Contacts of the strand formed by residues 301 - 306 (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 PHE 301 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ILE* 3.8 28.9 - - + -
270C MSE 4.0 17.0 - - - -
301C PHE* 4.5 2.7 - + - -
303C SER* 3.6 32.5 - - - -
314C LEU* 5.0 11.9 - - + -
317C TYR* 3.8 34.5 - + + +
318C VAL* 5.9 0.9 - - + -
325C LEU* 3.8 19.5 - - + -
267D THR 2.9 18.3 + - - +
268D ILE* 3.5 14.2 - - + +
269D GLU 3.0 24.1 + - - -
299D GLY 3.4 3.0 + - - -
300D ILE* 1.3 69.6 - - - +
302D PRO* 1.4 82.6 - - + +
303D SER* 3.5 9.2 + - - -
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Residues in contact with PRO 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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314C LEU* 3.8 18.8 - - + +
317C TYR* 4.3 10.3 - - + -
258D ARG* 5.9 0.9 - - - +
269D GLU 3.8 4.0 - - - +
285D TRP* 3.6 24.0 - - + -
286D LYS* 3.6 26.5 - - - +
289D PHE* 4.6 5.8 - - + -
290D GLY* 3.7 28.3 - - - +
300D ILE* 3.3 11.2 - - + +
301D PHE* 1.4 99.1 - - + +
303D SER* 1.3 59.2 + - - +
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Residues in contact with SER 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PHE* 3.5 23.6 - - - -
303C SER* 4.9 3.7 + - - -
268D ILE* 4.1 12.6 - - - -
269D GLU 2.8 14.6 + - - +
270D MSE 3.9 16.2 - - - +
271D LEU 3.0 17.5 + - - -
285D TRP* 3.3 9.4 - - - -
286D LYS* 4.2 6.3 - - - +
301D PHE* 3.5 8.4 + - - -
302D PRO* 1.3 75.0 - - - +
304D SER* 1.3 74.9 + - - +
314D LEU* 5.7 1.2 - - - +
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Residues in contact with SER 304 (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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286C LYS* 5.1 7.6 + - - -
270D MSE 4.4 5.1 - - - +
271D LEU* 3.2 19.1 - - - +
282D ALA* 3.9 26.8 - - - +
283D GLU* 4.4 2.9 + - - -
286D LYS* 3.9 22.7 + - - +
303D SER* 1.3 85.9 + - - +
305D ALA* 1.3 65.5 + - - +
306D ASN* 5.5 1.8 + - - -
310D ASP* 4.8 0.3 - - - +
314D LEU* 5.3 4.2 - - - +
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Residues in contact with ALA 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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270D MSE 3.6 24.9 - - + -
271D LEU 3.0 7.2 + - - +
272D ILE* 3.4 8.7 - - + +
273D ASN* 3.3 23.4 + - - -
304D SER* 1.3 77.7 - - - +
306D ASN* 1.3 68.4 + - - +
307D PHE* 3.7 19.8 + - + -
310D ASP* 3.4 15.0 - - + +
314D LEU* 5.2 4.7 - - + -
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Residues in contact with ASN 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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283C GLU* 6.4 0.4 - - - -
273D ASN* 2.9 35.0 + - - +
276D PRO* 5.5 7.6 - - + -
279D GLN* 3.9 38.7 + - - +
282D ALA* 5.4 3.1 - - - +
304D SER* 5.5 1.4 + - - -
305D ALA* 1.3 75.6 + - - +
307D PHE* 1.3 62.9 + - - +
309D THR* 3.3 11.4 - - + +
310D ASP* 2.8 40.1 + - - +
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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