Contacts of the strand formed by residues 251 - 255 (chain I) 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 ASN 251 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249I ALA* 3.5 23.8 - - - +
250I LYS* 1.3 73.3 + - - +
252I HIS* 1.3 59.9 + - - +
280I CYS 4.0 2.2 + - - -
281I MET* 3.5 23.2 - - - +
282I ALA 3.2 21.0 + - - +
283I LEU* 3.5 12.8 - - + +
284I SER* 3.2 11.1 + - - -
285I VAL* 3.2 22.7 + - - +
410I ASN* 3.8 2.4 - - - +
411I GLY* 2.7 47.8 + - - +
439I PRO 5.2 3.7 - - - +
441I PRO* 5.4 1.2 - - - +
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Residues in contact with HIS 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I LYS* 2.7 30.6 + - + -
251I ASN* 1.3 74.6 - - - +
253I ALA* 1.3 60.1 + - - +
254I ILE 4.2 0.2 - - - -
283I LEU* 3.9 2.3 - - - +
285I VAL* 3.2 33.2 - - + +
287I VAL* 3.8 16.6 - - + -
379I TYR* 2.7 34.4 + + - -
402I LEU* 4.5 4.0 - - + +
403I ILE* 3.6 38.9 - - + +
406I HIS* 4.0 21.8 - + + -
411I GLY 3.9 2.8 + - - -
412I THR* 2.8 24.8 + - - +
413I CYS* 3.1 8.3 + - - +
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Residues in contact with ALA 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252I HIS* 1.3 72.7 - - - +
254I ILE* 1.3 62.7 - - - +
255I VAL* 3.6 3.4 + - + +
268I LEU* 4.3 3.8 - - + -
283I LEU* 3.4 33.9 - - + -
285I VAL 3.0 6.8 + - - +
286I ALA* 3.5 4.2 - - + -
287I VAL* 2.8 27.5 + - - +
413I CYS* 3.2 10.5 - - + +
415I PHE* 3.9 22.7 - - + -
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Residues in contact with ILE 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ALA* 1.3 71.9 - - - +
255I VAL* 1.3 58.8 + - - +
256I MET* 3.8 30.2 + - + -
287I VAL* 3.5 10.5 - - + +
289I VAL* 4.2 9.0 - - + -
396I MET* 4.4 7.9 - - + +
399I ALA* 3.7 30.5 - - + -
400I MET* 3.8 12.3 - - + -
403I ILE* 4.0 14.4 - - + -
413I CYS 2.9 10.6 + - - +
414I ILE* 3.4 7.4 - - + -
415I PHE* 2.8 34.0 + - - -
425I PHE* 3.5 34.1 - - + -
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Residues in contact with VAL 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ALA 4.2 7.6 - - - +
254I ILE* 1.3 73.3 - - - +
256I MET* 1.3 63.9 + - - +
257I PRO 4.0 0.2 - - - -
259I ALA* 4.4 9.6 - - + -
261I MET* 3.8 36.3 - - + -
264I ALA* 4.8 4.5 - - + -
268I LEU* 4.6 6.7 - - + -
286I ALA* 4.9 2.2 - - + -
287I VAL 3.0 12.7 + - - +
288I ALA* 4.6 5.2 - - - -
289I VAL* 3.1 23.5 + - - +
293I ALA* 4.0 7.4 - - + +
297I LEU* 4.4 25.6 - - + -
415I PHE* 3.9 22.2 - - + -
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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