Contacts of the helix formed by residues 295 - 306 (chain D) in PDB entry 3ECS
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 ALA 295 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291D LEU* 4.3 12.6 - - + -
292D THR* 2.9 26.9 + - - +
294D SER* 1.3 76.8 - - - +
296D VAL* 1.3 64.3 + - - +
297D SER 3.3 0.7 - - - -
298D ASP* 3.4 13.5 + - - +
299D GLU* 3.3 23.4 + - + +
294F SER* 4.7 3.6 - - - -
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D VAL* 4.0 11.4 - - + -
201D VAL 3.6 24.7 - - - +
202D GLU* 4.0 4.7 - - - +
204D GLY* 3.8 12.1 - - - +
235D PHE* 4.0 13.7 - - + -
284D LEU* 4.1 23.1 - - + -
291D LEU* 4.2 15.3 - - + -
292D THR 4.1 8.3 - - - +
293D PRO 3.3 15.7 - - - +
294D SER 3.1 1.2 - - - -
295D ALA* 1.3 78.8 - - - +
297D SER* 1.3 65.4 + - - +
299D GLU* 3.2 6.7 + - - +
300D LEU* 2.8 23.2 + - + +
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Residues in contact with SER 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLU 3.6 19.2 + - - -
294D SER 3.3 15.3 + - - -
296D VAL* 1.3 78.4 - - - +
298D ASP* 1.3 65.7 + - - +
300D LEU* 3.8 3.4 - - - +
301D ILE* 3.1 32.7 + - - +
202F GLU 5.1 1.1 - - - -
203F ASN* 4.3 16.9 + - - -
239F PHE* 3.8 22.4 - - - -
294F SER* 4.4 9.2 + - - -
297F SER* 4.5 7.6 + - - -
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Residues in contact with ASP 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D SER 4.1 2.3 - - - +
295D ALA* 3.4 8.2 + - + +
296D VAL 3.2 0.6 - - - -
297D SER* 1.3 76.1 + - - +
299D GLU* 1.3 73.1 + - - +
301D ILE* 3.5 9.0 + - - +
302D LYS* 3.1 23.2 + - - +
203F ASN 5.6 0.4 - - - -
278F PRO* 4.0 28.3 - - - +
279F SER* 4.9 3.3 + - - -
293F PRO* 5.2 1.2 - - - +
294F SER* 3.0 34.4 + - - -
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Residues in contact with GLU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D PHE* 4.0 9.6 - - + -
288D LEU* 4.0 35.2 - - + +
291D LEU* 3.8 30.8 - - + +
295D ALA* 3.3 13.9 + - + +
296D VAL 3.2 6.1 + - - +
298D ASP* 1.3 82.3 - - - +
300D LEU* 1.3 58.0 + - - +
302D LYS* 3.4 28.6 + - - +
303D LEU* 2.8 31.2 + - - +
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D VAL 4.6 0.2 - - - +
201D VAL 4.5 2.7 - - - -
202D GLU* 3.6 35.2 - - + +
235D PHE* 3.7 32.3 - - + -
236D VAL 3.6 15.9 - - - +
237D ARG* 4.3 10.3 - - + -
296D VAL* 2.8 17.8 + - + +
297D SER* 3.8 5.8 - - - +
299D GLU* 1.3 74.4 - - - +
301D ILE* 1.3 61.0 + - - +
303D LEU* 4.3 2.0 - - - -
304D TYR* 3.1 46.7 + - + +
239F PHE* 4.1 21.8 - - + -
241F LEU* 4.8 2.9 - - + -
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Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D SER 3.1 19.2 + - - +
298D ASP* 3.7 7.9 - - - +
299D GLU 3.2 0.2 - - - -
300D LEU* 1.3 75.4 - - - +
302D LYS* 1.3 60.8 + - - +
303D LEU 3.2 0.3 + - - -
304D TYR 3.3 1.2 + - - -
305D LEU* 2.8 59.3 + - + +
203F ASN* 4.0 19.3 - - + +
239F PHE* 3.9 16.6 - - + -
240F PRO 5.5 0.2 - - - +
241F LEU* 4.4 16.4 - - + +
275F TYR* 4.7 2.2 - - - +
277F ALA* 5.7 5.4 - - + -
278F PRO* 3.4 34.8 - - + -
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Residues in contact with LYS 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D LEU* 5.7 7.9 - - + -
298D ASP 3.1 14.6 + - - +
299D GLU* 3.7 28.3 - - - +
301D ILE* 1.3 81.1 - - - +
303D LEU* 1.3 56.4 + - - +
305D LEU* 4.8 2.9 - - - -
306D ALA* 2.9 38.5 + - + +
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.5 42.4 - - + +
232D SER* 3.5 27.1 - - - +
235D PHE* 4.3 5.6 - - + -
288D LEU* 4.3 23.5 - - + +
299D GLU 2.8 22.0 + - - +
300D LEU* 3.8 5.6 - - - +
301D ILE 3.2 0.2 - - - -
302D LYS* 1.3 77.5 - - - +
304D TYR* 1.3 70.9 + - + +
305D LEU 3.3 0.3 + - - -
306D ALA* 3.5 18.4 + - + +
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Residues in contact with TYR 304 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D SER* 4.4 9.5 + - - -
70D GLU* 3.6 18.9 + - + -
71D LEU* 3.8 33.1 - - + +
74D ARG* 3.0 48.9 + - - +
235D PHE 2.8 29.8 + - - -
236D VAL* 4.0 6.4 - - - +
237D ARG* 3.5 30.4 + - + +
300D LEU* 3.1 41.4 + - + +
301D ILE 4.0 1.8 - - - +
303D LEU* 1.3 89.2 - - + +
305D LEU* 1.3 60.5 + - - +
306D ALA 4.7 1.5 - - - +
307D ALA* 5.5 1.4 - - - +
241F LEU* 3.8 19.3 - - + -
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ARG* 4.9 4.9 - - - +
301D ILE* 2.8 41.0 + - + +
302D LYS* 4.3 3.1 - - - +
304D TYR* 1.3 77.6 - - - +
306D ALA* 1.3 70.5 + - - +
307D ALA* 2.8 15.6 + - - +
241F LEU* 3.7 37.2 - - + +
242F ASN* 4.9 10.3 - - + +
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 4.4 12.1 - - - -
302D LYS* 2.9 25.3 + - + +
303D LEU* 3.5 15.4 + - + +
304D TYR 4.7 1.2 - - - +
305D LEU* 1.3 74.0 - - - +
307D ALA* 1.3 62.6 + - - +
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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