Contacts of the strand formed by residues 235 - 240 (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 LYS 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D SER 2.8 18.7 + - - +
212D THR* 3.3 16.4 - - + +
213D LEU 2.9 23.7 + - - +
233D LEU 4.4 9.4 - - - +
234D ILE* 1.3 72.8 - - - +
236D GLY* 1.3 62.9 + - - +
237D ILE* 5.4 1.1 - - + -
253D GLY* 4.4 8.6 - - - +
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Residues in contact with GLY 236 (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 3.5 6.3 - - - -
224D LEU* 4.0 11.4 - - - -
228D ILE* 3.5 22.1 - - - +
234D ILE* 4.7 0.7 - - - -
235D LYS* 1.3 73.5 - - - +
237D ILE* 1.3 65.7 + - - +
253D GLY 3.3 12.5 + - - +
254D ILE* 3.4 2.3 - - - -
255D GLU* 2.8 26.4 + - - +
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Residues in contact with ILE 237 (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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212D THR* 4.0 23.8 - - + -
213D LEU 2.9 12.0 + - - +
214D VAL* 3.3 11.1 - - + +
215D ASP 2.8 27.7 + - - -
224D LEU* 3.5 2.4 - - - +
235D LYS* 5.4 0.9 - - + -
236D GLY* 1.3 77.4 - - - +
238D ASN* 1.3 63.2 + - - +
239D PHE 3.5 0.7 + - - -
255D GLU* 3.3 21.3 - - + +
257D VAL* 3.8 27.8 - - + -
266D PRO* 4.0 23.1 - - + -
267D GLN 4.1 11.7 - - - +
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Residues in contact with ASN 238 (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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215D ASP* 4.0 6.8 - - - +
218D GLY* 3.1 38.4 - - - -
219D GLY 2.9 20.9 - - - +
221D GLY* 3.4 18.4 + - - -
224D LEU* 3.6 7.8 - - + +
236D GLY 4.1 0.2 - - - -
237D ILE* 1.3 70.3 - - - +
239D PHE* 1.3 58.5 + - - +
245D ILE* 3.8 6.7 - - - +
254D ILE* 3.9 13.4 - - + +
255D GLU 2.9 7.5 + - - +
256D HIS* 3.2 29.5 + - + +
257D VAL 2.8 27.5 + - - +
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Residues in contact with PHE 239 (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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214D VAL* 4.1 16.2 - - + -
215D ASP 2.9 15.2 + - - +
216D VAL* 4.3 17.7 - - + -
217D GLY 2.6 32.6 + - - -
218D GLY 3.0 6.4 + - - -
237D ILE* 3.5 1.3 + - + -
238D ASN* 1.3 73.7 - - - +
240D ASP* 1.3 57.6 + - - +
257D VAL* 3.1 27.4 - - + -
258D GLY 4.2 0.2 - - - -
259D GLY* 3.5 22.0 - - - -
260D ASP 3.5 18.8 - - - -
261D MET* 3.8 24.5 - - + -
264D SER 3.4 23.3 - - - -
265D VAL* 4.3 2.5 - - + -
266D PRO* 3.5 33.4 - - + -
1699D SAH 4.4 4.9 - + - -
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Residues in contact with ASP 240 (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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217D GLY* 3.3 8.0 - - - -
219D GLY 2.8 22.5 + - - +
239D PHE* 1.3 74.8 - - - +
241D LEU* 1.3 77.5 + - - +
244D VAL* 3.4 17.2 - - + +
245D ILE* 3.8 17.8 - - + +
257D VAL 3.2 5.3 + - - -
258D GLY* 3.2 5.9 - - - -
259D GLY 2.8 23.2 + - - -
1699D SAH 2.3 63.9 + - - -
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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