Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 1W7L
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 THR 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A CYS* 3.3 10.9 - - + +
212A THR* 3.7 21.5 - - + -
229A ILE* 3.8 10.3 - - + +
230A ALA* 3.7 27.9 - - + -
235A MET* 2.8 42.9 + - - +
236A TRP* 3.5 4.0 + - - +
238A ARG* 1.3 80.6 + - - +
240A LEU* 1.3 66.7 + - - +
241A THR* 3.8 2.0 - - - +
260A LEU 4.0 0.2 - - - +
261A GLY* 3.8 4.0 - - - -
262A PRO* 3.4 23.7 - - - +
265A ILE* 4.4 1.2 - - - +
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Residues in contact with LEU 240 (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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107A ALA* 4.0 16.6 - - + -
111A LEU* 3.8 22.7 - - + -
209A VAL* 4.5 6.9 - - + +
210A CYS 2.9 8.9 + - - +
211A ILE* 3.7 11.3 - - + +
212A THR* 2.8 34.4 + - - +
239A THR* 1.3 80.0 - - - +
241A THR* 1.3 59.1 + - - +
242A ILE* 4.8 2.1 - - + +
259A VAL* 3.8 10.8 - - + -
260A LEU 3.5 1.6 - - - -
261A GLY* 4.2 5.8 - - - -
265A ILE* 3.7 23.6 - - + -
266A MET* 3.8 28.0 - - - -
269A LEU* 3.7 24.9 - - + -
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Residues in contact with THR 241 (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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80A PHE* 6.5 0.4 - - + -
84A LEU* 4.9 9.5 - - + +
212A THR* 3.4 13.6 - - + +
214A GLU* 3.6 35.2 - - + +
217A GLN* 5.9 0.9 - - - +
228A SER* 5.1 2.0 - - - +
230A ALA* 3.5 23.6 - - - +
236A TRP* 5.6 0.5 - - - -
239A THR* 3.8 0.3 - - - +
240A LEU* 1.3 73.5 - - - +
242A ILE* 1.3 66.2 + - - +
243A GLY 4.2 0.3 + - - -
258A TRP* 3.7 1.0 - - - +
259A VAL* 3.2 3.8 - - - -
260A LEU* 2.8 63.6 + - + +
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Residues in contact with ILE 242 (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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100A GLY* 4.0 14.6 - - - +
103A ALA* 3.9 22.2 - - + +
104A LEU* 3.7 40.2 - - + +
107A ALA* 4.8 3.6 - - + -
211A ILE* 3.9 18.8 - - + -
212A THR 2.8 16.6 + - - +
213A ASP* 4.3 7.0 - - - +
214A GLU* 3.0 32.4 + - - +
215A VAL* 4.4 7.9 - - + -
240A LEU* 4.9 2.2 - - + +
241A THR* 1.3 80.9 - - - +
243A GLY* 1.3 68.2 + - - +
258A TRP* 3.4 2.9 - - - -
259A VAL* 3.9 22.7 - - + -
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Residues in contact with GLY 243 (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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100A GLY* 4.0 2.3 - - - -
214A GLU 4.8 1.8 - - - -
215A VAL* 4.0 10.5 - - - -
242A ILE* 1.3 80.7 - - - +
244A SER* 1.3 61.7 + - - -
257A GLY* 3.2 3.5 - - - -
258A TRP* 3.1 54.6 + - - +
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Residues in contact with SER 244 (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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100A GLY 4.1 1.3 - - - -
215A VAL* 3.6 28.7 - - - +
243A GLY* 1.3 75.6 - - - -
245A ALA* 1.3 61.8 + - - +
246A GLY* 3.3 11.3 + - - -
247A LYS* 3.4 14.0 + - - +
248A THR* 2.8 26.8 + - - -
256A VAL 3.7 4.7 - - - -
257A GLY* 4.1 0.4 - - - -
258A TRP* 3.7 6.8 - - - -
1247A PLP 2.6 29.8 + - - -
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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