Contacts of the strand formed by residues 198 - 202 (chain A) in PDB entry 1EUB
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 ASP 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP 3.9 0.3 - - - +
164A MET* 4.0 28.4 - - + +
172A HIS* 6.0 0.2 - - - +
187A HIS* 3.1 17.4 - - + +
188A ALA* 3.5 6.6 - - - -
189A PHE* 3.8 10.6 + - + +
194A ASN 3.7 2.2 - - - +
195A TYR* 2.9 54.6 - - + +
196A GLY 2.5 9.8 + - - +
197A GLY* 1.3 72.3 - - - +
199A ALA* 1.3 59.2 + - - +
200A HIS* 3.1 16.5 + - + +
277A CA 2.6 27.0 - - - -
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Residues in contact with ALA 199 (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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164A MET* 2.6 28.6 + - - +
165A ILE* 3.9 4.7 - - + -
166A SER* 2.8 29.7 + - - +
187A HIS 4.0 0.7 - - - -
197A GLY 3.0 4.8 + - - +
198A ASP* 1.3 70.1 - - - +
200A HIS* 1.3 58.4 + - - +
201A PHE* 4.2 1.8 - - + -
223A GLU* 3.5 29.4 - - + -
224A PHE* 3.7 19.1 - - + -
227A SER* 4.1 5.8 - - - +
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Residues in contact with HIS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET* 3.1 26.4 - - + +
166A SER* 3.1 25.5 + - - -
167A PHE 4.6 1.0 + - - -
168A GLY* 3.5 17.9 - - - +
169A ILE* 5.3 5.2 - - + +
171A GLU* 5.2 11.2 - - + -
172A HIS* 4.3 4.5 - + - -
187A HIS* 2.9 54.9 + - + +
195A TYR* 4.7 7.6 - + - -
198A ASP* 3.1 15.9 + - + +
199A ALA* 1.3 77.5 - - - +
201A PHE* 1.3 65.4 + - - +
202A ASP 3.9 0.3 + - - -
223A GLU* 4.4 0.8 - - - +
275A ZN 2.1 29.8 - - - -
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Residues in contact with PHE 201 (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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124A ASN* 3.6 29.8 - - - -
165A ILE* 3.7 21.5 - - + -
166A SER 3.1 14.0 + - - -
167A PHE* 3.7 4.2 - - - -
168A GLY* 2.8 19.8 + - - +
185A LEU* 2.9 22.0 - - + +
186A ALA* 3.1 20.0 - - + -
187A HIS* 5.9 0.2 - - - -
199A ALA* 4.9 2.0 - - + -
200A HIS* 1.3 74.3 - - - +
202A ASP* 1.3 51.4 + - - +
203A ASP* 2.4 23.0 + - - -
207A TRP* 3.5 26.5 - + + +
216A LEU* 4.8 1.3 - - + -
219A VAL* 3.1 30.7 - - + -
220A ALA* 3.8 17.7 - - + -
223A GLU* 3.5 16.8 - - + -
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Residues in contact with ASP 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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168A GLY 4.5 0.7 - - - -
177A PRO* 2.4 35.3 - - - +
178A PHE* 2.7 8.9 + - - +
179A ASP* 2.3 32.5 - - - +
184A LEU* 2.4 40.3 - - - +
185A LEU 3.1 8.5 + - - -
200A HIS 3.9 1.6 + - - -
201A PHE* 1.3 67.1 - - - +
203A ASP* 1.3 51.4 + - - +
204A ASP 2.4 4.2 + - - -
205A GLU* 2.4 51.3 + - + +
207A TRP* 3.1 1.2 - - - -
278A CA 2.5 0.5 - - - -
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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