Contacts of the helix formed by residues 204 - 208 (chain A) in PDB entry 4WMB
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A MET* 5.4 8.1 - - + -
105A THR* 6.0 2.0 - - - -
200A SER 3.7 17.3 - - - -
201A ASP* 3.1 34.5 + - + +
203A ILE* 1.3 87.8 - - + +
205A PHE* 1.3 62.7 + - + +
206A LEU 3.5 0.7 - - - -
327A LEU 5.5 1.8 - - - +
328A GLY* 4.6 10.1 - - - -
329A ASP* 3.0 33.1 + - - +
402A UDP 5.4 20.6 - + - -
50D GLN 6.1 4.5 - - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.3 1.4 - - - +
184A VAL* 3.5 24.5 - - + +
187A MET* 3.8 20.6 - - + -
188A GLN* 3.6 22.7 - - + -
191A PHE* 3.6 30.3 - + + -
192A SER* 3.3 27.4 - - - -
201A ASP* 3.3 20.4 - - + -
202A SER 2.9 10.6 + - - +
204A PHE* 1.3 81.3 - - + +
206A LEU* 1.3 64.1 + - - +
207A SER 3.2 2.9 - - - -
208A VAL* 3.0 23.6 + - + +
209A ALA 3.8 1.2 + - - -
328A GLY* 3.6 37.7 - - - -
329A ASP* 3.9 7.0 - - - -
332A PHE* 5.0 0.7 - - + -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.9 20.2 - - + -
103A MET* 4.4 8.5 - - - -
141A VAL* 4.0 16.8 - - + -
176A LEU* 4.2 11.2 - - + -
180A LEU* 3.7 29.1 - - + +
202A SER 3.9 0.8 + - - -
203A ILE* 3.1 18.9 + - + +
204A PHE 3.5 1.2 - - - -
205A PHE* 1.3 77.1 - - - +
207A SER* 1.3 64.1 + - - +
209A ALA* 3.2 4.2 + - - -
210A MET* 2.9 43.3 + - + -
213A ILE* 3.9 29.8 - - + -
223A GLN* 4.6 6.1 - - - +
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 1.3 78.1 - - - +
208A VAL* 1.3 62.7 + - - +
209A ALA 3.3 0.5 + - - -
210A MET* 3.4 13.6 + - - +
223A GLN* 3.3 25.0 + - - +
292A MET* 3.7 15.5 - - - -
294A LEU* 3.8 19.9 - - - +
299A MET* 4.5 5.2 - - - +
305A TYR* 4.5 1.0 + - - -
329A ASP* 2.9 32.8 + - - +
333A PHE* 3.4 15.8 - - - -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 5.6 0.4 - - + -
184A VAL* 3.8 20.0 - - + -
187A MET* 4.0 18.4 - - + -
205A PHE* 3.0 22.8 + - + +
207A SER* 1.3 76.9 - - - +
209A ALA* 1.3 61.6 + - + +
211A HIS* 3.5 5.0 + - - -
305A TYR* 2.6 39.9 + - - +
309A LEU* 4.1 9.3 - - + +
329A ASP* 3.8 27.4 - - + -
332A PHE* 3.9 22.7 - - + -
333A PHE* 3.7 8.1 - - + -
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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