Contacts of the helix formed by residues 220 - 224 (chain A) in PDB entry 2E98
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 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP 4.0 2.2 - - - -
27A GLY* 3.7 18.2 - - - +
30A ARG* 3.5 39.7 - - + +
31A TRP* 3.6 40.4 - - + +
34A LYS* 3.8 26.9 - - + +
195A THR* 4.8 0.2 - - - -
196A GLY* 4.2 2.7 - - - -
218A ASP 3.8 10.5 - - - +
219A VAL* 1.3 75.9 - - - +
221A TRP* 1.3 68.5 + - - +
222A PRO* 3.3 5.4 - - + -
223A ASP* 2.9 21.4 + - - +
224A PHE 3.2 8.0 + - - -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.8 26.2 - - + -
25A MET* 3.4 37.8 - - + -
26A ASP 3.0 24.9 + - - +
28A ASN* 3.3 30.5 - - - +
46A GLY* 3.2 26.7 + - - -
49A SER* 2.7 46.3 + - - -
50A VAL* 3.7 11.6 - - - +
53A ALA* 3.9 19.7 - - + -
67A LEU* 5.2 0.9 - - + -
195A THR* 3.6 20.2 - - + +
219A VAL 3.7 0.6 + - - -
220A LEU* 1.3 69.6 - - - +
222A PRO* 1.4 68.2 - - + +
224A PHE* 3.1 35.9 + + + +
501A B29 4.5 2.7 - + - -
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 4.0 0.2 - - - +
28A ASN* 3.0 35.7 - - + +
31A TRP* 3.5 49.9 - - + -
42A GLY 4.2 0.7 - - - +
45A ALA* 3.8 15.9 - - + +
46A GLY 4.2 6.7 - - - +
49A SER* 4.1 9.8 - - - -
52A ARG* 3.0 20.4 + - - -
220A LEU 3.4 4.5 - - - -
221A TRP* 1.4 89.4 - - + +
223A ASP* 1.3 56.4 + - - +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.1 35.9 + - - -
52A ARG* 4.2 2.9 - - - +
219A VAL* 3.7 12.6 - - + +
220A LEU* 2.9 17.3 + - - +
222A PRO* 1.3 75.2 - - - +
224A PHE* 1.3 59.9 + - - +
225A ASP* 3.1 14.7 + - - +
228A ASP* 3.2 8.1 - - - +
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Residues in contact with PHE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.6 3.8 - - + -
49A SER* 3.1 8.8 + - - +
52A ARG* 3.0 17.7 + - - -
53A ALA* 5.2 2.9 - - + +
193A ILE* 4.1 28.3 - - + -
195A THR* 3.6 20.4 - - + -
215A TYR* 5.4 2.9 - + - -
217A THR* 4.1 14.1 - - + -
219A VAL* 3.6 10.1 - - + +
220A LEU 3.2 4.6 + - - +
221A TRP* 3.1 47.3 + + + +
223A ASP* 1.3 74.7 - - - +
225A ASP* 1.3 60.0 + - - +
228A ASP* 3.5 26.5 - - + -
229A PHE* 3.7 45.8 - + + -
232A ALA* 5.2 0.2 - - + -
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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