Contacts of the strand formed by residues 251 - 255 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249L ALA* 3.6 22.2 - - - +
250L LYS* 1.3 72.3 - - - +
252L HIS* 1.3 60.4 + - - +
280L CYS 3.8 2.9 + - - -
281L MET* 3.2 25.3 - - - +
282L ALA 3.1 21.4 + - - +
283L LEU* 3.6 10.4 - - + +
284L SER* 3.2 8.8 + - - -
285L VAL* 3.1 25.1 + - - +
410L ASN* 3.7 3.0 - - - +
411L GLY* 2.8 48.6 + - - +
412L THR* 5.1 0.2 - - - -
439L PRO 5.1 2.4 - - - +
441L PRO* 5.5 1.0 - - - +
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Residues in contact with HIS 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L LYS* 2.9 29.4 + - + -
251L ASN* 1.3 74.6 - - - +
253L ALA* 1.3 58.2 + - - +
283L LEU* 4.0 3.0 - - - +
285L VAL* 3.1 30.0 - - + +
287L VAL* 3.8 16.2 - - + -
379L TYR* 2.7 37.4 + + - -
402L LEU* 4.4 4.4 - - + +
403L ILE* 3.5 40.0 - - + +
406L HIS* 4.0 23.6 - + + -
411L GLY 3.8 3.4 + - - -
412L THR* 2.7 28.9 + - - +
413L CYS* 3.3 7.3 + - - +
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Residues in contact with ALA 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252L HIS* 1.3 73.6 - - - +
254L ILE* 1.3 59.8 + - - +
255L VAL* 3.6 2.5 + - + +
268L LEU* 4.5 3.8 - - + -
283L LEU* 3.4 33.0 - - + -
285L VAL 2.7 9.6 + - - +
286L ALA* 3.5 4.0 - - + -
287L VAL* 2.7 33.2 + - - +
413L CYS* 3.4 9.6 - - + +
415L PHE* 3.9 22.2 - - + -
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Residues in contact with ILE 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L ALA* 1.3 72.1 - - - +
255L VAL* 1.3 63.2 + - - +
256L MET* 3.7 32.0 + - + -
287L VAL* 3.4 8.1 - - + +
289L VAL* 4.0 11.0 - - + -
396L MET* 4.3 9.0 - - + +
399L ALA* 3.8 30.1 - - + -
400L MET* 4.0 12.3 - - + -
403L ILE* 4.2 11.7 - - + -
413L CYS 3.0 6.6 + - - +
414L ILE* 4.0 9.1 - - + +
415L PHE* 2.9 30.1 + - - +
425L PHE* 3.4 36.6 - - + -
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Residues in contact with VAL 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L ALA 4.4 6.7 - - - +
254L ILE* 1.3 74.1 - - - +
256L MET* 1.3 65.9 + - - +
259L ALA* 4.5 9.4 - - + -
261L MET* 3.7 36.8 - - + -
264L ALA* 4.8 7.0 - - + -
268L LEU* 4.7 8.1 - - + -
286L ALA* 4.9 2.7 - - + -
287L VAL 2.9 10.8 + - - +
288L ALA* 4.0 7.3 - - + -
289L VAL* 3.0 25.9 + - - +
293L ALA* 4.5 5.3 - - + +
297L LEU* 4.3 24.9 - - + -
415L PHE* 4.1 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
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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