Contacts of the helix formed by residues 143 - 152 (chain B) in PDB entry 3FEO
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 ASP 143 (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 3.1 0.8 - - - -
142B PRO* 1.3 79.7 - - + +
144B PHE* 1.3 64.9 + - - +
145B SER 3.4 2.0 - - - -
146B GLN* 3.0 20.1 + - + +
147B LYS* 2.8 54.0 + - + +
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Residues in contact with PHE 144 (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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36B MET* 3.7 22.2 - - + -
39B CYS 5.1 3.1 - - - -
40B TRP* 4.5 4.0 - + - -
43B ILE* 3.8 29.8 - - + -
95B ILE* 3.6 30.3 - - + -
96B CYS* 4.3 10.5 - - - -
100B ILE 5.3 4.0 - - - -
102B PRO* 5.9 3.6 - - + -
140B LEU* 3.8 28.3 - - + -
141B PRO* 3.1 36.8 + - + +
142B PRO 3.2 2.2 - - - -
143B ASP* 1.3 77.1 - - - +
145B SER* 1.3 68.6 + - - +
147B LYS* 3.0 10.6 + - + +
148B VAL* 3.0 39.8 + - + +
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Residues in contact with SER 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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100B ILE 4.3 14.0 + - - -
101B HIS* 4.8 10.6 + - - -
142B PRO 5.0 0.8 + - - -
143B ASP 3.4 0.6 - - - -
144B PHE* 1.3 82.1 - - - +
146B GLN* 1.3 67.9 + - - +
148B VAL* 3.2 8.5 + - - +
149B SER* 2.9 27.8 + - - -
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Residues in contact with GLN 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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142B PRO 3.7 10.4 + - - +
143B ASP* 3.3 25.7 - - + +
145B SER* 1.3 84.0 - - - +
147B LYS* 1.3 57.4 + - + +
149B SER* 3.5 6.5 + - - +
150B GLU* 2.9 50.0 + - - +
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Residues in contact with LYS 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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36B MET* 3.5 24.6 - - + +
39B CYS* 4.8 18.4 - - + +
141B PRO* 4.7 16.7 - - + +
143B ASP* 2.8 50.7 + - + +
144B PHE* 3.6 6.5 - - - +
146B GLN* 1.3 74.9 - - + +
148B VAL* 1.3 54.9 + - - +
150B GLU* 3.1 11.8 + - - +
151B SER* 2.6 37.9 + - - -
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Residues in contact with VAL 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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36B MET* 3.7 17.2 - - + -
96B CYS* 3.5 46.4 - - + +
144B PHE* 3.0 30.8 + - + +
145B SER* 3.2 8.7 + - - +
147B LYS* 1.3 74.7 - - - +
149B SER* 1.3 64.5 + - - +
151B SER* 2.7 24.2 + - - +
152B MET* 3.2 33.5 - - + +
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Residues in contact with SER 149 (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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145B SER 2.9 18.8 + - - -
146B GLN* 4.0 6.1 - - - -
148B VAL* 1.3 76.0 - - - +
150B GLU* 1.3 61.3 + - - +
152B MET* 3.3 9.1 + - - +
153B GLN* 2.9 29.1 + - - +
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Residues in contact with GLU 150 (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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146B GLN* 2.9 41.2 + - - +
147B LYS* 3.5 12.0 + - - +
149B SER* 1.3 73.2 - - - +
151B SER* 1.3 57.8 + - - +
152B MET 2.7 11.4 + - - -
153B GLN* 2.8 29.3 + - + +
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Residues in contact with SER 151 (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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35B PRO* 3.2 31.9 - - - +
36B MET* 3.8 19.8 + - - +
147B LYS 2.6 19.3 + - - -
148B VAL* 2.7 19.9 + - - -
150B GLU* 1.3 69.8 - - - +
152B MET* 1.3 59.7 + - - +
153B GLN 3.5 1.6 - - - -
154B TYR* 3.4 18.7 + - - -
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Residues in contact with MET 152 (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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35B PRO* 4.7 5.4 - - + -
36B MET* 6.4 0.7 - - + -
148B VAL* 3.2 36.6 - - + +
149B SER* 3.3 7.2 + - - +
150B GLU 2.7 5.5 + - - -
151B SER* 1.3 79.1 - - - +
153B GLN* 1.3 71.1 + - - +
154B TYR* 3.6 34.7 + - + +
423B LEU* 3.4 52.9 - - + +
424B THR* 4.6 9.9 - - - -
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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