Contacts of the strand formed by residues 248 - 255 (chain A) in PDB entry 3CWL
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 ALA 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.8 23.6 - - + -
190A PHE* 5.3 1.6 - - + -
244A TYR* 2.8 38.8 + - + +
246A GLY 3.6 2.8 + - - -
247A ASN* 1.3 78.2 - - - +
249A THR* 1.3 67.1 + - - +
374A MET* 5.4 1.6 - - + -
375A ILE 3.2 13.0 - - - +
376A GLU* 4.4 0.4 - - - -
377A GLN* 3.5 5.6 - - - +
383A LEU* 4.2 19.7 - - + -
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Residues in contact with THR 249 (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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241A LEU* 4.2 18.2 - - + -
242A MET 3.6 16.2 - - - +
243A LYS* 3.8 10.8 - - + +
244A TYR* 4.7 1.3 - - - -
248A ALA* 1.3 72.0 + - - +
250A ALA* 1.3 71.5 + - - +
251A ILE* 3.8 1.1 + - + +
276A LEU* 4.2 23.4 - - + +
373A LEU 3.6 1.0 - - - +
374A MET* 3.2 3.5 - - - -
375A ILE* 2.7 40.9 + - - +
377A GLN* 2.8 31.7 + - - +
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Residues in contact with ALA 250 (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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194A TRP* 3.8 7.4 - - + -
240A LEU 3.6 0.7 - - - +
241A LEU* 3.2 4.5 - - - -
242A MET 2.8 38.7 + - - +
244A TYR* 3.7 23.0 - - + -
249A THR* 1.3 73.2 - - - +
251A ILE* 1.3 61.5 + - - +
252A PHE* 3.6 24.1 - - + -
373A LEU 3.4 4.9 - - - -
374A MET* 3.9 14.1 - - + -
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Residues in contact with ILE 251 (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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239A VAL* 3.8 19.3 - - + -
240A LEU 3.2 8.3 - - - +
241A LEU* 3.8 20.0 - - + -
249A THR* 4.5 2.2 - - + +
250A ALA* 1.3 76.6 - - - +
252A PHE* 1.3 63.6 + - - +
253A PHE* 3.5 33.2 - - + -
272A ILE* 4.5 13.9 - - + -
275A PHE* 3.9 16.2 - - + -
276A LEU* 5.1 4.3 - - + -
372A PHE* 3.1 6.5 - - - +
373A LEU* 2.7 60.5 + - + +
375A ILE* 4.2 15.9 - - + -
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Residues in contact with PHE 252 (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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194A TRP* 3.9 12.8 - + - -
238A TRP 3.5 0.9 - - - +
239A VAL* 3.4 7.1 - - - +
240A LEU* 2.7 56.6 + - + +
242A MET* 4.0 18.8 - - + -
250A ALA* 3.6 31.6 - - + -
251A ILE* 1.3 73.6 - - - +
253A PHE* 1.3 63.5 + - - +
288A LEU* 4.0 23.1 - - + -
340A ILE* 4.5 15.9 - - + -
366A PHE* 3.3 23.8 - + + -
370A PHE* 3.8 26.7 - + + -
371A VAL 3.5 3.4 - - - +
372A PHE* 3.9 15.9 - + + -
374A MET* 4.6 0.7 - - + -
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Residues in contact with PHE 253 (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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235A LEU* 3.9 10.1 - - + -
237A SER* 4.6 2.2 - - - -
238A TRP 3.4 2.5 - - - -
239A VAL* 3.6 33.2 - - + -
251A ILE* 3.5 33.2 - - + -
252A PHE* 1.3 73.4 - - - +
254A LEU* 1.3 60.9 + - - +
255A PRO* 3.3 5.2 - - - +
263A LEU* 3.8 33.7 - - + -
267A LEU* 3.5 33.2 - - + -
272A ILE* 4.5 8.3 - - + -
275A PHE* 4.1 6.3 - + - -
366A PHE* 4.4 0.2 - - - -
370A PHE* 3.2 5.2 - - - +
371A VAL 2.7 44.3 + - - +
373A LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 254 (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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237A SER* 3.4 2.4 - - - -
238A TRP* 2.9 57.5 + - + +
252A PHE 4.1 0.4 - - - -
253A PHE* 1.3 72.5 - - - +
255A PRO* 1.3 67.2 - - - +
256A ASP* 3.6 0.5 + - - +
364A VAL* 4.1 11.4 - - + -
365A LYS 3.2 30.3 - - - +
366A PHE* 3.6 32.3 - - + -
368A LYS* 3.8 48.0 + - + +
369A PRO 4.4 1.1 - - - +
370A PHE* 4.2 3.4 - - + -
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Residues in contact with PRO 255 (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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236A SER 4.2 0.2 - - - +
237A SER* 3.3 16.5 - - - +
253A PHE 3.3 12.6 - - - +
254A LEU* 1.3 83.5 - - + +
256A ASP* 1.3 66.4 + - - +
259A LYS 3.7 7.0 - - - +
260A LEU* 3.6 46.4 - - + +
263A LEU* 4.3 8.7 - - + -
368A LYS* 3.2 22.2 + - - -
369A PRO 3.4 22.0 - - - +
370A PHE* 4.2 2.0 - - - -
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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