Contacts of the helix formed by residues 130 - 135 (chain F) in PDB entry 4O9U
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 130 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F MET 5.7 0.3 - - - +
120F ILE* 4.1 12.7 - - - +
121F PRO 3.8 7.6 - - - +
122F ARG* 2.8 37.7 + - - -
126F ALA 3.4 12.3 + - - +
127F GLN* 3.6 19.9 + - - +
128F SER 3.7 0.4 - - - -
129F MET* 1.3 74.2 - - - +
131F ALA* 1.3 65.8 + - - +
132F LEU* 3.6 3.6 + - - +
133F SER* 2.9 41.5 + - - +
134F SER* 3.4 11.3 + - - -
329F ASN* 3.1 13.0 + - - +
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 4.4 6.3 - - + -
117F MET* 3.6 40.7 + - + +
120F ILE* 5.4 1.2 - - - +
129F MET 3.0 5.3 + - - -
130F ASP* 1.3 69.0 + - - +
132F LEU* 1.3 53.0 + - - +
133F SER 3.1 3.8 - - - -
134F SER* 2.7 24.7 + - - -
135F GLN* 2.7 26.7 + - - +
326F TYR* 3.8 22.2 - - + -
329F ASN* 4.1 3.6 - - - +
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Residues in contact with LEU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.5 24.9 - - + -
96F GLN* 5.7 1.6 - - - +
117F MET 4.4 3.6 + - - +
118F GLU* 3.8 32.1 - - + +
122F ARG* 4.2 21.1 - - - +
130F ASP* 3.6 1.9 + - - +
131F ALA* 1.3 77.0 - - - +
133F SER* 1.3 56.1 + - - +
135F GLN* 3.4 13.8 - - + +
136F ALA* 2.8 35.9 + - + +
500F NAD 5.1 8.0 + - - +
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Residues in contact with SER 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 2.8 26.5 + - - +
127F GLN* 3.9 10.0 + - - -
130F ASP* 2.9 31.6 + - - +
131F ALA 3.1 0.2 - - - -
132F LEU* 1.3 76.5 - - - +
134F SER* 1.3 57.6 + - - +
135F GLN 3.0 4.6 + - - -
136F ALA 3.3 0.2 + - - -
137F THR* 3.1 30.8 + - - -
177F VAL* 3.3 14.7 - - - +
500F NAD 3.9 10.3 - - - -
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Residues in contact with SER 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ALA* 4.7 5.8 - - - -
130F ASP 3.4 3.9 + - - -
131F ALA* 2.7 20.8 + - - -
133F SER* 1.3 74.7 - - - +
135F GLN* 1.3 79.7 + - - +
136F ALA 3.6 0.2 - - - -
137F THR* 4.5 0.9 - - - -
138F VAL* 3.2 23.6 - - - +
325F MET* 3.6 29.8 - - - +
329F ASN* 2.5 31.8 + - - -
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Residues in contact with GLN 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 3.6 25.7 + - - +
94F PHE* 4.3 11.9 - - + -
131F ALA 2.7 19.3 + - - +
132F LEU* 3.4 16.4 - - + +
134F SER* 1.3 109.2 + - - +
136F ALA* 1.3 56.3 + - - +
137F THR 3.8 0.2 - - - -
138F VAL* 4.6 2.7 - - - -
139F ALA* 4.3 5.2 - - - +
315F PRO* 3.3 43.6 - - + +
322F ALA* 3.1 32.2 + - - +
326F TYR* 3.6 18.8 - - + +
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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