Contacts of the helix formed by residues 359 - 363 (chain A) in PDB entry 2WXW
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 LEU 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.4 35.7 - - + +
109A THR* 3.8 15.3 - - + -
110A LEU* 5.1 5.6 - - + +
113A LEU* 6.2 0.7 - - + -
357A TYR* 3.9 7.6 - - + +
358A ASP* 1.3 71.7 - - - +
360A GLN* 1.3 53.6 + - - +
362A LEU* 3.6 11.2 - - + +
363A LEU* 2.7 53.7 + - + +
369A PRO* 4.6 0.3 - - - +
373A HIS* 5.1 4.9 - - + +
391A VAL* 3.0 36.0 + - + +
393A ASN* 3.7 37.0 - - + +
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Residues in contact with GLN 360 (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 GLY 4.7 6.5 + - - -
358A ASP* 3.2 24.1 + - - +
359A LEU* 1.3 77.7 - - - +
361A ASP* 1.3 70.6 + - - +
363A LEU 2.8 18.0 - - - +
364A ALA* 4.6 2.6 - - - +
369A PRO* 4.7 0.4 - - - -
370A ALA* 3.7 25.4 - - + +
373A HIS* 3.8 26.8 - - + +
374A THR* 6.1 0.3 - - - +
388A VAL* 4.2 18.2 + - - +
389A GLY 3.2 22.5 + - - +
390A GLU* 4.0 9.6 - - - -
391A VAL* 3.8 9.5 - - + +
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Residues in contact with ASP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 4.3 11.4 - - - +
94A VAL* 4.2 22.0 - - + +
96A HIS* 5.1 7.8 + - - -
235A MET* 6.1 0.5 - - - +
358A ASP* 3.1 24.5 + - + +
360A GLN* 1.3 88.1 + - - +
362A LEU* 1.3 64.6 + - - +
363A LEU 3.4 3.4 + - - +
364A ALA* 4.8 4.8 - - - +
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Residues in contact with LEU 362 (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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84A ILE* 3.2 47.3 - - + +
87A MET* 3.3 27.9 - - - +
91A LEU* 3.6 30.3 - - + +
94A VAL* 4.4 13.9 - - + +
101A LEU* 4.4 12.1 - - + -
106A VAL* 4.9 1.8 - - + -
357A TYR* 4.1 23.6 - - + -
358A ASP 2.7 21.8 + - - +
359A LEU* 3.6 15.9 - - + +
361A ASP* 1.3 75.3 - - - +
363A LEU* 1.3 61.2 + - + +
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Residues in contact with LEU 363 (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 LEU* 5.0 3.4 - - + -
83A ARG* 6.0 0.7 - - + -
84A ILE* 3.5 31.4 - - + -
110A LEU* 3.7 30.3 - - + -
128A ILE* 4.1 10.3 - - + -
359A LEU* 2.7 28.9 + - + +
360A GLN 2.8 25.5 - - - +
362A LEU* 1.3 81.7 - - + +
364A ALA* 1.3 62.6 + - - +
367A GLU* 4.1 27.6 - - + +
369A PRO* 3.3 30.8 - - + +
370A ALA 4.6 0.3 + - - -
373A HIS* 6.2 0.2 - - - +
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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