Contacts of the strand formed by residues 68 - 73 (chain B) 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 ASN 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE* 4.0 16.9 - - - +
66B PHE* 4.7 1.4 - - - +
67B LYS* 1.3 78.1 - - - +
69B ILE* 1.3 61.8 + - - +
345B PHE* 3.7 1.4 - - - +
346B ALA* 3.1 37.8 + - + +
351B SER* 2.7 38.3 + - - +
352B GLU* 3.7 25.3 + - - +
354B PHE* 5.9 0.9 - - - -
355B ILE* 3.8 23.3 - - + +
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS 4.2 0.3 - - - +
69A ILE* 3.7 45.0 + - + +
70A GLY* 4.4 0.2 - - - -
71A LEU* 4.1 20.4 - - + -
355A ILE* 5.6 0.2 - - - +
356A GLY* 3.8 29.2 - - - +
357A ILE* 4.2 3.6 - - + -
66B PHE* 4.6 3.8 - - + +
67B LYS 3.3 13.8 + - - +
68B ASN* 1.3 80.5 - - - +
70B GLY* 1.3 68.6 + - - +
71B LEU* 5.3 1.8 - - + -
343B PRO* 5.2 4.0 - - + -
344B VAL 3.2 9.4 - - - +
345B PHE* 3.8 32.5 - - + -
354B PHE 4.3 0.4 - - - -
355B ILE* 3.4 22.0 - - - +
356B GLY 3.9 0.3 + - - -
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.4 2.0 - - - -
69B ILE* 1.3 77.2 - - - +
71B LEU* 1.3 70.1 + - - +
343B PRO* 3.5 0.7 - - - +
344B VAL* 2.8 36.1 + - - +
354B PHE 3.4 18.3 + - - -
355B ILE* 3.9 0.4 - - - -
356B GLY 3.2 14.1 - - - -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.0 38.6 - - + -
69A ILE* 4.2 14.8 - - + -
71A LEU* 6.2 4.0 - - + -
343A PRO* 5.4 3.6 - - + -
345A PHE* 3.9 30.7 - - + -
69B ILE* 5.3 1.6 - - + -
70B GLY* 1.3 84.6 - - - +
72B ILE* 1.3 65.5 + - - +
341B LEU* 4.4 11.9 - - + -
342B ILE 3.3 3.4 - - - +
343B PRO* 3.8 18.2 - - + -
344B VAL* 4.6 0.8 - - - +
356B GLY 2.9 7.3 + - - +
357B ILE* 3.4 24.7 - - + +
358B TYR* 3.0 26.8 + - - -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 1.3 72.1 - - - +
73B LYS* 1.3 60.7 + - - +
74B THR* 3.9 7.0 + - + +
91B PHE* 3.6 22.9 - - + -
299B THR* 3.5 19.3 - - + +
300B SER 3.6 16.2 - - - +
341B LEU* 3.3 9.5 - - - -
342B ILE* 2.8 50.4 + - + +
344B VAL* 3.6 12.6 - - + -
358B TYR* 3.1 41.5 - - + +
360B ASN* 4.0 20.4 - - + -
363B ILE* 4.2 4.0 - - + -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 3.3 37.4 + - + +
55A TYR* 3.5 41.2 - - + +
72B ILE* 1.3 71.7 - - - +
74B THR* 1.3 60.4 + - - +
75B SER* 3.6 8.5 - - - +
96B LYS* 3.5 9.2 + - - -
340B THR 6.0 0.2 - - - -
341B LEU* 3.5 20.6 - - + +
357B ILE* 5.9 1.6 - - + -
358B TYR 3.0 12.2 + - - +
359B GLU* 3.5 28.9 + - - +
360B ASN 2.9 22.1 + - - -
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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