Contacts of the strand formed by residues 133 - 136 (chain C) in PDB entry 4HHM
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 VAL 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C PRO* 3.4 13.7 + - + +
88C MET* 3.2 12.0 - - + +
89C ALA* 3.0 24.9 + - - +
131C ALA* 3.5 2.5 - - - +
132C LYS* 1.3 89.2 - - + +
134C TYR* 1.3 64.3 + - - +
135C VAL 4.1 0.2 - - - -
176C ILE* 4.3 1.8 - - - -
177C ARG* 3.4 12.1 - - + +
179C ALA* 4.3 12.8 - - + -
242C PHE* 4.3 15.7 - - + +
243C HIS* 4.0 33.0 - - + -
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA* 3.1 20.4 - - + -
90C THR 4.0 3.8 - - - -
91C THR* 2.7 29.9 + - - -
119C THR* 3.7 16.2 + - + -
122C ASN* 2.9 52.2 + - - +
123C ILE* 3.9 15.7 - - + -
126C ALA* 4.0 14.1 - - + -
133C VAL* 1.3 73.4 - - - +
135C VAL* 1.3 72.7 + - - +
136C ALA* 3.9 2.6 + - + -
176C ILE* 3.8 14.3 - - + +
177C ARG 2.7 9.8 + - - +
178C PHE* 3.2 38.5 - + + -
179C ALA 3.0 21.3 + - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 3.5 34.3 - - + -
89C ALA 3.1 6.5 + - - -
90C THR* 2.7 42.1 + - + +
91C THR* 4.1 1.2 + - - -
133C VAL* 4.1 0.4 - - + -
134C TYR* 1.3 84.0 - - - +
136C ALA* 1.3 68.6 + - - +
137C TRP* 4.2 2.2 - - + +
179C ALA* 3.4 18.8 - - + +
181C GLU* 3.6 25.4 - - + +
215C ASN* 3.8 20.4 - - - +
243C HIS* 4.2 4.3 - - + +
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Residues in contact with ALA 136 (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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104C PHE* 5.3 6.7 - - + -
134C TYR* 5.0 5.2 - - + +
135C VAL* 1.3 79.7 - - - +
137C TRP* 1.3 60.1 + - - +
138C GLY 3.9 2.0 + - - -
162C PHE* 3.8 34.2 - - + -
165C LEU* 6.2 0.9 - - + -
178C PHE* 5.7 4.5 - - + -
179C ALA 3.0 8.7 + - - +
180C ILE* 3.7 8.5 - - + +
181C GLU 3.0 22.0 + - - +
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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