Contacts of the helix formed by residues 131 - 135 (chain E) in PDB entry 6UWZ
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 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E ILE* 1.3 71.4 - - - +
132E VAL* 1.3 64.6 + - - +
133E THR* 3.2 9.2 + - - +
134E TYR* 4.3 3.9 + - + -
138E ASP* 3.8 13.7 - - - +
139E TRP 4.8 6.7 - - - +
140E GLN* 3.1 27.2 - - - +
279E ASN* 5.6 2.9 - - - -
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Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ILE* 3.7 13.1 + - + +
131E ALA* 1.3 71.4 - - - +
133E THR* 1.3 68.8 + - - +
134E TYR 3.1 2.5 - - - -
135E PHE* 2.6 28.7 + - + +
274E PRO* 3.2 38.1 - - + +
276E THR* 3.7 18.2 - - - +
278E LEU* 6.0 0.4 - - + -
279E ASN* 3.2 41.2 + - + +
281E PRO* 3.2 21.8 - - + +
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Residues in contact with THR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ALA* 3.2 6.9 - - - +
132E VAL* 1.3 77.7 + - - +
134E TYR* 1.3 90.3 + - + +
279E ASN* 3.4 31.2 + - + +
280E VAL 3.6 12.6 - - - +
281E PRO 3.6 2.4 - - - -
282E LEU* 3.3 24.9 + - - +
285E LYS* 4.6 9.7 + - - +
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Residues in contact with TYR 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ALA* 4.3 5.4 + - + -
132E VAL 2.8 1.4 + - - -
133E THR* 1.3 101.8 - - + +
135E PHE* 1.3 56.2 + - - +
137E PHE* 2.6 41.5 + - + +
138E ASP* 4.1 2.9 - - - -
282E LEU* 4.1 10.9 - - + +
469E THR* 3.8 31.9 - - + -
470E GLY* 4.8 2.5 - - - -
473E ASN* 3.4 49.1 - - + +
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Residues in contact with PHE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLU* 4.7 7.9 - - + -
130E ILE* 5.7 2.0 - - + -
132E VAL* 2.6 32.6 + - + +
133E THR 3.4 0.2 - - - -
134E TYR* 1.3 71.5 - - - +
136E PRO* 1.3 71.0 - - + +
137E PHE 3.7 0.4 - - - +
138E ASP* 3.8 8.3 - - - +
217E ARG* 3.3 42.4 - - - -
222E TYR* 3.6 31.9 - + - -
269E ILE* 5.6 0.2 - - + -
272E LYS 3.8 15.5 - - - -
273E VAL* 3.7 25.4 - - + -
274E PRO* 4.7 10.3 - - + -
281E PRO* 4.0 7.4 - - + -
282E LEU* 3.2 24.8 + - - +
283E ILE* 3.4 21.2 + - + -
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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