3.7 5.0 - - - +
433A MET 3.2 11.0 - - - -
441A PRO* 5.2 2.0 - - - -
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASN* 5.1 1.1 - - - -
252A HIS 2.8 23.5 + - - +
283A LEU* 5.8 0.9 - - - -
403A ILE* 3.9 11.8 - - - +
411A GLY* 1.3 76.1 - - - -
413A CYS* 1.3 56.4 + - - +
425A PHE* 3.2 33.9 - - + -
429A ILE* 4.1 9.9 - - + -
431A VAL* 3.4 29.6 - - + -
433A MET 2.9 5.5 + - - -
434A VAL* 4.0 8.1 - - - -
435A GLY 2.8 27.9 + - - -
439A PRO 5.3 1.1 - - - -
441A PRO* 3.4 11.3 - - - +
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Residues in contact with CYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS 3.1 6.2 + - - +
253A ALA* 3.2 12.0 - - + -
254A ILE 3.0 21.1 + - - -
283A LEU* 4.3 2.5 - - + -
412A THR* 1.3 74.9 + - - +
414A ILE* 1.3 85.9 + - - +
415A PHE* 3.8 18.8 - - - -
425A PHE* 3.7 11.1 - - - -
435A GLY 3.4 7.6 - - - -
437A ASN 3.9 1.3 - - - -
438A ILE 3.3 43.7 - - - +
439A PRO* 3.7 12.6 - - + -
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Residues in contact with ILE 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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254A ILE* 3.5 18.4 - - + +
256A MET* 4.0 16.4 - - + -
396A MET* 3.7 29.6 - - + -
413A CYS* 1.3 79.8 - - - +
415A PHE* 1.3 67.3 + - - +
416A THR* 3.8 17.2 + - + -
421A ALA* 4.4 3.8 - - + +
422A ALA* 4.6 1.3 - - - -
425A PHE* 3.4 35.9 - - + -
435A GLY 3.1 2.8 + - - +
436A ILE* 3.7 23.3 - - + -
437A ASN* 2.7 31.4 + - - -
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Residues in contact with PHE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 3.8 23.1 - - + -
254A ILE 2.8 12.8 + - - +
255A VAL* 3.9 21.8 - - + -
256A MET* 3.2 25.6 + - - +
259A ALA* 3.4 19.9 - - + +
260A ASP 5.6 0.9 - - - -
263A ASN* 5.1 1.6 - - - -
264A ALA* 3.9 28.3 - - + -
267A GLN* 4.0 19.7 - - + -
268A LEU* 4.0 31.2 - - + -
413A CYS* 3.8 17.9 - - - -
414A ILE* 1.3 69.4 - - - +
416A THR* 1.3 63.2 + - - +
437A ASN* 3.3 21.8 - - + +
439A PRO* 4.2 10.5 - - + -
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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