Contacts of the strand formed by residues 201 - 207 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ILE* 5.0 0.4 - - - -
200B LEU* 1.3 75.1 - - - +
202B LEU* 1.3 66.0 - - - +
203B LEU* 3.6 11.0 + - - +
223B LEU* 3.2 11.1 - - - +
224B ARG* 2.7 37.3 + - - -
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG* 4.2 9.2 - - + +
195B ILE* 5.0 6.9 - - + +
196B CYS* 6.6 0.4 - - - -
200B LEU 4.3 0.6 + - - -
201B SER* 1.3 75.1 - - - +
203B LEU* 1.3 62.6 + - - +
204B ALA 3.4 28.3 - - - +
205B GLU* 3.7 26.0 - - + +
221B PHE* 3.7 23.1 - - + -
222B ALA 3.9 1.6 - - - +
223B LEU* 3.8 18.6 - - + +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PHE* 3.9 19.7 - - + -
163B ILE* 3.5 31.6 - - + -
201B SER* 4.1 12.6 - - - +
202B LEU* 1.3 80.9 - - - +
204B ALA* 1.3 59.7 + - - +
222B ALA 2.7 18.9 + - - +
223B LEU 3.6 17.7 - - - +
224B ARG* 3.7 40.2 - - + +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.0 18.4 - - + -
52B PHE* 3.9 21.8 - - + -
202B LEU* 3.4 8.8 - - - +
203B LEU* 1.3 82.3 - - - +
205B GLU* 1.3 62.6 + - - +
221B PHE* 3.4 3.8 - - - -
222B ALA 2.9 25.6 + - - -
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.5 0.7 - - - -
192B ARG* 2.3 51.4 + - - -
202B LEU* 3.7 12.9 - - + +
204B ALA* 1.3 76.8 - - - +
206B GLU* 1.3 65.8 + - - +
219B TYR* 4.1 22.4 - - + -
220B SER 3.3 5.4 - - - +
221B PHE* 3.3 24.1 - - + -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 4.5 11.6 - - - +
47B LYS* 6.0 2.8 - - - +
48B PHE* 3.7 41.4 + - + +
205B GLU* 1.3 77.2 - - - +
207B ARG* 1.3 73.3 + - - +
208B GLN* 3.6 1.9 + - - -
209B GLU* 5.9 1.3 - - - +
219B TYR* 3.4 4.3 - - - -
220B SER* 2.8 41.0 + - - -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLU* 1.3 83.6 - - - +
208B GLN* 1.3 75.5 + - - +
209B GLU* 3.7 15.4 + - + +
217B HIS* 3.0 46.1 + - - +
218B VAL 3.5 12.1 - - - +
219B TYR* 3.7 38.4 - - + +
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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