Contacts of the helix formed by residues 141 - 151 (chain I) 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 PHE 141 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140I ALA* 1.3 91.1 - - + +
142I GLY* 1.3 63.4 + - - +
144I GLU* 4.2 1.4 + - - +
145I GLY* 2.9 49.1 + - - -
146I VAL* 4.2 5.6 - - + +
149I MET* 4.0 19.7 - - + -
250I LYS 5.5 0.2 - - - -
272I ALA* 6.2 0.9 - - - -
275I GLY* 3.8 24.0 - - - -
276I LEU 3.9 7.2 - - - -
277I ALA* 3.7 33.2 - - + -
311I ASP* 3.0 13.3 + - - +
360I LYS* 3.7 15.5 + - - +
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Residues in contact with GLY 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I PRO* 3.7 12.9 - - - +
141I PHE* 1.3 81.2 - - - +
143I ILE* 1.3 66.3 + - - -
144I GLU 3.3 0.2 - - - -
146I VAL* 3.1 23.7 + - - +
311I ASP* 3.2 17.5 + - - -
360I LYS* 4.4 6.5 - - - -
361I ALA 3.0 16.8 - - - -
363I PHE* 5.1 0.2 - - - -
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Residues in contact with ILE 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLY* 1.3 72.5 - - - +
144I GLU* 1.3 66.1 + - - +
146I VAL* 3.9 0.3 - - - -
147I ARG* 3.0 38.7 + - - +
338I ARG* 3.5 39.9 - - + -
361I ALA* 2.9 24.6 + - + +
362I ALA 3.5 22.2 - - - +
363I PHE* 3.8 31.9 - - + -
364I PRO* 4.2 3.4 - - + -
385I ASP* 4.3 17.7 - - + +
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Residues in contact with GLU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I PHE 4.7 2.5 - - - +
142I GLY 3.3 0.4 - - - -
143I ILE* 1.3 80.5 - - - +
145I GLY* 1.3 58.4 + - - +
147I ARG* 3.9 5.0 - - - +
148I LYS* 2.9 33.1 + - - +
360I LYS* 5.4 8.5 - - - +
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Residues in contact with GLY 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I PHE* 2.9 44.7 + - - -
144I GLU* 1.3 77.8 - - - +
146I VAL* 1.3 56.6 + - - +
148I LYS* 3.6 7.6 - - - +
149I MET* 2.9 28.1 + - - +
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Residues in contact with VAL 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I PHE* 4.3 11.2 - - + -
142I GLY 3.1 17.9 + - - +
143I ILE 4.0 2.2 - - - +
145I GLY* 1.3 74.2 - - - +
147I ARG* 1.3 68.0 + - - +
149I MET* 3.0 12.4 + - + +
150I LEU* 2.9 38.3 + - + +
157I ILE* 5.1 5.4 - - + -
251I HIS* 4.5 9.9 - - + +
277I ALA* 4.6 0.7 - - + -
311I ASP* 4.6 5.6 - - + -
312I GLN* 3.3 38.4 - - + +
363I PHE* 4.0 17.7 - - + -
387I VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ILE* 3.0 26.5 + - - +
144I GLU* 3.9 4.9 - - - +
146I VAL* 1.3 76.5 - - - +
148I LYS* 1.3 54.0 + - - +
150I LEU* 3.3 2.2 + - - -
151I GLU* 2.6 32.6 + - - -
152I ILE* 3.0 44.3 + - - +
153I LYS* 3.4 25.6 + - - +
154I ASP 3.2 5.8 + - - -
155I ARG 2.9 29.3 + - - -
156I PRO* 4.2 0.8 - - - +
157I ILE* 4.2 6.6 - - + +
363I PHE* 3.8 22.4 - - + -
384I THR 3.2 17.2 + - - -
385I ASP* 2.8 32.5 + - - +
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Residues in contact with LYS 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I GLU 2.9 20.1 + - - +
145I GLY* 3.6 8.3 - - - +
147I ARG* 1.3 77.0 - - - +
149I MET* 1.3 64.6 + - - +
151I GLU* 3.2 20.9 + - - +
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Residues in contact with MET 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I PHE* 4.0 24.9 - - + -
145I GLY 2.9 11.0 + - - +
146I VAL* 3.0 13.4 + - - +
148I LYS* 1.3 78.6 - - - +
150I LEU* 1.3 77.7 + - + +
151I GLU* 4.6 0.2 - - - +
223I LYS* 3.5 18.7 - - - +
250I LYS* 3.6 38.7 + - + +
251I HIS* 3.6 33.0 - - + -
277I ALA* 3.9 18.4 - - + -
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Residues in contact with LEU 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I VAL* 2.9 26.9 + - + +
147I ARG* 4.3 1.6 - - - +
149I MET* 1.3 92.4 - - + +
151I GLU* 1.3 71.9 + - - +
152I ILE* 3.1 24.6 + - + +
157I ILE* 4.0 28.0 - - + -
186I ASP* 4.5 6.3 - - + -
187I TYR* 5.4 0.4 - - + -
223I LYS* 3.4 33.8 + - + +
224I LYS 4.1 10.5 - - - +
225I THR* 4.0 35.4 - - + -
227I PHE* 6.1 0.9 - - + -
250I LYS* 4.9 1.1 - - - +
251I HIS* 5.3 0.7 - - + -
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Residues in contact with GLU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I ARG 2.6 15.1 + - - -
148I LYS* 3.2 14.3 + - - +
149I MET 4.6 0.4 - - - +
150I LEU* 1.3 76.9 - - - +
152I ILE* 1.3 58.2 + - - +
153I LYS* 4.1 1.5 + - - -
222I GLU* 6.1 0.7 - - - -
223I LYS* 3.5 32.5 + - + +
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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