Contacts of the helix formed by residues 129 - 134 (chain F) in PDB entry 3KDO
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 PRO 129 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F LYS 3.7 7.9 - - - +
22F LYS 3.4 33.0 - - - +
23F ARG 4.5 3.8 - - - -
24F ASP 3.4 27.1 - - - +
25F ILE* 3.6 15.0 - - + -
93F PHE* 4.6 3.1 - - + -
127F TYR* 3.7 9.8 - - + +
128F PHE* 1.3 89.6 - - + +
130F GLU* 1.3 66.8 + - - +
131F LYS* 4.2 3.4 - - + +
132F LEU* 2.7 34.2 + - + +
133F ILE* 3.1 5.4 + - - -
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Residues in contact with GLU 130 (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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66B ARG* 2.8 36.1 + - - -
21F LYS 4.9 0.8 + - - -
22F LYS* 2.7 31.4 + - - +
127F TYR* 4.9 1.2 + - - -
128F PHE 3.8 0.8 + - - -
129F PRO* 1.3 71.9 - - - +
131F LYS* 1.3 62.5 + - - +
133F ILE* 3.6 4.4 - - - +
134F ARG* 2.6 67.1 + - + +
357F TYR* 3.3 39.4 + - + +
169G SER* 4.4 0.5 - - - -
198G TRP* 4.0 8.6 - - + -
199G TYR 5.2 0.7 - - - +
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Residues in contact with LYS 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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93B PHE* 5.4 2.0 - - - -
94B HIS* 4.8 4.1 - - + +
98B GLU* 5.3 1.9 + - - -
22F LYS 4.6 11.8 + - - +
93F PHE* 3.1 40.9 - - + -
98F GLU* 4.0 19.2 + - - +
129F PRO* 2.8 6.0 + - + +
130F GLU* 1.3 78.7 - - - +
132F LEU* 1.3 75.0 + - + +
134F ARG* 3.6 4.2 + - - +
135F GLU* 3.3 33.5 + - - +
198G TRP* 3.3 67.1 - - + +
201G ARG* 6.0 0.4 - - - +
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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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25F ILE* 3.0 35.9 - - + -
93F PHE* 3.8 29.4 - - + +
96F PHE* 6.4 0.4 - - + -
104F LEU* 4.0 8.1 - - + -
128F PHE* 3.7 31.9 - - + -
129F PRO* 2.7 20.5 + - + +
131F LYS* 1.3 78.9 - - + +
133F ILE* 1.3 65.3 + - - +
134F ARG 3.1 1.6 - - - -
135F GLU* 2.8 37.6 + - - +
136F PHE* 3.2 15.6 - - + -
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Residues in contact with ILE 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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128F PHE* 3.7 21.3 - - + +
129F PRO 3.1 12.0 + - - +
130F GLU* 3.6 13.0 - - - +
132F LEU* 1.3 76.3 - - - +
134F ARG* 1.3 61.5 + - + +
136F PHE* 3.0 31.6 + - - +
303F LYS* 5.5 0.2 - - + -
307F LEU* 3.9 22.0 - - + -
354F GLN* 3.6 19.5 - - - +
355F LYS 3.8 13.5 - - - +
356F PHE* 3.6 28.0 - - + +
357F TYR* 4.1 12.1 - - + -
359F ILE* 3.8 15.1 - - + +
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Residues in contact with ARG 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 GLU* 2.6 55.1 + - + +
131F LYS* 3.6 5.4 + - - +
133F ILE* 1.3 77.9 - - + +
135F GLU* 1.3 59.6 + - - +
136F PHE 3.2 10.5 + - - +
357F TYR* 3.7 23.3 - - + +
358F SER* 3.9 8.7 + - - -
169G SER* 3.4 14.7 + - - -
170G PRO* 4.5 6.4 - - - +
171G GLU* 3.1 41.4 + - - -
198G TRP* 4.0 24.7 - - + +
199G TYR* 4.7 9.0 + - - +
204G GLU* 4.9 12.5 + - - +
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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