Contacts of the strand formed by residues 251 - 255 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249G ALA* 3.5 24.0 - - - +
250G LYS* 1.3 74.3 - - - +
252G HIS* 1.3 61.1 + - - +
280G CYS 3.9 1.2 + - - -
281G MET* 3.4 29.3 - - - +
282G ALA 3.7 16.6 + - - +
283G LEU* 3.8 12.5 - - + +
284G SER* 3.4 9.2 + - - -
285G VAL* 3.2 23.2 + - - +
410G ASN* 3.8 2.6 - - - +
411G GLY* 2.8 47.3 + - - +
412G THR* 5.0 0.4 - - - -
439G PRO 5.1 2.3 - - - +
441G PRO* 5.4 1.9 - - - +
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Residues in contact with HIS 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G LYS* 2.8 40.2 + - + -
251G ASN* 1.3 76.9 - - - +
253G ALA* 1.3 61.7 + - - +
283G LEU* 3.7 4.9 - - - +
285G VAL* 3.3 30.5 - - + +
287G VAL* 3.7 16.4 - - + -
379G TYR* 2.8 36.2 + + - -
402G LEU* 4.7 3.3 - - + +
403G ILE* 3.5 40.7 - - + +
406G HIS* 4.2 12.8 - + + -
411G GLY 3.8 3.8 + - - -
412G THR* 3.2 7.7 + - - +
413G CYS 3.1 21.3 + - - -
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Residues in contact with ALA 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252G HIS* 1.3 75.5 - - - +
254G ILE* 1.3 60.9 + - - +
255G VAL* 3.6 3.4 + - + +
268G LEU* 4.4 3.4 - - + -
283G LEU* 3.5 29.4 - - + -
285G VAL 2.9 7.8 + - - +
286G ALA* 3.6 3.7 - - - -
287G VAL* 2.7 34.3 + - - +
413G CYS* 3.4 10.3 - - + -
415G PHE* 3.8 22.7 - - + -
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Residues in contact with ILE 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ALA* 1.3 72.4 - - - +
255G VAL* 1.3 59.2 + - - +
256G MET* 3.6 32.2 + - + +
287G VAL* 3.6 6.7 - - + +
289G VAL* 4.4 8.3 - - + -
396G MET* 4.4 5.6 - - + +
399G ALA* 3.7 31.6 - - + -
400G MET* 3.9 12.8 - - + -
403G ILE* 4.1 15.0 - - + -
413G CYS 3.0 7.0 + - - +
414G ILE* 3.5 14.1 - - + -
415G PHE* 2.8 33.0 + - - +
425G PHE* 3.4 34.8 - - + -
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Residues in contact with VAL 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ALA 4.2 5.6 - - - +
254G ILE* 1.3 72.3 - - - +
256G MET* 1.3 64.3 + - - +
259G ALA* 4.5 5.4 - - + -
261G MET* 3.7 38.6 - - + -
264G ALA* 5.1 2.9 - - + -
268G LEU* 4.8 5.8 - - + -
286G ALA* 4.9 2.9 - - + -
287G VAL 3.0 15.7 + - - +
288G ALA* 4.5 5.6 - - + -
289G VAL* 3.2 23.0 + - - +
293G ALA* 4.3 9.7 - - + +
297G LEU* 4.6 25.4 - - + -
415G PHE* 4.0 22.4 - - + -
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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