Contacts of the strand formed by residues 251 - 255 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D ALA* 3.5 22.2 - - - +
250D LYS* 1.3 74.1 - - - +
252D HIS* 1.3 61.4 + - - +
280D CYS 4.2 3.1 - - - -
281D MET* 3.4 27.3 - - - +
282D ALA 3.2 19.4 + - - +
283D LEU* 3.7 10.1 - - + -
284D SER* 3.1 26.3 + - - -
285D VAL 3.2 8.3 + - - +
410D ASN* 3.7 3.2 - - - +
411D GLY* 2.9 47.2 + - - +
412D THR* 5.1 0.4 - - - -
439D PRO 6.0 0.4 - - - +
441D PRO* 5.6 1.2 - - - +
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Residues in contact with HIS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D LYS* 2.8 31.2 + - + -
251D ASN* 1.3 75.6 - - - +
253D ALA* 1.3 60.2 + - - +
283D LEU* 3.9 4.2 - - - +
285D VAL* 3.2 26.0 - - + +
287D VAL* 3.8 23.6 - - + -
379D TYR* 2.8 34.6 + + - -
402D LEU* 4.6 2.7 - - + -
403D ILE* 3.6 43.6 - - + +
406D HIS* 4.1 18.6 - + + -
411D GLY 3.9 3.6 + - - -
412D THR* 2.9 21.8 + - - +
413D CYS 3.1 9.2 + - - -
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Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D HIS* 1.3 74.2 - - - +
254D ILE* 1.3 60.1 + - - +
255D VAL* 3.8 2.3 + - + +
268D LEU* 4.3 3.6 - - + -
283D LEU* 3.5 24.9 - - + -
285D VAL 2.9 7.2 + - - +
286D ALA* 3.5 3.9 - - - +
287D VAL* 2.7 35.1 + - - +
413D CYS* 3.2 10.3 - - + +
415D PHE* 3.8 28.3 - - + -
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Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ALA* 1.3 72.9 - - - +
255D VAL* 1.3 61.9 + - - +
256D MET* 4.0 28.0 + - + -
287D VAL* 3.3 6.7 - - + +
289D VAL* 4.0 10.8 - - + -
396D MET* 4.3 9.2 - - + +
399D ALA* 3.5 33.4 - - + -
400D MET* 3.7 15.9 - - + -
403D ILE* 4.0 15.5 - - + -
413D CYS 3.0 6.0 + - - +
414D ILE* 3.6 9.8 - - + -
415D PHE* 2.9 31.7 + - - +
425D PHE* 3.7 30.1 - - + -
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ALA* 4.6 4.9 - - + +
254D ILE* 1.3 72.8 - - - +
256D MET* 1.3 67.3 + - - +
259D ALA* 4.6 9.4 - - + -
261D MET* 3.7 36.6 - - + -
264D ALA* 4.6 7.4 - - + -
268D LEU* 4.6 10.3 - - + -
286D ALA* 5.0 2.5 - - + -
287D VAL 2.9 14.9 + - - +
288D ALA* 3.9 7.3 - - + -
289D VAL* 3.2 24.9 + - - +
293D ALA* 4.2 4.3 - - + +
297D LEU* 4.5 19.3 - - + -
415D PHE* 3.9 21.8 - - + -
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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