Contacts of the helix formed by residues 142 - 149 (chain B) in PDB entry 3UFJ
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 GLY 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B PRO* 1.3 76.4 - - - +
143B LEU* 1.3 67.1 + - - -
144B MET 3.2 2.9 - - - -
145B ALA* 3.2 5.3 + - - +
146B ALA* 2.8 22.3 + - - +
196B THR* 3.8 0.9 - - - -
197B THR 3.7 7.4 - - - -
198B PRO 3.9 1.8 - - - -
11F UF2 3.3 42.0 - - - -
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Residues in contact with LEU 143 (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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143A LEU* 4.2 18.0 - - + +
144A MET* 4.0 40.4 - - + +
147A TYR* 3.8 35.4 - - + -
142B GLY* 1.3 70.7 - - - +
144B MET* 1.3 64.6 + - - +
146B ALA* 3.4 3.5 + - + +
147B TYR* 3.0 22.7 + - - +
196B THR* 4.2 12.6 - - + +
197B THR 3.8 7.1 + - - -
198B PRO* 3.8 25.2 + - + +
10F A 4.5 14.8 - - - +
11F UF2 4.3 1.7 + - - +
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.9 18.7 - - + +
198A PRO* 4.7 18.4 - - + -
142B GLY* 3.2 0.8 - - - -
143B LEU* 1.3 76.6 - - - +
145B ALA* 1.3 68.5 + - - +
147B TYR* 2.8 7.5 + - - +
148B LYS* 2.7 40.4 + - + +
153B PRO* 3.9 24.5 - - + -
154B GLY* 4.4 21.3 - - - +
9D C 5.3 5.2 - - - +
10D A 3.8 27.1 - - - +
16E G 6.2 3.1 - - - -
10F A 6.2 4.5 - - - -
11F UF2 4.5 12.7 + - - +
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Residues in contact with ALA 145 (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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124B LEU* 3.9 12.8 - - + +
141B PRO* 4.2 0.2 - - + -
142B GLY 3.2 12.7 + - - +
144B MET* 1.3 78.7 - - - +
146B ALA* 1.3 54.3 + - - +
148B LYS 3.6 0.2 - - - -
149B GLY* 2.8 32.2 + - - -
150B HIS 3.5 17.5 + - - +
153B PRO* 3.4 17.3 - - + +
11F UF2 3.5 35.4 + - + +
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Residues in contact with ALA 146 (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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123B THR* 4.5 13.1 - - - +
124B LEU* 5.1 7.6 - - - +
141B PRO* 4.6 5.3 - - + +
142B GLY 2.8 19.1 + - - +
143B LEU* 3.6 5.4 - - + +
145B ALA* 1.3 74.8 - - - +
147B TYR* 1.3 62.0 + - - +
149B GLY* 3.5 8.1 + - - -
196B THR* 3.4 30.5 - - + +
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Residues in contact with TYR 147 (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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121A THR* 5.9 7.6 - - - -
143A LEU* 3.6 22.7 - - + -
195A ARG* 5.0 4.2 + - - -
196A THR* 3.6 24.9 - - + -
197A THR* 3.5 19.1 - - - +
198A PRO* 3.3 32.0 - - + +
202A ASP* 4.9 6.0 + - - +
143B LEU 3.0 11.6 + - - +
144B MET* 2.8 17.4 + - - +
146B ALA* 1.3 74.5 - - - +
148B LYS* 1.3 79.2 + - + +
149B GLY* 3.2 1.0 + - - -
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Residues in contact with LYS 148 (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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198A PRO* 6.1 1.1 - - + -
202A ASP* 6.2 0.2 - - - +
144B MET* 2.7 38.0 + - + +
145B ALA 3.9 2.7 - - - +
147B TYR* 1.3 87.2 - - + +
149B GLY* 1.3 57.1 + - - +
150B HIS* 3.1 25.8 - - + +
153B PRO* 4.4 11.7 - - + -
175B HIS* 3.6 34.5 - - + +
176B MET* 6.2 0.2 - - - -
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.5 15.5 - - - +
125B PRO* 4.5 11.7 - - - +
145B ALA 2.8 11.7 + - - -
146B ALA 3.5 6.5 + - - -
147B TYR 3.2 4.8 - - - -
148B LYS* 1.3 76.1 - - - +
150B HIS* 1.3 67.8 + - - -
178B ASP* 4.6 1.4 - - - +
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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