Contacts of the helix formed by residues 141 - 146 (chain K) in PDB entry 1UW9
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 141 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ASP 3.3 25.8 - - - +
34K THR* 3.2 26.2 - - - +
35K ASP 3.5 11.0 - - - +
36K ILE* 3.7 19.7 - - + -
105K ILE* 4.8 0.2 - - + -
139K ARG* 3.3 19.0 - - - +
140K ILE* 1.3 83.9 - - - +
142K PRO* 1.3 73.3 - - + +
143K ALA 4.3 2.9 - - - +
144K TYR* 2.9 24.8 + - + +
145K VAL* 2.9 11.4 + - - +
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Residues in contact with PRO 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H THR* 4.4 14.4 - - + -
143H ALA* 4.4 1.1 - - + -
33K ASP 4.6 5.8 - - - +
139K ARG* 5.6 1.8 - - - +
140K ILE 3.8 2.4 - - - +
141K PRO* 1.3 85.5 - - + +
143K ALA* 1.3 56.8 + - - +
145K VAL* 3.1 11.2 + - + +
146K LYS* 2.9 37.5 + - - +
367K ASP* 3.8 38.6 - - + +
369K SMC 3.9 26.2 - - + -
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Residues in contact with ALA 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H PRO* 4.3 3.6 - - + -
143H ALA* 3.7 32.7 - - + +
146H LYS* 3.5 25.2 - - + +
369H SMC 5.6 0.2 - - - -
34K THR* 4.0 23.8 - - + -
105K ILE* 3.7 18.6 - - + -
141K PRO* 3.1 1.8 + - - +
142K PRO* 1.3 79.2 - - - +
144K TYR* 1.3 59.5 + - - +
146K LYS* 4.1 3.6 + - - +
147K THR* 3.6 5.9 - - - +
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Residues in contact with TYR 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H LYS* 5.7 1.3 - - - -
36K ILE* 4.2 14.6 - - + -
105K ILE* 3.6 20.4 - - + +
108K PHE* 3.5 28.1 - + + +
109K GLU 2.8 32.8 + - - -
110K GLU* 4.2 2.2 - - + -
112K SER 3.5 15.8 + - - -
116K MET* 4.0 18.7 + - + +
140K ILE* 4.0 14.8 - - + -
141K PRO* 2.9 22.5 + - + +
143K ALA* 1.3 77.6 - - - +
145K VAL* 1.3 63.3 + - - +
146K LYS 3.1 1.6 - - - -
147K THR* 2.7 40.9 + - + -
148K PHE* 3.2 30.4 - + - -
320K MET* 4.0 6.3 - - + -
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Residues in contact with VAL 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140K ILE* 3.6 30.2 - - + +
141K PRO 2.9 18.4 + - - +
142K PRO* 3.5 10.1 - - + +
144K TYR* 1.3 75.1 - - - +
146K LYS* 1.3 63.9 + - + +
148K PHE* 3.1 27.3 + - - +
320K MET* 5.7 0.7 - - + -
366K GLN* 4.4 0.2 - - - +
367K ASP 4.1 11.4 - - - +
368K TRP* 3.3 36.6 - - + +
369K SMC 4.7 4.5 - - + +
371K MET* 3.7 27.4 - - + +
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Residues in contact with LYS 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H ILE* 4.2 29.7 + - + +
106H ASP* 5.2 1.6 + - - -
108H PHE 5.2 1.0 + - - -
110H GLU* 3.0 46.7 + - - +
143H ALA* 3.5 24.7 - - + +
144H TYR* 5.6 1.6 - - - -
147H THR* 3.6 20.3 - - + +
142K PRO 2.9 21.8 + - - +
143K ALA 4.2 3.8 - - - +
144K TYR 3.1 0.4 - - - -
145K VAL* 1.3 77.2 - - + +
147K THR* 1.3 60.6 + - + +
148K PHE 3.3 6.1 + - - +
369K SMC 4.1 32.3 + - + +
210R PRO* 3.6 19.4 - - - +
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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