Contacts of the helix formed by residues 268 - 273 (chain A) in PDB entry 1ZD4
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 SER 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A HIS* 3.2 26.0 - - - +
267A GLU* 1.3 80.0 - - - +
269A TRP* 1.3 66.0 + - - +
270A TYR* 2.9 26.6 + - - +
271A SER* 3.0 18.5 + - - -
272A TRP* 4.4 0.3 - - - -
290A ASP* 3.9 9.9 - - - -
294A TYR* 5.1 2.7 - - - -
295A GLY* 5.5 1.8 - - - -
448A PHE* 3.9 9.8 - - - -
449A TYR* 4.2 8.0 - - - -
452A GLN* 5.0 9.2 - - - -
453A PHE* 4.9 5.2 - - - -
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Residues in contact with TRP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A CYS* 3.8 15.7 - - - -
232A PRO* 4.0 29.4 - - + -
235A MET* 4.0 6.5 - - + -
237A HIS* 4.5 6.8 - + - -
249A HIS* 3.8 19.4 - + + -
251A VAL* 3.3 31.7 - - + +
263A HIS* 4.2 0.9 - - - -
268A SER* 1.3 78.8 - - - +
270A TYR* 1.3 82.1 + + - +
271A SER 3.1 2.0 + - - -
272A TRP* 3.1 25.3 + - - +
273A ARG* 5.3 0.2 - - - -
276A ILE* 3.6 24.8 - - + +
288A ALA* 3.9 12.1 - - + +
289A MET 2.9 31.2 + - - +
290A ASP* 3.4 21.4 + - - -
296A GLU* 5.7 1.0 + - - +
448A PHE* 4.0 26.7 - + - -
452A GLN* 5.2 4.2 + - - -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 4.5 3.1 + - - -
230A CYS 4.0 12.0 + - - -
232A PRO* 4.0 22.4 - - + +
268A SER* 2.9 14.9 + - - +
269A TRP* 1.3 98.5 - + + +
271A SER* 1.3 55.5 + - - +
272A TRP 3.0 6.6 + - - -
273A ARG* 2.8 84.5 + - + +
445A GLU* 3.9 33.7 + - - +
448A PHE* 3.4 34.3 - + + -
449A TYR* 3.6 11.0 - + + +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS* 4.6 3.8 - - - -
267A GLU* 2.9 49.1 + - - +
268A SER 3.0 12.7 + - - -
270A TYR* 1.3 76.5 - - - +
272A TRP* 1.3 59.4 + - - +
273A ARG* 3.5 7.0 + - - +
274A TYR* 5.7 0.3 - - - -
275A GLN* 3.7 0.3 - - - +
449A TYR* 3.1 17.8 + - - -
526A GLN* 3.0 37.4 - - - +
527A MET* 4.1 5.1 + - - +
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Residues in contact with TRP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 3.5 48.5 - - + +
262A CYS 3.8 19.1 - - - -
263A HIS* 3.6 23.7 - - + +
268A SER 4.4 4.5 - - - -
269A TRP* 3.1 21.3 + - - +
270A TYR 3.0 1.4 - - - -
271A SER* 1.3 79.1 - - - +
273A ARG* 1.3 52.8 + - - +
274A TYR 2.7 7.4 + - - -
275A GLN* 2.7 57.2 + - + -
276A ILE* 2.9 18.2 + - + +
288A ALA* 4.7 2.2 - - + -
289A MET 5.4 0.2 - - - -
330A ILE* 3.9 26.2 - - + -
331A GLY 4.1 4.5 - - - -
332A HIS* 4.1 4.7 - - + -
356A LEU* 3.8 27.4 - - + -
526A GLN* 3.5 28.4 - - + +
533A VAL* 5.4 0.2 - - + -
537A LEU* 4.7 5.6 - - + -
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A THR 3.3 8.5 - - - +
229A SER* 3.4 24.7 - - - +
230A CYS* 3.4 17.9 + - - +
269A TRP 4.2 0.8 + - - -
270A TYR* 2.8 76.3 + - + +
271A SER* 3.9 5.2 - - - +
272A TRP* 1.3 77.3 - - - +
274A TYR* 1.3 75.9 + - + +
276A ILE* 4.5 1.1 - - - -
277A PRO* 3.2 18.3 - - - +
440A MET 4.6 0.6 + - - -
441A VAL* 3.5 15.0 - - - +
445A GLU* 2.6 30.7 + - - +
449A TYR* 3.0 20.6 + - - -
527A MET* 3.1 38.0 - - - +
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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
------------------------------------------------------------
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