Contacts of the helix formed by residues 269 - 279 (chain A) in PDB entry 3GZN
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 GLU 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LYS 4.7 1.2 - - - +
216A HIS* 2.8 38.3 + - - +
217A SER* 3.3 34.0 + - - -
258A ILE* 3.7 13.6 - - + +
259A LEU* 3.3 26.1 + - - +
267A GLU* 3.2 18.4 + - + -
268A ASP* 1.3 73.4 - - - +
270A GLU* 1.3 64.0 + - - +
271A ASN* 3.3 11.7 - - - +
272A PHE* 3.3 21.3 + - + +
273A GLU* 3.3 15.0 + - - +
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Residues in contact with GLU 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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268A ASP* 3.4 13.1 + - + +
269A GLU* 1.3 68.4 - - - +
271A ASN* 1.3 58.2 + - - +
272A PHE 3.1 2.0 - - - -
273A GLU* 2.9 16.6 + - + +
274A GLU* 2.7 42.6 + - + +
340A ILE* 4.9 8.3 - - + -
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Residues in contact with ASN 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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216A HIS 2.7 28.9 + - - -
217A SER* 3.3 30.1 + - - +
219A THR 3.4 20.1 + - - +
221A TRP* 3.5 14.2 - - - +
224A ILE* 3.4 20.5 - - - +
269A GLU* 3.4 13.9 - - - +
270A GLU* 1.3 73.0 + - - +
272A PHE* 1.3 64.6 + - - -
274A GLU* 3.7 3.2 + - - +
275A ALA* 3.1 21.3 + - - +
340A ILE* 3.9 25.2 - - + +
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Residues in contact with PHE 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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208A LEU* 5.1 4.5 - - + -
216A HIS* 3.3 42.0 - + - -
219A THR* 6.2 0.2 - - - -
224A ILE* 3.6 25.4 - - + -
228A TYR* 3.6 36.8 - + - -
254A ILE* 3.6 29.9 - - + +
257A GLY 4.1 3.6 - - - -
258A ILE* 3.9 21.1 - - + -
269A GLU* 3.3 22.3 + - - +
270A GLU 3.1 0.6 - - - -
271A ASN* 1.3 92.4 - - - +
273A GLU* 1.3 59.2 + - - +
275A ALA* 3.2 6.1 + - - +
276A ILE* 2.9 34.7 + - - +
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Residues in contact with GLU 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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255A ARG* 3.3 40.0 + - - -
258A ILE* 4.1 9.0 - - + +
268A ASP* 5.9 2.2 - - - -
269A GLU 3.3 14.3 + - - +
270A GLU* 2.9 22.3 + - + +
272A PHE* 1.3 75.9 - - - +
274A GLU* 1.3 57.2 + - - +
276A ILE* 3.2 10.8 + - - +
277A LYS* 3.0 31.9 + - + +
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Residues in contact with GLU 274 (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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221A TRP* 3.1 25.3 - - + +
270A GLU* 2.7 22.0 + - + +
271A ASN* 3.7 5.5 - - - +
273A GLU* 1.3 70.0 - - - +
275A ALA* 1.3 59.6 + - - +
277A LYS* 3.1 8.5 + - + +
278A ASN* 2.9 40.6 + - - +
339A MET* 3.6 4.8 - - - +
340A ILE* 3.0 45.2 + - - +
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Residues in contact with ALA 275 (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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221A TRP* 3.7 17.4 - - + +
224A ILE* 3.9 20.2 - - + -
225A ILE* 3.4 24.5 - - + +
254A ILE* 4.5 6.7 - - + -
271A ASN 3.1 12.5 + - - +
272A PHE 3.2 9.6 + - - +
274A GLU* 1.3 79.0 - - - +
276A ILE* 1.3 62.1 + - - +
278A ASN 3.3 0.3 + - - -
279A VAL* 3.2 27.8 + - - +
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Residues in contact with ILE 276 (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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251A ARG* 2.8 63.9 + - + +
254A ILE* 3.7 21.1 - - + -
255A ARG* 3.7 48.2 - - - +
258A ILE* 4.5 4.5 - - + -
272A PHE 2.9 25.7 + - - +
273A GLU* 3.4 15.0 - - - +
274A GLU 3.2 0.2 - - - -
275A ALA* 1.3 77.3 - - - +
277A LYS* 1.3 62.2 + - + +
278A ASN 3.5 0.2 + - - -
279A VAL* 3.7 8.6 - - - +
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Residues in contact with LYS 277 (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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251A ARG* 3.7 5.6 + - - +
273A GLU* 3.0 17.4 + - + +
274A GLU* 3.1 12.3 + - + +
276A ILE* 1.3 79.8 - - + +
278A ASN* 1.3 66.1 + - - +
279A VAL 3.4 1.0 + - - -
280A ASN* 3.6 18.4 + - - +
28I GLU* 5.0 9.0 - - - +
31I GLU* 5.0 2.6 - - - +
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Residues in contact with ASN 278 (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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221A TRP* 3.5 52.8 - - + +
225A ILE* 4.2 2.9 - - - -
274A GLU* 2.9 30.4 + - - +
275A ALA 3.3 2.0 + - - +
276A ILE 3.3 0.2 - - - -
277A LYS* 1.3 79.3 - - - +
279A VAL* 1.3 61.3 + - - +
280A ASN* 2.9 7.5 + - - -
281A THR* 3.1 16.2 + - - +
282A ALA* 3.0 24.8 + - - +
31I GLU* 4.7 8.5 - - - +
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Residues in contact with VAL 279 (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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225A ILE* 4.1 7.4 - - + +
247A LYS* 3.7 46.3 - - + +
250A PHE* 3.8 19.5 - - + -
251A ARG* 3.9 15.3 - - + +
254A ILE* 3.8 23.3 - - + -
275A ALA 3.2 16.9 + - - +
276A ILE* 3.7 12.6 - - - +
277A LYS 3.3 0.2 - - - -
278A ASN* 1.3 76.3 - - - +
280A ASN* 1.3 62.1 + - - +
281A THR 3.5 0.2 + - - -
282A ALA* 5.5 0.2 - - - -
283A LEU* 4.0 23.8 + - + +
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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