Contacts of the helix formed by residues 129 - 134 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS 3.9 7.9 - - - +
22A LYS 3.5 30.3 - - - +
24A ASP 3.1 32.3 - - - +
25A ILE* 4.0 12.1 - - + -
93A PHE* 4.6 5.6 - - + -
127A TYR* 3.7 12.8 - - + +
128A PHE* 1.3 88.9 - - + +
130A GLU* 1.3 67.8 + - - +
131A LYS* 2.8 4.9 + - + +
132A LEU* 2.9 31.3 + - + +
133A ILE 3.1 5.5 + - - -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS 4.7 3.2 + - - -
22A LYS* 2.9 23.9 + - - +
127A TYR* 5.2 0.6 + - - -
128A PHE 3.9 0.4 + - - -
129A PRO* 1.3 72.5 - - - +
131A LYS* 1.3 61.1 + - - +
133A ILE* 3.6 4.5 - - - +
134A ARG* 2.6 64.8 + - - +
357A TYR* 3.1 41.1 + - + +
169B SER* 4.4 0.7 - - - -
198B TRP* 3.9 11.5 - - + -
199B TYR* 5.3 0.5 - - - +
66G ARG* 2.7 37.1 + - - -
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS 4.9 9.1 + - - +
93A PHE* 3.1 46.0 - - + -
98A GLU* 3.7 24.9 + - - +
129A PRO* 2.8 3.6 + - + +
130A GLU* 1.3 80.2 - - - +
132A LEU* 1.3 67.4 + - + +
134A ARG* 3.5 8.0 + - - +
135A GLU* 3.2 32.1 + - + +
198B TRP* 3.8 62.9 - - + +
201B ARG* 6.0 0.6 - - - +
93G PHE* 6.0 0.7 - - - -
94G HIS* 4.7 3.8 - - - +
98G GLU* 4.8 2.4 + - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.5 32.1 - - + -
93A PHE* 3.9 28.9 - - + +
96A PHE* 5.7 0.7 - - + -
104A LEU* 4.6 5.6 - - + -
128A PHE* 3.9 36.8 - - + -
129A PRO* 2.9 13.4 + - + +
131A LYS* 1.3 83.6 - - + +
133A ILE* 1.3 67.3 + - - +
134A ARG 3.0 1.8 - - - -
135A GLU* 2.9 32.7 + - - +
136A PHE* 3.2 19.7 - - + -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.5 33.7 - - + +
129A PRO 3.1 6.3 + - - +
130A GLU* 3.6 12.3 - - - +
132A LEU* 1.3 77.2 - - - +
134A ARG* 1.3 60.0 + - + +
135A GLU 3.2 0.2 - - - -
136A PHE* 3.3 27.4 + - - +
303A LYS* 5.5 0.7 - - + -
307A LEU* 4.0 22.2 - - + +
354A GLN* 3.6 24.0 - - + +
355A LYS 3.8 7.2 - - - +
356A PHE* 3.8 15.3 - - + +
357A TYR* 4.0 13.2 - - + -
359A ILE* 3.7 26.6 - - + +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 2.6 50.9 + - + +
131A LYS* 3.5 6.5 + - - +
132A LEU 3.0 0.8 - - - -
133A ILE* 1.3 79.0 - - + +
135A GLU* 1.3 58.0 + - - +
136A PHE 3.1 12.7 + - - +
357A TYR* 3.5 24.6 - - + +
358A SER* 4.0 9.2 + - - +
169B SER* 3.5 14.8 + - - -
170B PRO* 4.4 6.6 - - - +
171B GLU* 3.1 39.7 + - - +
198B TRP* 3.9 28.0 - - + +
199B TYR* 4.7 4.4 + - - +
204B GLU* 4.6 14.2 + - - +
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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