Contacts of the helix formed by residues 134 - 139 (chain C) in PDB entry 4R0C
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 ASP 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU* 3.3 5.8 + - - +
133C VAL* 1.3 90.4 - - - +
135C ALA* 1.3 55.9 + - - +
136C GLY 3.1 2.9 - - - -
137C TYR* 2.7 29.1 + - - +
138C VAL* 2.9 32.2 + - + +
441C TYR* 2.4 38.2 + - - -
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU* 3.3 14.1 + - + +
103C SER* 3.7 29.4 - - - +
106C LEU* 4.7 8.0 - - + +
129C SER* 5.0 0.4 - - - -
132C THR* 3.5 21.6 + - + +
134C ASP* 1.3 75.6 - - - +
136C GLY* 1.3 57.8 + - - +
138C VAL* 4.7 1.1 - - - +
139C VAL* 3.1 17.2 + - + +
140C LEU* 2.8 27.2 + - - +
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C SER* 3.6 26.7 + - - -
132C THR* 3.9 6.3 + - - -
133C VAL 4.7 1.8 + - - -
134C ASP 2.8 5.5 + - - -
135C ALA* 1.3 75.7 - - - +
137C TYR* 1.3 56.1 + - - +
140C LEU* 3.2 12.1 - - - +
141C ILE* 3.1 31.7 + - - +
166C VAL* 3.8 12.0 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL 4.1 13.9 - - - -
134C ASP 2.7 10.6 + - - +
136C GLY* 1.3 73.3 - - - +
138C VAL* 1.3 60.3 + - + +
141C ILE* 3.6 18.6 - - + +
142C PRO* 3.3 13.0 - - - +
163C PHE* 4.2 8.5 - + - -
166C VAL* 3.9 20.4 + - + -
167C SER* 2.9 37.3 + - - -
170C PHE* 5.9 2.4 - - - -
433C ASN* 5.3 1.0 + - - -
439C MET* 4.2 6.0 - - + -
441C TYR* 3.4 71.5 - + + -
444C LEU* 4.5 2.7 - - + -
445C VAL* 4.4 3.6 - - + -
448C PHE* 3.2 22.7 - - + -
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 2.9 42.4 + - + +
135C ALA* 4.7 0.4 - - - +
137C TYR* 1.3 74.3 - - + +
139C VAL* 1.3 71.9 + - + +
142C PRO* 3.9 11.9 - - - +
244C ASP* 3.9 12.0 - - - +
441C TYR* 4.6 0.7 - - + -
444C LEU* 3.7 24.2 - - + -
448C PHE* 4.1 9.8 - - + -
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C SER* 3.2 38.4 - - - +
106C LEU* 6.4 0.7 - - + -
107C ALA* 4.7 4.9 - - + -
135C ALA* 3.1 13.6 + - + +
137C TYR 3.3 0.2 - - - -
138C VAL* 1.3 96.7 - - + +
140C LEU* 1.3 70.1 + - + +
141C ILE 3.5 0.7 - - - -
142C PRO* 3.2 4.0 - - - +
143C LEU* 3.2 25.8 + - + +
244C ASP* 4.0 14.3 - - - +
245C ALA* 3.7 28.0 - - + -
246C PRO* 4.7 2.0 - - + -
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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