Contacts of the strand formed by residues 235 - 240 (chain D) in PDB entry 6NFJ
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 TYR 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D PHE* 6.3 0.7 - - + -
188D GLU* 3.8 35.8 - - + +
189D PRO 4.0 6.2 + - - +
190D ILE* 3.4 36.0 - - + -
191D VAL 3.2 22.5 + - - -
233D VAL* 3.3 8.4 - - - +
234D LYS* 1.3 86.5 - - + +
236D TRP* 1.3 61.8 + - - +
295D TRP* 3.6 40.5 - + + -
369D PHE* 4.5 14.8 - + + -
413D LEU* 6.1 1.1 - - + -
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Residues in contact with TRP 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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191D VAL* 3.6 26.9 - - + -
193D LEU* 3.5 35.9 - - + -
225D CYS* 3.2 35.9 - - + -
226D PHE* 4.0 15.0 - + - -
229D PHE* 4.0 10.8 - + + -
230D GLY* 4.0 12.1 - - - -
233D VAL* 3.5 40.0 + - + -
234D LYS 4.6 0.2 - - - -
235D TYR* 1.3 76.5 - - - +
237D ILE* 1.3 69.0 + - - +
284D TYR* 3.6 32.3 - + - -
295D TRP 2.8 16.7 + - - +
296D LEU* 3.2 20.1 - - + -
297D SER 3.0 24.1 + - - -
369D PHE* 4.1 2.0 - - - -
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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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150D GLN* 5.3 3.1 - - - +
190D ILE* 4.0 21.5 - - + -
191D VAL 2.8 7.5 + - - +
192D THR* 3.2 26.4 - - + +
193D LEU* 2.9 31.3 + - - +
236D TRP* 1.3 84.4 - - - +
238D THR* 1.3 63.9 + - - +
239D ILE 4.0 7.4 - - - +
297D SER 3.6 9.0 - - - -
299D THR* 3.5 33.0 - - - +
369D PHE* 3.5 30.1 - - + -
371D ALA* 3.7 15.0 - - + -
413D LEU* 5.3 1.1 - - + -
415D ALA* 6.0 0.9 - - + -
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Residues in contact with THR 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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192D THR* 4.0 0.4 - - - +
193D LEU* 3.6 7.0 + - + +
194D TYR* 3.0 32.1 + - - +
218D PHE* 4.1 16.9 - - + -
237D ILE* 1.3 74.8 - - - +
239D ILE* 1.3 70.2 + - - +
277D HIS* 3.2 30.9 + - - +
280D VAL* 3.7 32.1 - - + -
296D LEU* 3.7 13.7 - - + -
297D SER 3.2 12.5 + - - -
298D ILE* 3.5 8.8 - - - +
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Residues in contact with ILE 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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194D TYR* 3.7 26.7 - - + -
209D TRP* 5.0 1.8 - - + -
218D PHE* 4.6 7.0 - - + -
237D ILE* 4.0 3.7 - - - +
238D THR* 1.3 86.3 + - - +
240D HIS* 1.3 63.4 + - - +
241D ASN 3.4 3.3 + - - -
242D PRO* 3.7 31.0 - - + -
245D VAL* 4.5 3.6 - - + -
273D LEU* 3.3 47.6 - - + +
276D ALA* 4.6 6.1 - - + -
277D HIS* 4.5 17.5 - - + +
298D ILE* 3.3 14.2 - - + +
299D THR 3.3 21.8 + - - -
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Residues in contact with HIS 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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91D THR 5.9 0.2 - - - -
150D GLN* 3.4 30.0 + - - -
192D THR* 3.9 7.1 + - + +
194D TYR 3.1 16.2 + - - +
195D HIS* 3.1 48.2 + + + -
196D TRP* 2.8 34.6 + + - -
239D ILE* 1.3 69.9 - - - +
241D ASN* 1.3 70.9 + - + +
299D THR* 3.7 25.8 + - + +
373D SER* 5.0 0.2 + - - -
377D ASN* 6.2 0.7 - - - -
415D ALA 4.4 8.7 - - - -
416D GLU* 2.7 30.0 + - + -
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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