Contacts of the strand formed by residues 268 - 273 (chain D) in PDB entry 3IFS
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C THR* 5.6 0.7 - - - +
268C ILE* 3.8 31.4 - - + -
301C PHE* 3.8 28.7 - - + -
266D LYS 3.5 0.2 - - - -
267D THR* 1.3 88.4 - - - +
269D GLU* 1.3 62.9 + - - +
270D MSE 4.2 4.5 - - + -
300D ILE* 4.2 1.1 - - - -
301D PHE* 3.5 14.1 - - + +
303D SER* 4.1 21.1 - - - -
324D ASP* 3.1 13.3 + - + +
325D LEU* 3.4 32.7 - - + -
326D PHE* 3.0 29.5 + - - +
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Residues in contact with GLU 269 (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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254D TYR* 2.6 20.2 + - - -
258D ARG* 2.9 34.3 + - - -
268D ILE* 1.3 73.0 - - - +
270D MSE 1.3 67.3 + - - +
285D TRP* 3.3 23.6 - - + -
300D ILE* 3.6 12.2 - - + +
301D PHE 3.0 7.3 + - - +
302D PRO* 3.7 1.4 - - - +
303D SER 2.8 28.8 + - - +
326D PHE* 3.4 32.4 - - + +
328D THR* 2.5 28.4 + - - +
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Residues in contact with MSE 270 (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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301C PHE* 4.0 18.8 - - + -
268D ILE* 4.2 9.6 - - + -
269D GLU* 1.3 76.9 - - - +
271D LEU* 1.3 61.2 + - - +
272D ILE* 3.4 16.1 + - + +
303D SER* 3.4 23.6 - - - +
304D SER 4.7 2.7 - - - +
305D ALA* 3.6 29.8 - - + -
307D PHE* 4.6 2.0 - - + -
314D LEU* 4.7 11.2 - - + -
318D VAL* 3.8 31.2 - - + -
325D LEU* 4.3 12.3 - - + -
326D PHE 2.9 14.1 + - - +
327D GLU* 3.3 12.4 - - + +
328D THR 3.0 23.1 + - - -
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Residues in contact with LEU 271 (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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269D GLU 3.9 1.0 + - - -
270D MSE 1.3 70.7 - - - +
272D ILE* 1.3 60.2 + - - +
273D ASN* 5.5 0.9 + - - -
281D PHE* 4.6 3.1 - - + -
282D ALA* 3.9 19.9 - - + +
285D TRP* 3.4 67.4 - - + +
303D SER 3.0 7.9 + - - +
304D SER* 3.2 7.2 - - - -
305D ALA 3.0 23.7 + - - +
328D THR* 3.4 29.2 - - + +
330D LEU* 4.1 34.8 - - + -
401D PHE* 4.4 3.4 - - + -
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Residues in contact with ILE 272 (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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270D MSE 3.6 36.8 - - + +
271D LEU* 1.3 78.3 - - - +
273D ASN* 1.3 70.0 + - - +
274D TYR* 4.0 12.8 - - + -
305D ALA* 3.4 16.2 - - + +
307D PHE* 3.3 31.9 - - + -
327D GLU* 3.7 33.7 - - + +
328D THR 2.8 7.4 + - - +
329D VAL* 3.9 16.6 - - + -
330D LEU* 2.8 33.2 + - - +
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Residues in contact with ASN 273 (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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271D LEU 5.5 0.8 + - - -
272D ILE* 1.3 75.9 - - - +
274D TYR* 1.3 64.6 + - - +
275D GLU 2.9 28.3 + - - +
278D LEU* 3.8 44.3 + - + +
279D GLN* 4.0 0.6 - - - +
282D ALA* 5.1 5.7 - - - +
305D ALA 3.3 4.6 + - - -
306D ASN* 2.9 35.4 + - - +
307D PHE* 2.8 31.5 + - - +
330D LEU* 3.9 11.0 - - + +
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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