Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 2AXT
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 TYR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ALA* 3.4 29.7 + - - +
126A TYR* 3.4 17.3 - + - -
127A MET* 3.7 26.0 - - + -
130A GLN* 3.4 21.3 - - - +
143A ILE 3.2 2.7 + - - +
144A CYS 4.0 4.3 - - - +
145A VAL 3.2 0.4 - - - -
146A ALA* 1.3 77.2 - - - +
148A SER* 1.3 57.4 + - - +
149A ALA 3.0 7.1 + - - -
150A PRO* 3.4 14.7 - - + +
151A LEU* 3.4 15.0 + - + +
558A CLA 3.6 22.6 - - + +
561A PHO 3.1 78.8 + + + +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 4.0 24.2 - - - -
144A CYS 3.5 5.5 + - - -
145A VAL* 2.8 19.5 + - - -
146A ALA 3.1 0.4 - - - -
147A TYR* 1.3 75.9 - - - +
149A ALA* 1.3 59.1 + - - +
151A LEU* 4.3 3.1 - - - -
152A ALA* 2.9 29.9 + - - +
284A TRP* 2.8 26.2 + - - -
435C PHE* 4.1 0.9 - - - -
439C VAL* 3.9 10.7 - - - +
442C LEU* 4.8 4.7 - - - -
507C DGD 4.4 6.8 - - - +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA 3.4 9.1 + - - +
148A SER* 1.3 78.3 + - - +
150A PRO* 1.3 77.5 - - + +
152A ALA* 3.2 3.8 + - - +
153A SER* 2.9 24.3 + - - -
280A VAL* 4.1 13.7 - - + +
283A VAL* 3.6 28.1 - - + +
284A TRP* 3.6 20.4 - - + +
287A ALA* 4.6 0.9 - - - +
561A PHO 5.1 2.2 - - + -
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Residues in contact with PRO 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA 3.6 4.5 - - - +
147A TYR* 3.4 18.6 - - + +
149A ALA* 1.3 96.7 - - + +
151A LEU* 1.3 55.0 + - - +
153A SER* 2.7 24.9 + - - -
154A ALA 2.8 10.2 + - - -
558A CLA 3.5 44.6 - - + +
561A PHO 3.3 49.4 - - + +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.9 1.3 - - + +
123A ALA* 3.5 46.4 - - + +
124A SER* 3.9 17.9 - - - +
127A MET* 3.9 20.4 - - + -
147A TYR* 3.4 22.3 + - + +
148A SER* 4.3 4.0 - - - +
149A ALA 3.3 0.2 - - - -
150A PRO* 1.3 78.3 - - - +
152A ALA* 1.3 52.2 + - - +
154A ALA* 2.8 11.1 + - + +
155A PHE* 2.7 55.5 + - + +
558A CLA 4.3 7.2 - - + +
507C DGD 3.8 18.2 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER 2.9 21.5 + - - +
149A ALA* 3.2 6.5 + - - +
151A LEU* 1.3 78.5 - - - +
153A SER* 1.3 57.4 + - - +
155A PHE* 3.7 4.5 - - - +
156A ALA* 3.1 26.0 + - - +
284A TRP* 4.5 0.7 - - + -
287A ALA* 3.5 16.0 - - + +
291A SER* 4.9 1.2 + - - -
435C PHE* 3.6 30.1 - - + -
507C DGD 4.1 9.4 - - + +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA 2.9 10.7 + - - -
150A PRO 2.7 18.0 + - - -
152A ALA* 1.3 71.4 - - - +
154A ALA* 1.3 61.5 + - - -
155A PHE 3.1 0.4 - - - -
156A ALA* 4.4 0.7 - - - -
157A VAL* 3.2 26.2 + - - +
283A VAL* 3.8 8.1 + - - +
286A THR* 4.8 0.3 + - - -
287A ALA* 3.6 16.4 + - - +
558A CLA 3.3 56.4 + - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 4.0 25.1 - - + -
120A LEU* 3.7 4.6 - - + +
150A PRO 2.8 9.9 + - - +
151A LEU* 2.8 11.6 + - + +
153A SER* 1.3 76.0 - - - +
155A PHE* 1.3 59.5 + - - +
157A VAL* 4.2 3.1 - - - -
158A PHE* 3.2 35.7 + - - +
558A CLA 3.9 21.7 - - + +
559A CLA 4.4 8.7 - - + -
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.8 29.6 - - + -
124A SER* 3.3 27.4 - - - -
151A LEU* 2.7 38.9 + - + +
152A ALA* 3.7 8.7 - - - +
154A ALA* 1.3 77.9 - - - +
156A ALA* 1.3 59.5 + - - +
159A LEU* 2.8 57.6 + - + +
160A ILE* 3.1 10.6 + - + -
507C DGD 3.5 44.9 - - + -
201I MGE 3.8 27.8 - - + -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA 3.1 17.3 + - - +
153A SER* 3.7 7.6 - - - +
155A PHE* 1.3 80.9 - - - +
157A VAL* 1.3 61.8 + - - +
160A ILE* 3.3 13.5 + - - +
161A TYR* 2.8 29.5 + - - +
287A ALA* 3.8 8.1 - - - +
290A ILE* 3.7 21.1 - - + -
291A SER* 3.4 19.5 - - - +
558A CLA 4.8 0.4 - - - -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 3.2 11.6 + - - +
154A ALA* 4.6 2.0 - - - +
156A ALA* 1.3 81.0 - - - +
158A PHE* 1.3 72.8 + - + +
161A TYR* 4.4 2.9 - - - +
162A PRO* 4.4 1.4 - - - +
171A GLY* 3.5 10.4 - - - -
172A MET* 3.2 49.3 + - + -
182A PHE* 3.6 23.1 - - + -
290A ILE* 4.2 6.5 - - + -
558A CLA 3.6 17.7 - - - +
559A CLA 3.5 23.8 - - + -
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 3.8 9.0 + - - -
116A ILE* 3.5 35.4 - - + +
119A PHE* 4.4 14.4 - + - -
120A LEU* 4.2 13.7 - - + -
154A ALA* 3.2 22.2 + - - +
157A VAL* 1.3 91.8 - - + +
159A LEU* 1.3 58.8 + - - +
162A PRO* 3.7 13.8 - - - +
168A PHE* 4.1 1.9 - - - -
172A MET* 3.3 36.8 - - + -
174A LEU* 3.5 21.3 - - + -
559A CLA 3.3 36.1 - - + -
561A PHO 3.6 15.0 - - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 5.9 0.4 - - + -
117A PHE* 5.1 6.5 - - + -
120A LEU* 3.7 17.5 - - + -
155A PHE* 2.8 43.8 + - + +
156A ALA 3.7 0.2 + - - -
158A PHE* 1.3 75.0 - - - +
160A ILE* 1.3 64.5 + - + +
162A PRO* 3.2 11.3 - - - +
163A ILE* 3.0 49.4 + - + +
168A PHE* 4.3 15.5 - - + -
507C DGD 4.0 39.9 - - + -
201I MGE 4.4 10.3 - - + -
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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