Contacts of the strand formed by residues 219 - 224 (chain P) in PDB entry 1E33
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 219 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22P ASN* 2.6 49.2 + - + -
23P ILE 3.0 32.8 + - - -
24P VAL* 5.0 3.4 - - + -
116P TYR* 3.5 7.9 - - - -
117P LEU 3.4 11.2 - - - +
208P LEU* 4.5 11.7 - - + +
209P MET* 3.6 46.2 - - + -
212P ALA* 3.7 25.1 - - + -
213P GLN 5.6 0.2 - - - -
217P ARG 3.6 0.4 + - - -
218P PRO* 1.4 76.9 - - - +
220P PHE* 1.3 59.9 + - - +
221P LEU* 4.0 17.5 - - + -
265P ILE* 5.0 2.2 - - + -
270P LEU* 3.8 19.1 - - + -
274P THR* 4.3 14.6 - - + -
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Residues in contact with PHE 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ILE* 3.3 26.7 - - + -
25P LEU* 4.1 26.9 - - + -
77P LEU* 5.5 2.0 - - + -
107P VAL* 4.6 13.5 - - + -
108P ALA* 4.0 16.2 - - + -
111P LEU* 3.8 25.6 - - + -
116P TYR* 3.9 5.8 - - + -
117P LEU 3.1 4.6 + - - +
118P THR* 4.0 25.4 - - + -
119P GLY 2.9 26.0 + - - +
141P PHE* 3.7 26.9 - + - -
208P LEU* 4.6 1.1 - - - -
219P PHE* 1.3 73.5 - - - +
221P LEU* 1.3 66.0 + - - +
222P TYR* 4.2 13.7 - + + -
340P LEU* 4.9 3.4 - - + -
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Residues in contact with LEU 221 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23P ILE 2.9 12.1 + - - +
24P VAL* 4.2 20.9 - - + -
25P LEU* 2.9 30.0 + - - +
119P GLY 3.3 12.3 - - - +
121P ALA* 4.6 3.6 - - + +
204P PHE* 4.4 14.6 - - + -
205P ALA* 3.7 30.5 - - + +
208P LEU* 4.1 19.3 - - + -
209P MET* 5.2 8.1 - - - -
219P PHE* 4.0 10.0 - - + -
220P PHE* 1.3 75.4 - - - +
222P TYR* 1.3 66.0 + - - +
223P TYR* 4.2 14.1 - - + +
261P LEU* 4.4 12.1 - - + -
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Residues in contact with TYR 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU* 3.7 22.0 - - + -
27P PHE* 3.6 39.6 - - + -
73P ARG* 4.3 10.9 + - - +
76P LEU* 3.8 19.7 - - + +
77P LEU* 4.2 23.5 - - + +
119P GLY 2.8 8.0 + - - +
120P MET* 3.2 35.2 - - + +
121P ALA 2.7 29.1 + - - +
123P LYS 4.9 1.5 + - - -
124P TRP* 5.3 1.6 - + - -
126P LEU* 5.8 0.4 - - + +
141P PHE* 3.7 30.5 - + + -
220P PHE* 4.1 8.7 - + + -
221P LEU* 1.3 71.4 - - - +
223P TYR* 1.3 57.5 + - - +
224P ALA* 3.9 18.1 - - + +
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Residues in contact with TYR 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P VAL* 5.0 0.2 - - + -
25P LEU 3.1 11.6 + - - +
26P ILE* 3.4 25.6 - - + -
27P PHE 2.9 24.6 + - - -
121P ALA* 3.6 15.7 - - + +
198P GLU* 4.6 6.6 - - - +
201P TYR* 4.1 26.5 - + + -
202P MET* 4.2 14.8 - - + +
221P LEU* 3.8 17.7 - - + -
222P TYR* 1.3 73.9 - - - +
224P ALA* 1.3 55.9 + - - +
225P SER* 3.5 26.4 + - - -
227P HIS* 5.6 1.9 - - - -
254P LEU* 4.0 21.8 - - + +
257P ALA* 3.5 28.3 - - + +
258P VAL* 5.5 0.4 - - + -
261P LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P PHE* 3.4 10.1 - - - +
73P ARG* 3.8 14.1 - - - +
120P MET* 4.5 0.7 - - + -
121P ALA 3.0 11.1 + - - +
122P GLY* 3.4 6.5 - - - -
123P LYS 3.0 45.0 + - - +
222P TYR* 3.8 22.8 + - + +
223P TYR* 1.3 68.2 - - - +
225P SER* 1.3 69.4 + - - +
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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