Contacts of the strand formed by residues 197 - 200 (chain D) in PDB entry 1EJI
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 LEU 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D VAL* 4.2 25.1 - - + -
128D TYR* 4.3 11.2 - - + -
131D LEU* 4.6 9.0 - - + -
132D VAL* 3.8 26.0 - - + -
137D ARG 3.5 1.8 + - - -
138D ILE* 3.5 14.4 - - + -
139D MSE 3.1 22.2 + - - -
195D PRO* 3.4 2.6 - - - +
196D LYS* 1.3 81.3 - - - +
198D ILE* 1.3 70.5 + - - +
199D ILE* 3.6 28.5 - - + -
223D ALA* 3.9 0.6 - - - +
224D TYR* 3.3 24.7 - - + +
226D MSE 4.2 15.3 - - + -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D MSE 3.5 14.4 - - + +
172D TYR* 4.5 11.2 - - + -
186D LEU* 4.8 7.2 - - + -
190D ALA* 4.9 2.7 - - + -
195D PRO* 3.9 26.7 - - + -
197D LEU* 1.3 80.1 - - - +
199D ILE* 1.3 70.7 + - - +
214D LEU* 4.7 12.3 - - + +
217D ILE* 4.3 16.6 - - + +
218D ALA* 4.0 31.6 - - + +
221D ASN* 5.4 0.4 - - + +
223D ALA* 4.8 2.2 - - + -
224D TYR 2.7 12.7 + - - +
225D LEU* 3.6 18.8 - - + +
226D MSE 2.9 26.3 + - - +
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Residues in contact with ILE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D TYR* 3.4 25.1 - - + +
138D ILE* 3.7 20.0 - - + -
139D MSE 2.7 16.5 + - - +
140D GLY* 4.3 5.6 - - - -
141D LEU 4.6 1.0 + - - -
151D HIS* 3.6 49.1 - - + +
172D TYR* 2.6 32.6 + - - -
197D LEU* 3.6 19.3 - - + -
198D ILE* 1.3 75.9 - - - +
200D ALA* 1.3 56.7 - - - +
201D GLY 3.9 4.8 + - - +
226D MSE 3.3 25.1 - - + +
228D ASP* 4.5 2.5 - - + -
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Residues in contact with ALA 200 (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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172D TYR* 4.2 4.3 - - - -
198D ILE 4.0 0.2 + - - -
199D ILE* 1.3 71.4 - - - +
201D GLY* 1.3 56.9 + - - +
209D LEU* 3.6 11.5 - - + +
211D TYR* 3.9 20.4 + - + -
214D LEU* 3.5 30.3 - - + -
225D LEU* 4.1 11.7 - - + -
226D MSE 2.8 12.4 + - - +
227D ALA* 3.2 10.3 - - + +
228D ASP 3.2 18.2 + - - -
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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