Contacts of the strand formed by residues 242 - 246 (chain D) in PDB entry 4PEI
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 THR 242 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D LEU* 3.8 23.0 - - + +
222D LYS* 3.6 21.5 - - - +
223D PRO* 2.8 25.6 + - + +
226D TRP* 3.8 33.0 - - + +
238D GLU* 3.7 6.2 - - - +
239D GLU* 2.8 37.8 + - + +
240D GLY 3.1 0.6 - - - +
241D PRO* 1.3 76.5 - - - +
243D HIS* 1.3 65.3 + - - +
244D PHE* 3.5 3.4 + - + +
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Residues in contact with HIS 243 (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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266B LYS* 6.4 0.2 - - - -
224D LYS* 2.9 28.7 + - + +
225D TYR* 3.3 38.8 + + + +
226D TRP 3.0 23.0 + - - +
237D ALA 4.0 0.7 - - - -
238D GLU* 3.0 35.4 + - - +
241D PRO 4.5 8.0 + - - -
242D THR* 1.3 72.5 - - - +
244D PHE* 1.3 61.5 + - - +
245D ILE* 3.9 4.6 + - + +
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Residues in contact with PHE 244 (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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182D TRP* 3.6 35.2 - + - -
183D PRO* 3.6 15.7 - - + -
186D ILE* 3.7 40.8 - - + -
226D TRP* 3.4 27.8 - + + +
228D SER* 3.4 25.6 - - - -
235D TYR* 4.1 10.8 - + - -
236D HIS* 3.3 6.2 - - - +
237D ALA* 2.7 52.7 + - + +
238D GLU* 5.5 0.2 - - - +
242D THR* 3.5 4.4 + - + +
243D HIS* 1.3 71.6 - - - +
245D ILE* 1.3 66.7 + - - +
246D ALA* 3.7 24.7 - - + -
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Residues in contact with ILE 245 (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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11D ILE* 4.1 15.7 - - + -
225D TYR* 4.0 26.7 - - + -
226D TRP 3.0 8.5 + - - +
227D ILE* 3.2 14.6 - - + +
228D SER 3.0 24.1 + - - -
234D GLU* 4.7 7.6 - - - +
235D TYR 3.3 7.0 - - - +
236D HIS* 4.6 17.7 - - + +
243D HIS* 4.4 6.5 - - + +
244D PHE* 1.3 84.3 - - - +
246D ALA* 1.3 69.9 + - - +
247D LEU* 4.1 18.6 - - + -
257D SER* 5.6 1.3 - - - +
259D LEU* 4.0 18.6 - - + -
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Residues in contact with ALA 246 (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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182D TRP* 3.2 47.3 - - + +
228D SER 3.3 4.9 - - - -
229D GLY 5.3 0.2 - - - +
231D MET* 5.4 0.4 - - + -
233D CYS* 3.4 5.8 - - - +
234D GLU* 3.4 3.8 - - - +
235D TYR* 2.8 33.0 + - + +
244D PHE* 3.7 8.5 - - + -
245D ILE* 1.3 75.4 - - - +
247D LEU* 1.3 67.5 + - - +
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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