Contacts of the strand formed by residues 208 - 212 (chain A) in PDB entry 2WEB
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 PHE 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ASN* 3.7 3.9 - - - +
195A VAL* 2.9 47.0 + - + +
198A TYR* 3.7 29.2 - + + -
206A ASP 3.7 6.3 - - - -
207A GLY* 1.3 78.4 - - - +
209A SER* 1.3 72.4 + - - +
221A LEU* 4.3 15.0 - - + -
222A ASP* 5.3 11.2 - - - +
225A VAL* 5.0 10.3 - - + -
256A PHE* 4.8 2.0 - + - -
258A VAL* 4.4 13.7 - - + -
295A PHE* 6.3 0.9 - - - -
296A SER* 3.5 21.1 - - - -
298A PHE* 3.8 22.2 - + - -
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Residues in contact with SER 209 (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 SER* 4.4 9.1 + - - -
193A PHE 3.3 7.2 - - - -
194A ASN* 3.2 24.9 - - - +
208A PHE* 1.3 86.6 - - - +
210A GLY* 1.3 60.2 + - - +
294A GLY 4.9 2.3 + - - -
295A PHE* 3.7 18.3 - - - +
296A SER 3.0 18.5 + - - -
298A PHE* 4.8 0.7 - - - -
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Residues in contact with GLY 210 (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 SER* 3.3 4.4 + - - -
193A PHE* 2.9 34.9 + - - +
209A SER* 1.3 77.8 - - - +
211A ILE* 1.3 65.9 + - - -
295A PHE* 4.6 2.9 - - - -
296A SER 3.0 15.0 - - - -
298A PHE* 3.7 19.5 - - - -
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Residues in contact with ILE 211 (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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35A GLY* 5.0 2.0 - - - -
190A PHE* 3.5 50.9 - - + -
191A TRP 3.4 6.5 - - - +
192A SER* 4.1 11.0 - - - +
193A PHE* 4.2 1.3 - - - -
210A GLY* 1.3 78.4 - - - +
212A ALA* 1.3 61.1 + - - +
213A ASP* 3.3 17.5 + - + +
295A PHE* 4.1 23.3 - - + -
296A SER 2.9 14.6 + - - +
297A ILE* 4.3 6.3 - - + -
298A PHE* 2.8 34.5 + - - +
326A PP4 3.9 23.3 - - + -
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Residues in contact with ALA 212 (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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34A THR* 2.8 22.9 + - - +
35A GLY* 5.1 0.3 - - - -
191A TRP* 3.0 20.0 + - - +
193A PHE* 3.9 7.8 - - + -
211A ILE* 1.3 70.1 - - - +
213A ASP* 1.3 59.1 + - - +
298A PHE* 3.8 9.6 - - + -
302A PHE* 6.5 0.2 - - + -
303A LEU* 4.8 11.0 - - + -
308A VAL* 5.2 2.5 - - + -
310A PHE* 3.8 28.3 - - + -
317A LEU* 4.2 15.3 - - + -
319A PHE* 5.6 1.8 - - + -
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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