Contacts of the strand formed by residues 268 - 274 (chain D) in PDB entry 1FP1
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 GLY 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212D THR* 3.9 20.4 - - - -
214D VAL* 4.1 7.0 - - - -
266D PRO 3.8 1.6 + - - -
267D GLN* 1.3 77.6 - - - +
269D ASP* 1.3 57.6 + - - -
270D ALA 3.2 5.6 - - - -
271D MET* 4.1 2.2 - - - +
295D ALA 3.5 2.8 + - - -
296D LEU* 3.4 12.3 - - - +
297D SER* 3.1 25.6 + - - -
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Residues in contact with ASP 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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209D GLY 4.5 1.6 - - - +
210D ILE* 3.3 20.1 - - - +
211D SER* 2.5 44.0 + - - -
212D THR* 3.0 17.5 + - - -
268D GLY* 1.3 72.6 - - - -
270D ALA* 1.3 59.6 + - - +
296D LEU* 3.6 4.0 - - - -
297D SER* 3.4 25.2 + - - +
299D ASN 6.0 0.4 - - - -
300D GLY* 3.0 28.7 - - - -
301D LYS* 3.3 3.1 + - - +
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Residues in contact with ALA 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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210D ILE* 3.5 39.0 - - + -
212D THR 3.4 5.0 + - - +
213D LEU* 3.7 10.5 - - + -
214D VAL* 2.9 23.7 + - - +
268D GLY 3.2 1.4 + - - -
269D ASP* 1.3 82.6 + - - +
271D MET* 1.3 67.6 + - - +
296D LEU* 3.7 0.6 - - - +
301D LYS* 3.2 15.7 - - + +
303D ILE* 5.1 5.2 - - + -
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Residues in contact with MET 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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213D LEU* 4.1 2.0 - - - -
214D VAL* 3.2 21.3 - - + +
216D VAL* 4.2 9.6 - - + -
265D VAL* 4.0 5.2 - - + -
266D PRO 3.5 22.4 - - - +
268D GLY 4.1 4.9 - - - +
270D ALA* 1.3 81.3 - - - +
272D ILE* 1.3 54.2 + - - +
273D LEU* 4.4 3.1 - - + -
292D CYS* 3.3 50.3 - - - +
295D ALA* 3.5 23.6 - - + +
296D LEU* 3.6 15.3 - - + +
301D LYS 3.1 5.1 + - - -
302D VAL* 3.2 12.3 - - + +
303D ILE* 2.6 33.5 + - - +
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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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197D MET* 5.6 2.9 - - + -
200D MET* 4.2 7.4 - - + -
207D PHE* 4.2 23.8 - - + -
213D LEU* 4.0 22.7 - - + -
214D VAL 2.9 8.1 + - - +
215D ASP* 3.3 33.6 - - + +
216D VAL 3.0 24.4 + - - -
223D ASN* 6.5 0.9 - - + -
224D LEU* 5.2 1.1 - - + -
227D ILE* 5.5 4.9 - - + -
271D MET* 1.3 75.4 - - - +
273D LEU* 1.3 67.0 + - - +
274D LYS* 4.0 8.5 - - + +
303D ILE* 3.2 21.8 - - + +
305D VAL* 3.9 23.3 - - + -
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Residues in contact with LEU 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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216D VAL* 3.7 38.6 - - + +
271D MET 4.4 1.6 - - - +
272D ILE* 1.3 81.3 - - - +
274D LYS* 1.3 59.5 - - - +
275D ALA 4.0 1.4 + - - -
276D VAL* 4.1 18.7 + - + -
277D CYS* 4.4 3.8 - - - -
288D PHE* 3.6 36.8 - - + -
289D LEU* 4.2 11.7 - - + -
292D CYS* 4.1 11.0 - - - -
302D VAL* 4.0 20.4 - - + -
303D ILE 2.7 9.0 + - - -
304D ILE* 3.5 17.9 - - + +
305D VAL 3.0 20.9 + - - +
306D GLU* 4.9 0.9 - - - +
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Residues in contact with LYS 274 (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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193D CYS* 3.6 18.9 - - - +
196D GLU* 2.8 35.6 + - - -
197D MET* 3.9 22.9 - - - -
215D ASP* 4.9 3.4 + - - +
216D VAL 4.8 0.2 + - - -
223D ASN* 3.8 11.4 - - + +
272D ILE* 4.0 10.1 + - + -
273D LEU* 1.3 72.3 - - - +
275D ALA* 1.3 81.0 + - + +
276D VAL* 3.2 4.6 + - - +
305D VAL* 3.5 34.3 - - + +
365D LEU* 6.2 0.2 - - - -
1699D SAH 3.1 47.2 + - - +
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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