Contacts of the helix formed by residues 350 - 355 (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 GLY 350 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.2 8.1 - - - -
32B LYS 3.4 19.3 + - - +
295B LEU* 4.3 3.6 - - - -
348B GLY 3.2 0.8 + - - -
349B PRO* 1.3 71.0 - - - +
351B SER* 1.3 64.1 + - - +
352B GLU* 3.1 13.8 + - - -
353B GLU* 3.1 22.1 + - - +
354B PHE* 3.8 3.9 - - - -
370B VAL* 3.6 20.6 - - - +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 2.7 30.9 + - - +
295B LEU* 3.8 8.7 - - - -
346B ALA* 3.4 43.6 + - - +
347B TYR* 3.6 6.9 - - - -
348B GLY 3.0 20.8 + - - -
349B PRO 3.3 1.2 + - - -
350B GLY* 1.3 78.0 - - - +
352B GLU* 1.3 65.3 + - - +
353B GLU 3.1 0.4 - - - -
354B PHE* 3.1 13.6 + - - +
355B ILE 4.4 0.2 + - - -
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Residues in contact with GLU 352 (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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31B LEU* 3.5 33.6 - - + +
32B LYS 5.6 0.3 + - - -
68B ASN* 3.9 26.5 + - - +
348B GLY 4.6 1.3 - - - +
350B GLY 3.1 6.4 + - - -
351B SER* 1.3 83.4 + - - +
353B GLU* 1.3 61.5 + - - +
354B PHE 3.0 1.8 + - - -
355B ILE* 3.3 29.7 - - + +
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Residues in contact with GLU 353 (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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31B LEU* 3.7 13.3 - - + +
350B GLY 3.1 15.4 + - - +
352B GLU* 1.3 78.6 - - - +
354B PHE* 1.3 59.1 + - + +
355B ILE* 3.4 2.6 + - - +
366B LYS* 2.7 73.4 + - + +
369B LYS* 3.2 39.8 + - + +
370B VAL* 3.7 19.6 - - + +
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Residues in contact with PHE 354 (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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68B ASN 5.9 0.7 - - - -
69B ILE 4.9 0.4 - - - -
70B GLY* 3.4 12.6 + - - -
295B LEU* 3.9 20.6 - - + -
297B ILE* 3.5 28.0 - - + -
344B VAL* 4.2 9.7 - - + +
346B ALA* 3.9 21.3 - - + -
350B GLY 3.8 12.1 - - - -
351B SER* 3.1 15.1 + - - +
352B GLU 3.0 1.8 - - - -
353B GLU* 1.3 81.4 - - + +
355B ILE* 1.3 61.9 + - - +
358B TYR* 2.7 37.5 + - - +
363B ILE* 4.0 25.4 - - + -
366B LYS* 3.6 31.6 - - + -
367B ILE* 3.8 13.5 - - + -
370B VAL* 4.5 4.5 - - + -
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Residues in contact with ILE 355 (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* 3.4 32.0 + - + +
68A ASN* 3.9 18.2 - - - +
69A ILE 6.1 0.2 - - - +
355A ILE* 6.3 2.7 - - + -
68B ASN* 3.8 36.3 - - + +
69B ILE 3.4 19.1 - - - +
352B GLU* 3.3 24.0 - - + +
353B GLU 3.4 4.5 - - - +
354B PHE* 1.3 79.6 - - - +
356B GLY* 1.3 69.8 + - - +
358B TYR* 3.3 10.2 - - - -
366B LYS* 4.8 1.2 + - - -
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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