Contacts of the helix formed by residues 268 - 278 (chain A) in PDB entry 3F4V
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 ILE 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.7 39.0 - - + -
243A ASP 3.8 11.2 - - - +
244A PHE* 3.7 45.3 - - + -
264A ARG 2.9 14.9 + - - +
267A HIS* 1.3 73.5 - - + +
269A GLY* 1.3 66.6 + - - +
270A TRP 3.2 2.0 - - - -
271A TYR* 3.1 6.1 + - + +
272A LEU* 2.9 45.2 + - + +
312A ILE* 3.9 13.7 - - + -
372A TYR* 4.1 15.5 - - + -
377A TYR* 5.1 0.7 - - - +
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Residues in contact with GLY 269 (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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264A ARG 3.2 9.9 + - - -
265A ASP* 3.2 12.1 + - - -
268A ILE* 1.3 78.6 - - - +
270A TRP* 1.3 62.0 + - - +
273A ASP* 2.9 27.4 + - - +
281A PRO* 3.3 17.3 - - - +
377A TYR* 3.5 22.7 - - - -
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Residues in contact with TRP 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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178A ARG* 3.7 11.0 - - + -
181A ALA* 3.7 24.2 - - + -
208A PRO* 3.5 13.7 - - + -
209A TYR* 3.7 24.7 + + - +
212A ALA* 3.3 28.1 - - + +
216A LEU* 4.0 2.3 - - - +
265A ASP 2.8 7.3 + - - -
266A PHE 3.5 12.1 - - - +
267A HIS 4.3 1.6 - - - +
269A GLY* 1.3 75.2 - - - +
271A TYR* 1.3 84.5 + + + +
274A PRO* 3.3 18.9 - - - +
280A TYR* 3.4 23.3 - + - -
281A PRO* 4.0 1.8 - - - -
284A MET* 3.4 30.8 - - + +
292A LEU* 4.4 1.6 - - - +
333A TYR* 3.3 47.1 - + - -
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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
----------------------------------------------------------
177A PRO* 3.4 25.5 + - + -
178A ARG* 3.3 39.7 + - + -
181A ALA* 4.2 0.3 - - - +
212A ALA* 3.3 41.8 - - + +
215A PHE* 5.0 1.3 - - + -
216A LEU* 4.0 22.4 - - + +
240A ILE* 5.7 0.9 - - + -
242A LEU* 3.8 32.1 - - + -
267A HIS 4.1 9.0 - - - -
268A ILE* 3.1 4.2 + - + +
269A GLY 3.1 0.2 - - - -
270A TRP* 1.3 107.9 - + + +
272A LEU* 1.3 59.5 + - - +
273A ASP 3.4 1.6 - - - -
274A PRO* 3.3 4.8 - - - +
275A LEU* 3.0 36.6 + - + +
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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
----------------------------------------------------------
242A LEU* 3.9 9.6 - - + -
268A ILE* 2.9 38.6 + - + +
271A TYR* 1.3 74.8 - - - +
273A ASP* 1.3 61.7 + - - +
275A LEU* 4.4 3.4 - - + +
276A ILE* 2.8 44.7 + - + +
310A ILE* 3.7 43.3 - - + -
373A ILE* 4.0 22.4 - - + -
377A TYR* 3.8 38.8 - - + -
380A PRO* 5.9 0.4 - - + -
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Residues in contact with ASP 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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265A ASP* 4.2 4.3 - - - +
269A GLY* 2.9 23.2 + - - +
272A LEU* 1.3 77.8 - - - +
274A PRO* 1.3 57.1 - - + +
277A ASN* 2.7 52.1 + - - +
278A GLY 2.9 6.4 + - - -
279A HIS* 2.9 29.2 - - + +
280A TYR 4.2 0.2 - - - -
281A PRO* 3.8 21.7 - - - +
376A LYS* 4.9 7.9 + - - -
377A TYR* 2.6 28.9 + - - -
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Residues in contact with PRO 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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216A LEU* 4.0 11.9 - - + -
269A GLY 3.4 3.6 - - - +
270A TRP 3.3 27.1 - - - +
271A TYR 3.3 7.4 - - - +
273A ASP* 1.3 88.7 - - + +
275A LEU* 1.3 60.1 + - - +
278A GLY* 3.0 23.4 + - - -
279A HIS 3.3 19.3 - - - +
280A TYR* 3.5 24.2 - - + -
295A PHE* 4.1 9.4 - - + -
303A VAL* 3.6 23.8 - - + +
304A LYS* 3.6 3.5 - - - -
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Residues in contact with LEU 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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216A LEU* 4.0 16.2 - - + -
219A HIS* 3.8 18.8 - - + +
240A ILE* 3.6 28.5 - - + -
242A LEU* 4.2 11.9 - - + -
271A TYR* 3.0 29.2 + - + +
272A LEU* 4.1 5.8 - - + +
274A PRO* 1.3 77.3 - - - +
276A ILE* 1.3 66.3 + - + +
303A VAL* 3.7 11.8 - - + +
305A GLY* 2.8 30.3 + - - -
306A SER* 3.4 26.7 + - - +
307A ALA* 4.5 7.6 + - + +
310A ILE* 4.6 9.6 - - + -
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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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272A LEU* 2.8 34.0 + - + +
275A LEU* 1.3 81.1 - - - +
277A ASN* 1.3 73.7 + - - +
278A GLY 3.7 0.2 - - - -
304A LYS* 3.6 21.8 - - - +
305A GLY* 4.9 1.2 + - - +
307A ALA* 5.9 2.9 - - + +
310A ILE* 4.5 14.8 - - + -
377A TYR* 3.7 39.5 - - + +
380A PRO* 4.1 24.9 - - + -
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Residues in contact with ASN 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 ASP* 2.7 39.5 + - - +
276A ILE* 1.3 88.5 - - - +
278A GLY* 1.3 60.7 + - - +
279A HIS* 3.4 26.8 + - - +
304A LYS* 4.1 15.2 + - - +
376A LYS* 5.3 3.2 + - - +
377A TYR* 3.8 18.5 - - - -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP 2.9 3.6 + - - -
274A PRO* 3.0 16.8 + - - -
276A ILE 3.7 0.8 - - - -
277A ASN* 1.3 77.2 - - - +
279A HIS* 1.3 62.7 + - - +
295A PHE* 4.9 2.3 - - - -
300A ALA* 3.3 32.0 - - - +
303A VAL* 5.7 0.4 - - - -
304A LYS* 3.8 17.3 - - - +
1003A MES 3.4 10.0 - - - -
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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