Contacts of the helix formed by residues 268 - 273 (chain A) in PDB entry 2Z1Z
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 PHE 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 5.0 0.2 - - + -
107A ILE* 4.7 4.5 - - + -
111A PHE* 4.3 2.5 - + - -
267A SER* 1.3 71.6 - - - +
269A SER* 1.3 58.1 + - - +
270A LYS 3.2 1.2 + - - -
271A TYR* 3.4 17.7 + + - -
272A ALA* 2.9 44.7 + - + +
273A GLY 3.8 0.2 + - - -
274A PHE* 3.8 22.0 - + + -
279A LEU* 2.8 35.9 + - + +
281A TRP* 3.6 26.0 - + - -
319A ALA* 3.3 32.8 - - + -
322A CYS* 3.8 19.5 - - + -
323A LEU* 3.7 36.1 - - + -
331A MET* 4.4 7.0 - - - -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.5 7.4 - - - +
267A SER* 3.1 12.5 + - - -
268A PHE* 1.3 76.3 - - - +
270A LYS* 1.3 64.2 + - - +
273A GLY* 3.2 24.9 + - - -
274A PHE* 3.4 20.7 + - - +
275A THR* 3.6 17.5 - - - +
278A ARG* 3.3 13.9 + - - -
279A LEU 4.2 2.7 + - - -
500A PLP 3.0 24.3 + - - -
94B TYR* 3.9 2.9 - - - -
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Residues in contact with LYS 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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64A GLY* 2.9 25.7 + - - -
66A THR* 3.9 11.4 - - + +
239A ALA* 4.2 17.9 - - + +
240A TYR* 2.9 41.5 + - + +
243A TYR* 2.7 31.5 + - + +
267A SER* 4.5 4.7 + - - +
268A PHE 3.3 0.6 - - - -
269A SER* 1.3 83.0 - - - +
271A TYR* 1.3 61.3 + - + +
273A GLY 4.4 0.6 + - - -
275A THR* 4.0 9.6 - - - -
334A VAL* 5.1 1.0 - - - +
335A ILE* 4.9 0.3 - - - +
338A TYR* 4.9 2.9 - - - -
408A PHE* 3.7 18.3 - - + -
433A MLT 3.9 5.9 - - - -
500A PLP 2.8 30.5 - - + +
94B TYR* 3.3 22.7 + - - -
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Residues in contact with TYR 271 (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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111A PHE* 4.1 24.8 - + - -
238A SER* 3.3 18.5 + - - -
239A ALA 2.9 28.0 + - - -
240A TYR 4.4 0.7 - - - -
241A ALA* 4.4 1.2 + - - +
242A MET* 3.6 50.2 - - + +
243A TYR* 4.8 4.5 - + - -
266A ALA* 4.0 13.5 - - - +
267A SER 3.6 21.3 - - - -
268A PHE* 4.1 12.3 - + - +
270A LYS* 1.3 82.6 - - + +
272A ALA* 1.3 58.5 + - + +
273A GLY 3.6 0.2 - - - -
281A TRP* 4.2 10.4 - + - -
331A MET* 3.8 33.1 - - + +
334A VAL* 3.7 20.5 - - - +
335A ILE* 4.4 12.4 - - + +
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Residues in contact with ALA 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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70A ILE* 3.7 22.0 - - - +
71A PRO* 4.2 10.3 - - - +
74A ILE* 5.3 2.9 - - + -
268A PHE* 2.9 18.8 + - + +
271A TYR* 1.3 76.8 - - - +
273A GLY* 1.3 60.8 + - - +
274A PHE* 3.3 17.0 - - + -
322A CYS* 3.7 30.3 - - - -
331A MET* 4.1 11.4 - - + -
334A VAL* 5.3 4.3 - - - -
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Residues in contact with GLY 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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66A THR* 3.5 20.0 - - - -
68A GLU 5.5 2.0 - - - -
70A ILE* 3.9 4.8 - - - +
269A SER 3.2 14.4 + - - -
270A LYS 4.4 0.8 + - - -
271A TYR 3.6 2.4 - - - +
272A ALA* 1.3 78.1 - - - +
274A PHE* 1.3 57.0 + - - +
275A THR 3.1 8.1 + - - -
276A GLY 4.7 0.3 + - - -
277A VAL* 5.0 0.3 - - - +
334A VAL* 5.4 3.0 - - - +
338A TYR* 6.3 0.2 - - - -
91B TYR* 2.5 33.1 + - - -
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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