Contacts of the strand formed by residues 411 - 415 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F LYS 4.8 0.7 - - - +
251F ASN* 3.1 42.7 + - - +
252F HIS 4.0 0.3 + - - -
281F MET* 3.6 9.9 - - - -
403F ILE* 5.9 0.3 - - - +
409F GLY 3.8 0.2 - - - -
410F ASN* 1.3 82.0 + - - +
412F THR* 1.3 64.4 + - - -
431F VAL* 3.7 5.6 - - - +
433F MET 3.3 8.5 - - - -
441F PRO* 4.9 0.7 - - - -
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Residues in contact with THR 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F ASN* 4.0 1.7 + - - -
252F HIS* 3.0 20.0 + - - +
283F LEU* 5.8 0.4 - - - -
403F ILE* 3.9 15.5 - - - +
411F GLY* 1.3 76.4 - - - -
413F CYS* 1.3 53.7 + - - +
425F PHE* 3.4 29.5 - - + -
429F ILE* 4.0 10.1 - - + -
431F VAL* 3.4 31.0 - - + -
433F MET 3.0 8.3 + - - +
434F VAL* 3.5 4.3 - - + -
435F GLY* 2.6 32.4 + - - -
439F PRO 5.8 0.4 - - - -
441F PRO* 3.8 6.7 - - - +
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Residues in contact with CYS 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F HIS 3.0 6.6 + - - +
253F ALA* 3.2 4.4 - - + -
254F ILE* 3.1 20.1 + - - +
283F LEU* 4.0 12.8 - - + -
412F THR* 1.3 76.8 + - - +
414F ILE* 1.3 76.8 + - - +
415F PHE* 3.6 31.4 - - - -
425F PHE* 3.7 9.9 - - - -
435F GLY 3.3 6.1 - - - -
437F ASN 4.2 0.4 - - - -
438F ILE 3.5 41.3 - - - +
439F PRO* 3.8 9.0 - - + -
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Residues in contact with ILE 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F ILE* 3.6 16.6 - - + +
256F MET* 3.9 20.0 - - + -
396F MET* 3.7 30.7 - - + -
413F CYS* 1.3 78.6 - - - +
415F PHE* 1.3 61.6 + - - +
416F THR* 3.9 18.5 + - + -
421F ALA* 4.4 4.0 - - + +
422F ALA* 4.8 2.2 - - - -
425F PHE* 3.1 38.6 - - + -
435F GLY 3.0 13.4 + - - +
436F ILE* 3.6 17.4 - - + +
437F ASN* 2.7 32.6 + - - +
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Residues in contact with PHE 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ALA* 3.9 16.4 - - + -
254F ILE 2.9 19.4 + - - +
255F VAL* 4.2 13.0 - - + -
256F MET* 3.1 24.6 + - - +
259F ALA* 3.6 18.3 - - + +
260F ASP 5.5 0.7 - - - +
263F ASN* 4.8 2.9 - - - -
264F ALA* 3.9 35.0 - - + -
267F GLN* 3.7 25.1 - - + -
268F LEU* 4.3 16.2 - - + -
413F CYS* 3.6 25.6 - - - -
414F ILE* 1.3 70.6 - - - +
416F THR* 1.3 66.2 + - - +
437F ASN* 3.2 22.0 - - + +
439F PRO* 4.2 15.7 - - + -
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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