Contacts of the strand formed by residues 201 - 207 (chain A) in PDB entry 2EX4
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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY 4.2 0.9 + - - -
200A LEU* 1.3 72.7 - - - +
202A LEU* 1.3 61.5 + - - +
203A LEU* 3.5 16.2 + - - +
223A LEU* 3.2 28.4 - - - +
224A ARG* 2.8 21.1 + - - -
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Residues in contact with LEU 202 (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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192A ARG* 4.7 13.9 - - + +
195A ILE* 5.1 7.6 - - + -
200A LEU 3.9 1.6 + - - -
201A SER* 1.3 71.0 - - - +
203A LEU* 1.3 60.3 + - - +
204A ALA 3.3 27.4 - - - +
205A GLU* 3.7 24.2 - - + +
221A PHE* 3.8 21.1 - - + -
222A ALA 3.7 0.9 - - - -
223A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 203 (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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52A PHE* 3.9 21.5 - - + -
163A ILE* 3.6 31.2 - - + -
201A SER* 3.9 26.5 - - - +
202A LEU* 1.3 73.4 - - - +
204A ALA* 1.3 60.8 + - - +
222A ALA 2.7 14.5 + - - +
223A LEU 3.7 17.7 - - - +
224A ARG* 3.8 30.1 - - + +
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Residues in contact with ALA 204 (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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48A PHE* 3.7 25.8 - - + -
52A PHE* 3.9 15.7 - - + -
202A LEU* 3.3 10.1 - - - +
203A LEU* 1.3 80.8 - - - +
205A GLU* 1.3 61.0 + - - +
221A PHE* 3.3 5.4 - - - -
222A ALA* 2.9 25.2 + - - +
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Residues in contact with GLU 205 (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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48A PHE* 4.5 0.4 - - - -
188A LEU* 5.0 0.2 - - - -
192A ARG* 2.9 55.5 + - - -
202A LEU* 3.7 19.1 - - + +
204A ALA* 1.3 76.5 - - - +
206A GLU* 1.3 65.9 + - - +
219A TYR* 4.1 19.8 - - + -
220A SER 3.3 4.5 - - - -
221A PHE* 3.6 23.4 - - + -
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Residues in contact with GLU 206 (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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44A SER* 4.1 16.3 + - - +
47A LYS* 6.1 1.0 - - - +
48A PHE* 3.7 41.5 + - + +
205A GLU* 1.3 78.2 - - - +
207A ARG* 1.3 74.5 + - - +
208A GLN* 3.7 1.2 + - - -
219A TYR* 3.4 4.4 - - - -
220A SER* 2.8 41.5 + - - -
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Residues in contact with ARG 207 (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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206A GLU* 1.3 84.5 - - - +
208A GLN* 1.3 75.3 + - - +
209A GLU* 3.6 21.5 + - + +
217A HIS* 3.4 44.8 + - - +
218A VAL 3.5 7.0 - - - +
219A TYR* 3.6 42.9 - - + -
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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