Contacts of the helix formed by residues 268 - 273 (chain P) in PDB entry 1ZD2
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P HIS* 3.2 31.4 + - - +
267P GLU* 1.3 81.4 - - - +
269P TRP* 1.3 66.3 + - - +
270P TYR* 2.8 28.8 + - - +
271P SER* 2.9 12.3 + - - -
272P TRP* 4.1 0.3 - - - -
290P ASP* 3.8 11.0 - - - -
294P TYR* 5.4 0.9 - - - -
295P GLY 5.5 1.1 - - - -
448P PHE* 3.9 8.6 - - - -
449P TYR* 3.9 10.2 - - - -
452P GLN* 5.1 7.6 - - - -
453P PHE* 4.9 4.3 - - - -
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Residues in contact with TRP 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230P CYS* 4.1 12.8 - - - -
232P PRO* 3.8 39.3 - - + -
235P MET* 3.9 8.7 - - + -
237P HIS* 4.3 6.9 - + - -
249P HIS* 3.9 25.1 - + + -
251P VAL* 3.4 24.2 - - + -
263P HIS* 4.3 0.7 - - - -
268P SER* 1.3 80.3 - - - +
270P TYR* 1.3 81.4 + + - +
271P SER 3.0 0.2 - - - -
272P TRP* 2.9 32.6 + - - +
273P ARG* 5.2 0.4 - - - -
276P ILE* 3.7 24.4 - - + +
288P ALA* 3.7 16.3 - - + +
289P MET 3.1 27.3 + - - +
290P ASP* 3.5 17.3 + - + -
296P GLU* 5.5 0.6 + - - -
448P PHE* 3.8 18.9 - + - -
452P GLN* 5.0 3.9 + - - -
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Residues in contact with TYR 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229P SER* 4.4 2.9 + - - -
230P CYS 3.7 22.8 + - - -
232P PRO* 3.7 19.1 - - + +
268P SER* 2.8 14.1 + - - +
269P TRP* 1.3 101.1 - + + +
271P SER* 1.3 53.8 + - - +
272P TRP 2.9 6.5 - - - -
273P ARG* 2.9 75.0 + - + +
445P GLU* 3.9 30.1 + - - +
448P PHE* 3.3 36.3 - + + +
449P TYR* 3.7 9.9 - + + -
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Residues in contact with SER 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P HIS* 4.2 3.6 - - - -
267P GLU* 2.5 48.5 + - - +
268P SER 2.9 14.3 + - - -
270P TYR* 1.3 79.0 - - - +
272P TRP* 1.3 59.2 + - - +
273P ARG* 3.4 5.5 + - - +
274P TYR* 5.2 0.7 + - - -
449P TYR* 3.0 19.9 + - - -
526P GLN* 2.9 39.3 - - - +
527P MET* 4.8 3.3 + - - +
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Residues in contact with TRP 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P LEU* 3.6 43.8 - - + +
262P CYS 3.8 17.9 - - - -
263P HIS* 3.2 31.5 - - + +
268P SER 4.1 0.4 - - - -
269P TRP* 2.9 19.8 + - - +
270P TYR 2.9 1.2 - - - -
271P SER* 1.3 81.7 - - - +
273P ARG* 1.3 50.4 + - - +
274P TYR 2.6 19.9 + - - -
275P GLN* 2.9 41.1 + - + -
276P ILE* 3.1 14.8 + - + +
288P ALA* 4.8 1.6 - - + -
330P ILE* 3.8 36.1 - - + -
331P GLY 4.4 1.1 - - - -
332P HIS* 4.1 6.7 - - + -
356P LEU* 4.0 18.6 - - + -
526P GLN* 3.3 32.1 - - + -
537P LEU* 4.7 5.2 - - + -
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Residues in contact with ARG 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228P THR 3.3 13.5 - - - +
229P SER* 3.4 21.4 - - - +
230P CYS* 3.5 19.5 + - - -
269P TRP 4.0 1.2 + - - -
270P TYR* 2.9 68.3 + - + +
271P SER* 4.0 3.2 - - - +
272P TRP* 1.3 75.8 - - - +
274P TYR* 1.3 72.9 + - + +
276P ILE* 4.4 1.3 - - - -
277P PRO* 3.5 8.8 - - - +
440P MET 4.1 2.0 + - - -
441P VAL* 3.3 16.0 - - - +
445P GLU* 2.8 38.6 + - - +
449P TYR* 2.8 33.4 + - - -
527P MET* 3.2 31.4 - - - +
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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
------------------------------------------------------------
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