Contacts of the strand formed by residues 294 - 299 (chain A) in PDB entry 2W5X
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 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASN* 3.2 25.9 + - + +
38A ILE* 3.9 30.5 - - + -
287A PHE* 3.5 8.8 - - + -
288A ALA* 3.9 33.0 + - + +
291A ASP* 2.8 24.4 + - - -
292A GLY* 3.6 1.8 - - - -
293A ASN* 1.3 75.2 - - - +
295A LEU* 1.3 70.1 + - - +
296A VAL* 3.8 1.8 + - + -
347A TYR* 3.8 0.7 - - - +
348A GLY* 3.7 16.1 - - - -
349A PRO* 3.7 4.9 - - - +
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Residues in contact with LEU 295 (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 PRO* 3.7 20.9 - - + +
36A ASN 2.9 9.2 + - - +
37A VAL* 3.3 12.7 - - + +
38A ILE 2.9 25.6 + - - +
294A THR* 1.3 72.5 - - - +
296A VAL* 1.3 66.5 + - - +
297A ILE* 3.7 21.8 - - + -
346A ALA* 4.4 0.7 - - + -
347A TYR 3.3 16.8 - - - +
348A GLY* 4.5 0.7 - - - -
349A PRO 3.6 15.0 - - - +
351A SER* 3.9 21.5 - - - -
354A PHE* 3.6 26.0 - - + -
367A ILE* 5.1 0.9 - - + -
370A VAL* 3.8 21.1 - - + -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.4 14.6 - - + +
40A LEU* 4.4 5.2 - - + -
66A PHE* 4.1 2.0 - - + -
284A ALA* 4.0 24.5 - - + +
285A LEU* 4.0 24.9 - - + -
288A ALA* 3.5 31.2 - - + -
294A THR* 4.3 6.3 - - + +
295A LEU* 1.3 76.2 - - - +
297A ILE* 1.3 62.7 + - - +
298A VAL* 4.2 19.3 - - + -
345A PHE 3.7 0.5 - - - +
346A ALA* 3.2 4.9 - - - +
347A TYR* 2.8 37.0 + - + +
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Residues in contact with ILE 297 (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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37A VAL* 4.1 10.1 - - + -
38A ILE 2.9 7.8 + - - +
39A LEU* 3.4 20.8 - - + +
40A LEU* 2.8 27.9 + - - +
295A LEU* 3.7 20.2 - - + -
296A VAL* 1.3 77.7 - - - +
298A VAL* 1.3 68.7 + - - +
299A THR* 4.8 1.6 - - + +
344A VAL* 4.2 18.8 - - + -
345A PHE 3.4 7.4 - - - +
346A ALA* 4.6 3.1 - - + -
354A PHE* 3.5 32.8 - - + -
363A ILE* 4.7 11.2 - - + -
367A ILE* 3.6 26.2 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.4 24.9 - - + -
42A SER* 5.2 0.7 - - - +
63A TYR* 4.2 12.3 - - + +
66A PHE* 3.4 27.8 - - + -
277A PHE* 3.7 30.5 - - + -
281A ILE* 4.0 13.2 - - + -
296A VAL* 4.2 1.8 - - + -
297A ILE* 1.3 79.0 - - - +
299A THR* 1.3 67.5 + - - +
344A VAL* 3.5 1.2 - - - +
345A PHE* 2.8 51.5 + - + +
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Residues in contact with THR 299 (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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39A LEU* 4.7 15.5 - - + +
40A LEU 3.1 7.1 + - - +
41A ILE* 3.3 6.9 - - + -
42A SER* 3.0 26.3 + - - -
72A ILE* 3.6 3.1 - - + +
91A PHE* 3.8 31.4 - - + -
297A ILE* 4.2 3.8 - - + -
298A VAL* 1.3 78.9 - - - +
300A SER* 1.3 70.8 + - - +
342A ILE* 3.6 6.6 - - - +
343A PRO 2.8 20.3 + - - -
344A VAL* 3.5 20.7 - - + +
345A PHE* 5.3 1.3 - - - -
363A ILE* 5.1 4.3 - - + -
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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