Contacts of the helix formed by residues 130 - 138 (chain F) in PDB entry 5UQ9
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 GLY 130 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F VAL* 4.2 0.4 - - - -
129F SER* 1.3 78.1 + - - +
131F GLY* 1.3 65.7 + - - +
132F GLU 3.5 0.7 + - - -
133F GLU* 4.0 2.1 + - - +
134F GLY* 3.0 34.8 + - - -
135F ALA 4.9 0.7 - - - -
139F PRO* 5.0 0.4 - - - -
365F GLY* 3.8 14.6 - - - -
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Residues in contact with GLY 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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14F MET* 3.2 30.7 - - - +
128F VAL* 5.3 2.7 + - - +
130F GLY* 1.3 79.3 - - - +
132F GLU* 1.3 60.1 + - - -
135F ALA* 3.5 8.3 - - - +
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Residues in contact with GLU 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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13F VAL* 3.9 22.9 - - + +
14F MET* 5.2 3.4 - - + -
17F ASN* 3.3 27.2 + - - +
130F GLY 3.5 0.2 + - - -
131F GLY* 1.3 71.4 - - - -
133F GLU* 1.3 94.7 + - + +
134F GLY 3.2 1.3 - - - -
135F ALA* 3.4 2.4 + - - -
136F ARG* 3.1 18.9 + - - +
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Residues in contact with GLU 133 (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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130F GLY 4.0 1.9 + - - +
132F GLU* 1.3 97.1 - - + +
134F GLY* 1.3 61.9 + - - +
136F ARG* 3.4 3.8 + - - +
137F TYR* 3.2 46.9 + - + +
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Residues in contact with GLY 134 (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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130F GLY* 3.0 30.0 + - - -
133F GLU* 1.3 75.3 - - - +
135F ALA* 1.3 60.8 + - - +
138F GLY 2.7 40.5 + - - -
139F PRO* 2.9 13.4 - - - -
365F GLY* 5.9 1.1 - - - -
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Residues in contact with ALA 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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14F MET* 3.8 16.6 - - + +
17F ASN* 2.9 26.9 - - + +
18F LEU* 3.4 31.8 - - + +
21F ASN* 3.2 14.7 + - - +
128F VAL* 5.2 1.1 - - + -
130F GLY 4.6 0.4 - - - -
131F GLY 3.5 19.7 + - - +
132F GLU* 3.4 5.4 + - - +
134F GLY* 1.3 75.3 - - - +
136F ARG* 1.3 56.1 + - - +
139F PRO* 3.9 8.7 - - + +
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Residues in contact with ARG 136 (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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17F ASN* 3.4 36.0 + - + +
20F LEU* 3.5 46.0 + - - +
21F ASN* 3.2 15.0 + - - +
24F ASP* 3.1 30.7 + - - -
132F GLU 3.1 16.0 + - - +
133F GLU* 3.8 4.0 - - - +
134F GLY 3.1 1.2 - - - -
135F ALA* 1.3 74.5 - - - +
137F TYR* 1.3 97.4 + - + +
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Residues in contact with TYR 137 (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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21F ASN* 3.3 10.3 + - - +
24F ASP* 5.1 4.5 - - - -
25F HIS* 5.1 6.6 + - - -
133F GLU* 3.2 34.1 + - + +
134F GLY 3.2 1.4 + - - -
136F ARG* 1.3 117.0 + - + +
138F GLY* 1.3 58.0 + - - +
160F ILE 4.2 2.6 - - - +
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Residues in contact with GLY 138 (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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21F ASN* 3.4 1.2 - - - +
133F GLU 4.3 0.4 + - - -
134F GLY* 2.7 21.5 + - - +
137F TYR* 1.3 75.8 - - - +
139F PRO* 1.3 67.5 - - - +
160F ILE 3.4 9.0 - - - -
161F ALA 4.6 0.2 - - - -
162F ALA* 3.3 27.9 - - - +
365F GLY* 4.2 8.0 - - - -
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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