Contacts of the helix formed by residues 129 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LYS 3.7 13.0 - - - +
22B LYS 3.3 31.9 - - - +
23B ARG 4.1 3.8 - - - +
24B ASP 3.5 20.4 - - - +
25B ILE* 3.7 29.4 - - + -
93B PHE* 4.5 2.2 - - + -
127B TYR* 3.8 2.6 - - - +
128B PHE* 1.3 90.8 - - + +
130B GLU* 1.3 67.7 + - - +
131B LYS* 3.1 2.9 - - + +
132B LEU* 2.9 26.7 + - + +
133B ILE 3.2 7.1 + - - -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS 4.7 1.4 + - - -
22B LYS* 2.7 43.1 + - - +
127B TYR* 5.1 0.4 + - - -
128B PHE 3.9 0.2 + - - -
129B PRO* 1.3 72.5 - - - +
131B LYS* 1.3 62.5 + - - +
133B ILE* 3.2 4.1 + - - +
134B ARG* 2.7 62.2 + - - +
357B TYR* 3.4 37.0 + - + +
169C SER* 4.4 0.5 - - - -
198C TRP* 3.8 12.4 - - + -
199C TYR 5.0 1.2 - - - +
66F ARG* 2.8 32.5 + - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS 5.0 9.3 + - - +
93B PHE* 3.7 45.5 - - + -
98B GLU* 3.2 28.5 + - - +
129B PRO* 3.0 2.7 + - + +
130B GLU* 1.3 79.0 - - - +
132B LEU* 1.3 67.5 + - + +
134B ARG* 3.7 4.0 + - - +
135B GLU* 3.4 32.8 + - - +
198C TRP* 3.6 65.5 - - + +
93F PHE* 5.8 1.3 - - - -
94F HIS* 4.7 4.7 - - + -
98F GLU* 4.6 3.5 + - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.6 28.0 - - + -
93B PHE* 3.6 35.4 - - + +
96B PHE* 5.6 2.7 - - + -
104B LEU* 3.9 17.3 - - + -
128B PHE* 3.9 26.0 - - + -
129B PRO* 2.9 16.5 + - + +
131B LYS* 1.3 81.1 - - + +
133B ILE* 1.3 65.1 + - - +
134B ARG 3.1 1.8 - - - -
135B GLU* 2.9 35.0 + - - +
136B PHE* 3.2 19.4 - - + -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 3.7 21.5 - - + +
129B PRO 3.2 15.6 + - - +
130B GLU* 3.5 12.1 - - - +
132B LEU* 1.3 77.0 - - - +
134B ARG* 1.3 58.4 + - + +
136B PHE* 3.2 30.5 + - - +
307B LEU* 3.9 23.3 - - + -
354B GLN* 3.6 24.5 - - + +
355B LYS 4.0 8.5 - - - +
356B PHE* 3.7 17.7 - - + +
357B TYR* 4.2 8.1 - - + -
359B ILE* 3.7 28.7 - - + +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.7 52.1 + - + +
131B LYS* 3.7 7.2 + - - +
132B LEU 3.1 0.2 - - - -
133B ILE* 1.3 76.9 - - + +
135B GLU* 1.3 58.4 + - - +
136B PHE 3.1 13.9 + - - +
357B TYR* 3.6 24.3 - - + +
358B SER* 3.9 9.1 + - - +
169C SER* 3.2 13.9 + - - -
170C PRO* 4.0 8.6 - - - +
171C GLU* 2.9 43.4 + - - -
198C TRP* 3.9 28.0 - - + +
199C TYR* 4.6 3.9 + - - +
204C GLU* 4.4 13.8 + - - +
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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