Contacts of the helix formed by residues 141 - 150 (chain B) in PDB entry 3BFT
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B TYR* 5.0 1.8 - - - -
62B GLY 4.7 3.4 - - - -
63B ALA* 4.6 6.8 - - - +
96B ARG* 3.7 10.8 - - - -
138B LEU* 5.8 0.2 - - - -
140B SER* 1.3 77.5 - - - +
142B SER* 1.3 65.5 + - - -
143B THR 3.3 3.3 + - - -
144B LYS* 3.6 3.2 + - - +
145B GLU* 3.2 22.5 + - - +
148B ARG* 5.4 1.8 + - - +
1440B S2P 3.2 16.2 - - - -
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Residues in contact with SER 142 (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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91B THR* 3.2 29.7 + - - +
93B THR* 3.7 29.6 - - - -
96B ARG* 3.8 4.4 - - - +
141B GLY* 1.3 69.4 - - - -
143B THR* 1.3 60.7 + - - +
145B GLU* 3.5 7.0 + - - +
146B PHE* 2.9 28.9 + - - +
193B GLU* 3.5 4.9 + - - -
218B LYS* 4.4 9.1 + - - -
1440B S2P 2.8 17.7 + - - -
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Residues in contact with THR 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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111B ILE* 3.9 28.0 - - + +
137B THR* 3.5 31.9 - - + -
138B LEU* 5.3 2.0 - - - -
141B GLY 3.3 1.0 - - - -
142B SER* 1.3 76.6 + - - +
144B LYS* 1.3 68.0 + - - +
146B PHE* 3.0 18.5 + - - +
147B PHE* 3.3 18.8 + - + -
191B LEU 3.8 10.1 - - - +
192B LEU* 4.6 1.4 - - - -
193B GLU* 4.1 5.7 + - - +
218B LYS* 5.0 0.2 + - - -
1440B S2P 2.6 31.4 + - - -
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Residues in contact with LYS 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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137B THR* 3.6 14.0 + - - +
138B LEU* 3.5 15.8 + - - +
139B ASP* 2.9 51.2 + - - +
140B SER* 4.5 1.5 - - - -
141B GLY 3.6 9.9 + - - +
143B THR* 1.3 78.7 - - - +
145B GLU* 1.3 63.3 + - - +
147B PHE* 3.2 7.3 + - - +
148B ARG* 3.0 40.1 + - - +
159B TRP* 4.0 24.5 - - + -
162B MET* 6.1 0.2 - - - -
170B PHE* 3.8 29.5 - - + -
1439B CAC 5.4 1.8 - - - +
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Residues in contact with GLU 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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93B THR* 6.6 0.4 - - + -
95B VAL* 5.2 19.8 - - + +
141B GLY 3.2 17.6 + - - +
142B SER* 3.5 9.6 - - - +
144B LYS* 1.3 79.3 - - - +
146B PHE* 1.3 62.7 + - - +
148B ARG* 2.6 36.2 + - - +
149B ARG* 2.8 72.8 + - + +
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Residues in contact with PHE 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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111B ILE* 3.5 21.1 - - + -
142B SER 2.9 14.4 + - - +
143B THR 3.0 9.4 + - - +
145B GLU* 1.3 77.2 - - - +
147B PHE* 1.3 75.4 + + - +
149B ARG* 3.7 3.2 - - - +
150B SER* 2.9 33.5 + - - -
152B ILE* 5.9 2.0 - - + -
155B PHE* 3.6 45.5 - + + -
215B LEU* 4.4 13.5 - - + -
216B ASP* 3.6 29.6 - - + -
218B LYS* 4.7 2.2 - - - +
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Residues in contact with PHE 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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111B ILE* 4.4 4.7 - - + -
137B THR* 4.2 11.9 - - + -
143B THR* 3.3 30.2 + - + -
144B LYS* 3.2 7.6 + - - +
146B PHE* 1.3 88.2 - + - +
148B ARG* 1.3 66.0 + - - +
149B ARG 3.3 0.5 + - - -
150B SER* 3.6 14.2 + - - +
155B PHE* 3.7 34.8 - + + +
156B ASP* 5.0 0.3 - - - -
158B MET* 3.6 31.2 - - + -
159B TRP* 3.1 37.0 - - + +
162B MET* 4.7 6.5 - - + -
191B LEU* 3.6 27.1 - - + -
215B LEU* 3.6 24.2 - - + -
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Residues in contact with ARG 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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140B SER* 6.2 1.2 - - - +
141B GLY 5.4 1.8 + - - +
144B LYS* 3.0 34.9 + - - +
145B GLU* 2.6 41.8 + - - +
147B PHE* 1.3 77.3 - - - +
149B ARG* 1.3 82.4 + - - +
150B SER 5.0 1.1 - - - +
159B TRP* 3.5 52.8 + - + +
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Residues in contact with ARG 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 GLU* 2.8 44.4 + - + +
146B PHE* 4.2 2.5 - - - +
148B ARG* 1.3 99.9 + - - +
150B SER* 1.3 64.6 + - - +
151B LYS* 3.6 18.3 + - - +
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Residues in contact with SER 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 PHE* 2.9 22.8 + - - -
147B PHE 3.6 8.9 + - - +
148B ARG 5.0 1.0 - - - +
149B ARG* 1.3 81.7 - - - +
151B LYS* 1.3 67.3 + - - +
152B ILE* 3.2 17.4 + - - +
155B PHE* 3.2 39.6 - - - +
156B ASP* 3.9 19.9 - - - +
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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