Contacts of the helix formed by residues 269 - 278 (chain A) in PDB entry 4CAA
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 PRO 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER 4.8 5.6 - - - +
31A VAL* 3.7 24.9 - - + +
32A ASP* 3.4 46.0 - - + +
35A PHE* 3.9 13.0 - - + -
267A LEU 4.6 0.4 - - - +
268A LEU* 1.3 83.6 - - + +
270A GLU* 1.3 73.4 + - + +
272A LEU* 3.8 3.9 + - + +
273A LYS* 3.4 20.4 + - - +
380B GLN* 5.5 0.7 - - - +
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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 LEU* 2.7 29.0 + - + +
269A PRO* 1.3 94.8 - - + +
271A THR* 1.3 63.2 + - - +
273A LYS* 3.5 6.3 + - - +
274A ARG* 3.1 23.4 + - - +
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Residues in contact with THR 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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235A LEU* 3.9 13.1 - - + +
266A MET* 2.5 34.6 + - - +
267A LEU* 4.8 1.1 - - - -
268A LEU* 2.7 21.1 + - - +
270A GLU* 1.3 72.0 - - - +
272A LEU* 1.3 63.7 + - - +
274A ARG* 3.0 15.6 + - - +
275A TRP* 2.9 61.8 + - + +
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Residues in contact with LEU 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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31A VAL* 4.9 7.0 - - + -
35A PHE* 4.0 31.6 - - + -
251A LEU* 3.8 28.0 - - + -
253A ILE* 6.4 0.2 - - + -
268A LEU 3.3 3.0 + - - -
269A PRO* 4.1 8.1 - - + +
270A GLU 3.4 0.2 - - - -
271A THR* 1.3 78.6 - - - +
273A LYS* 1.3 61.9 + - - +
275A TRP* 3.2 20.0 + - + +
276A ARG* 2.9 35.8 + - + +
373B ILE* 4.2 16.2 - - + -
375B VAL* 4.7 9.6 - - + -
380B GLN* 4.4 16.4 - - - +
382B ILE* 4.1 18.8 - - + -
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Residues in contact with LYS 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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269A PRO 3.4 14.9 + - - +
270A GLU* 4.0 6.7 - - - +
271A THR 3.3 0.6 - - - -
272A LEU* 1.3 78.2 - - - +
274A ARG* 1.3 59.6 + - - +
276A ARG* 3.7 6.0 - - - +
277A ASP* 2.8 57.8 + - - +
380B GLN* 4.6 10.7 + - - +
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Residues in contact with ARG 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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230A PHE* 3.9 20.8 - - - -
232A ASP* 3.3 34.9 + - - -
234A GLU* 4.8 8.1 - - - +
235A LEU* 3.8 22.6 - - - +
270A GLU 3.1 13.0 + - - +
271A THR* 3.0 16.3 + - - +
273A LYS* 1.3 77.2 - - - +
275A TRP* 1.3 62.8 + - - +
277A ASP* 3.6 5.1 - - - +
278A SER* 2.8 42.3 + - - +
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Residues in contact with TRP 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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35A PHE* 6.3 0.2 - + - -
230A PHE* 3.8 18.0 - + - -
232A ASP* 2.9 22.8 + - - -
235A LEU* 3.9 7.0 - - + -
237A CYS* 3.7 21.8 - - - -
239A VAL* 3.5 34.5 - - + +
251A LEU* 5.5 2.5 - - + -
253A ILE* 3.9 33.0 - - + -
263A VAL* 4.4 7.9 - - + -
266A MET 6.3 0.2 - - - -
267A LEU* 4.1 24.7 - - + -
271A THR* 2.9 37.0 + - + -
272A LEU* 3.5 26.5 - - + +
274A ARG* 1.3 82.0 - - - +
276A ARG* 1.3 63.6 + - - +
278A SER* 2.9 34.9 + - - -
373B ILE* 5.3 2.0 - - + -
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Residues in contact with ARG 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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241A GLU* 3.2 28.3 + - - -
249A SER* 4.0 8.3 + - - -
251A LEU* 3.9 20.1 - - + +
272A LEU* 2.9 34.7 + - + +
273A LYS* 3.7 6.3 - - - +
275A TRP* 1.3 77.0 - - - +
277A ASP* 1.3 69.6 + - - +
278A LEU* 3.4 24.5 + - - +
375B VAL* 3.7 12.9 - - - +
376B PRO 3.6 21.6 + - - -
377B THR* 4.4 11.7 + - - +
380B GLN* 3.6 28.8 - - - +
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Residues in contact with ASP 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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273A LYS* 2.8 48.7 + - - +
274A ARG* 3.6 5.8 - - - +
276A ARG* 1.3 85.7 - - - +
278A SER* 1.3 61.6 + - - +
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Residues in contact with SER 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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229A TYR 4.1 0.3 - - - +
230A PHE* 3.5 49.6 - - - -
274A ARG* 2.8 29.3 + - - +
275A TRP 2.9 3.0 + - - -
277A ASP* 1.3 79.3 - - - +
278A LEU* 1.3 64.1 + - - +
279A GLU* 3.3 16.7 + - - +
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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