Contacts of the helix formed by residues 143 - 152 (chain B) in PDB entry 3R9X
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 4.4 9.4 - - - +
142B THR* 1.3 78.7 - - - +
144B TRP* 1.3 70.0 + - - +
145B LEU* 3.4 2.2 - - - -
146B SER* 3.2 16.9 + - - -
147B VAL* 3.6 3.3 + - - +
201B PHE* 3.7 23.1 - - - -
204B ARG* 4.7 1.1 - - - -
1512C U 4.7 7.2 - - - -
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Residues in contact with TRP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 6.0 2.0 - - - -
112B GLU* 3.3 44.6 - - + -
143B GLY* 1.3 69.7 - - - -
145B LEU* 1.3 95.4 + - + +
146B SER 2.9 1.4 + - - -
147B VAL* 3.0 6.9 + - - +
148B PHE* 2.9 48.3 + + + +
194B LYS* 3.5 40.6 - - + -
197B LEU* 3.7 25.3 - - + +
198B THR* 3.8 15.2 + - - -
201B PHE* 3.3 29.9 - - + +
1511C G 3.3 27.4 + - - -
1512C U 6.1 0.9 - - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 3.5 42.0 - - - +
111B ILE* 3.9 14.4 - - + -
112B GLU* 4.2 20.4 - - + -
132B VAL* 6.4 1.1 - - + -
136B LEU* 3.8 18.4 - - + -
143B GLY 3.4 1.0 - - - -
144B TRP* 1.3 110.1 - - + +
146B SER* 1.3 55.8 + - - +
148B PHE* 3.4 4.2 - - + +
149B VAL* 2.8 45.2 + - + +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 2.9 27.2 + - - +
136B LEU* 2.8 26.4 + - - +
138B GLY* 3.7 0.2 - - - -
142B THR* 3.2 10.6 - - - +
143B GLY 3.2 13.5 + - - -
144B TRP 3.1 0.4 - - - -
145B LEU* 1.3 78.9 - - - +
147B VAL* 1.3 57.6 + - - +
149B VAL* 3.3 2.9 + - - +
150B ARG* 2.7 57.1 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 4.8 4.5 - - + -
143B GLY 3.6 1.3 + - - +
144B TRP 3.0 6.2 + - - +
146B SER* 1.3 74.4 + - - +
148B PHE* 1.3 66.8 + - - +
150B ARG* 3.2 15.8 + - - +
151B THR* 2.8 27.2 + - - -
193B TYR* 4.2 5.8 - - - +
197B LEU* 3.6 24.9 - - + -
201B PHE* 3.6 32.1 - - + -
233B LEU* 4.2 12.2 - - + +
236B PHE* 3.8 33.2 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 4.2 14.6 - - + -
115B VAL* 3.4 36.3 - - + -
116B TYR* 4.4 14.1 - + - -
144B TRP* 2.9 34.0 + + + +
145B LEU* 3.4 17.0 - - + +
147B VAL* 1.3 74.7 - - - +
149B VAL* 1.3 63.8 + - - +
151B THR* 3.4 5.7 + - - -
152B PHE* 3.4 30.9 - + - -
190B LEU* 3.9 28.9 - - + -
193B TYR* 3.7 19.1 - + - -
194B LYS* 4.0 12.6 - - + -
197B LEU* 3.4 26.2 - - + +
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Residues in contact with VAL 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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111B ILE* 3.6 29.8 - - + -
115B VAL* 3.7 17.5 - - + -
136B LEU* 4.1 11.2 - - + -
145B LEU* 2.8 30.9 + - + +
146B SER 3.7 3.6 - - - +
148B PHE* 1.3 74.5 - - + +
150B ARG* 1.3 59.1 + - - +
152B PHE* 3.2 3.6 + - - +
153B TYR* 2.8 41.1 + - + +
155B VAL* 3.9 24.5 - - + -
179B LEU* 4.4 13.9 - - + -
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Residues in contact with ARG 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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136B LEU 2.8 25.4 - - - -
137B GLN* 3.4 20.0 + - - +
138B GLY* 4.1 7.7 + - - -
139B LYS* 5.3 7.5 - - - +
142B THR* 4.0 8.7 - - - +
146B SER* 2.7 48.6 + - - +
147B VAL* 3.2 16.3 + - - +
149B VAL* 1.3 76.0 - - - +
151B THR* 1.3 58.4 + - - +
152B PHE 3.2 0.2 - - - -
153B TYR 3.3 8.1 - - - +
154B ASP* 5.6 0.2 - - - -
155B VAL* 3.8 22.2 - - + +
184B LYS* 2.8 37.3 + - - -
233B LEU* 3.9 33.5 - - + +
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Residues in contact with THR 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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147B VAL* 2.8 15.3 + - - +
148B PHE 3.5 9.2 - - - -
149B VAL 3.2 0.2 - - - -
150B ARG* 1.3 78.4 - - - +
152B PHE* 1.3 77.0 + - + +
184B LYS* 2.9 27.1 + - - +
185B PHE* 3.8 18.3 + - + +
193B TYR* 2.7 39.2 + - + +
233B LEU* 4.8 0.2 - - - +
237B PHE* 3.5 22.7 - - + -
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.3 29.4 - - + -
118B LYS* 4.2 11.2 - - + -
148B PHE* 3.4 35.4 - + - -
149B VAL 3.2 2.2 + - - -
151B THR* 1.3 99.6 - - + +
153B TYR* 1.3 78.7 + - + +
181B LYS* 3.8 6.7 - - + +
182B ASN 3.0 29.5 + - - -
183B GLU* 2.8 32.5 + - - +
185B PHE 4.1 2.9 - - - -
187B VAL* 3.8 19.7 - - + -
190B LEU* 3.4 30.7 - - + -
193B TYR* 4.0 6.3 - + - -
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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