Contacts of the helix formed by residues 129 - 134 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21H LYS 3.8 10.8 - - - +
22H LYS 3.4 26.2 - - - +
23H ARG 4.0 2.5 - - - -
24H ASP 3.1 39.5 - - - +
25H ILE* 3.7 23.3 - - + -
93H PHE* 4.9 1.6 - - + -
127H TYR* 3.7 2.2 - - + +
128H PHE* 1.3 89.8 - - + +
130H GLU* 1.3 67.8 + - - +
131H LYS* 2.8 9.2 + - + +
132H LEU* 2.9 19.5 + - + -
133H ILE* 3.1 7.0 + - - -
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Residues in contact with GLU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG* 2.8 37.9 + - - +
21H LYS 4.7 0.6 + - - -
22H LYS* 2.8 32.4 + - - +
127H TYR* 5.0 1.6 + - - -
128H PHE 3.8 0.8 + - - -
129H PRO* 1.3 72.4 - - - +
131H LYS* 1.3 62.4 + - - +
133H ILE* 3.2 5.2 + - - +
134H ARG* 2.8 62.9 + - - +
357H TYR* 3.4 38.3 + - + +
169I SER* 4.4 0.7 - - - -
198I TRP* 3.9 12.7 - - + -
199I TYR* 5.3 0.9 - - - +
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Residues in contact with LYS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E PHE* 6.1 0.8 - - - -
94E HIS* 5.1 1.3 - - - -
98E GLU* 4.6 3.4 + - - -
22H LYS 4.7 5.8 + - - +
93H PHE* 4.0 42.0 - - + -
98H GLU* 2.5 37.0 + - - +
129H PRO* 2.8 9.5 + - + +
130H GLU* 1.3 81.1 - - - +
132H LEU* 1.3 69.3 + - + +
134H ARG* 3.4 9.5 + - - +
135H GLU* 3.5 24.7 + - + +
198I TRP* 3.6 64.6 - - + +
201I ARG* 6.0 0.4 - - - +
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Residues in contact with LEU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ILE* 3.6 19.3 - - + -
93H PHE* 3.8 31.2 - - + +
96H PHE* 5.7 2.9 - - + -
104H LEU* 3.9 11.9 - - + -
128H PHE* 3.3 44.6 - - + -
129H PRO* 2.9 12.6 + - + +
131H LYS* 1.3 81.4 - - + +
133H ILE* 1.3 66.6 + - - +
135H GLU* 2.9 36.5 + - - +
136H PHE* 3.1 19.8 - - + -
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Residues in contact with ILE 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PHE* 3.7 22.0 - - + +
129H PRO 3.1 14.1 + - - +
130H GLU* 3.4 13.7 - - - +
132H LEU* 1.3 76.5 - - - +
134H ARG* 1.3 60.4 + - + +
136H PHE* 3.1 30.3 + - - +
303H LYS* 5.8 0.4 - - + -
307H LEU* 3.9 23.1 - - + +
354H GLN* 3.5 23.6 - - + +
355H LYS 4.0 9.2 - - - +
356H PHE* 3.7 26.2 - - + +
357H TYR* 4.1 12.3 - - + -
359H ILE* 3.9 15.4 - - + +
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Residues in contact with ARG 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H GLU* 2.8 49.5 + - + +
131H LYS* 4.0 4.9 - - - +
132H LEU 3.2 0.4 - - - -
133H ILE* 1.3 77.4 - - + +
135H GLU* 1.3 58.3 + - - +
136H PHE 3.0 14.2 + - - +
357H TYR* 3.6 23.0 - - + +
358H SER* 4.1 8.2 + - - +
359H ILE* 6.0 0.4 - - - -
169I SER* 3.4 16.7 - - - -
170I PRO* 4.1 10.3 - - - +
171I GLU* 3.0 39.7 + - - -
198I TRP* 4.2 26.0 - - + +
199I TYR* 4.8 5.8 + - - +
204I GLU* 5.2 4.8 + - - -
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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