Contacts of the helix formed by residues 147 - 156 (chain A) in PDB entry 2X8Y
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 PRO 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LEU 3.4 6.3 - - - +
146A ASP* 1.3 93.4 - - - +
148A GLU* 1.3 82.0 + - - +
150A GLU* 3.6 3.5 + - + +
151A GLU* 3.0 33.4 + - + +
327A LYS* 3.7 16.2 - - + +
356A ARG* 3.8 23.1 - - + +
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Residues in contact with GLU 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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140A LYS* 6.1 3.1 - - - +
142A ASP 4.1 5.8 - - - +
143A LEU* 3.8 34.0 - - + +
144A ALA* 2.9 32.9 + - - +
147A PRO* 1.3 100.6 - - + +
149A ILE* 1.3 62.5 + - - +
151A GLU* 3.4 15.6 + - - +
152A VAL* 3.4 13.2 + - - +
327A LYS* 4.5 2.4 + - - -
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Residues in contact with ILE 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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130A VAL* 5.1 1.6 - - + -
132A VAL* 3.6 43.3 - - + -
143A LEU* 3.9 7.0 - - + +
144A ALA 2.9 19.3 + - - +
145A LEU* 3.6 25.8 - - + +
148A GLU* 1.3 72.6 - - - +
150A GLU* 1.3 57.8 + - - +
152A VAL* 3.1 8.3 + - - +
153A ILE* 3.0 25.6 + - + +
165A TYR* 4.0 28.0 - - + +
169A PHE* 4.1 14.8 - - + -
262A MET* 3.6 28.5 - - + -
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Residues in contact with GLU 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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145A LEU* 2.9 43.6 + - + +
146A ASP* 4.4 16.5 - - - +
147A PRO* 4.1 3.8 - - + +
149A ILE* 1.3 73.9 - - - +
151A GLU* 1.3 57.6 + - - +
153A ILE* 4.0 8.0 - - + +
154A SER* 2.7 37.5 + - - -
261A ASN* 5.3 2.6 + - - -
262A MET* 5.4 5.0 + - + +
263A TRP* 3.5 27.2 - - + -
356A ARG* 4.5 15.3 + - - +
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Residues in contact with GLU 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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147A PRO* 3.0 21.7 + - + +
148A GLU* 3.4 8.5 - - - +
150A GLU* 1.3 77.0 - - - +
152A VAL* 1.3 64.1 + - + +
154A SER* 3.1 14.5 + - - -
155A LYS* 3.1 58.2 + - + +
356A ARG* 5.5 6.8 + - - -
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Residues in contact with VAL 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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143A LEU* 5.6 2.9 - - + -
148A GLU 3.7 12.8 - - - +
149A ILE* 3.1 7.9 + - - +
151A GLU* 1.3 77.8 - - + +
153A ILE* 1.3 63.0 + - - +
155A LYS* 5.1 0.4 - - - -
156A SER* 2.8 52.9 + - - +
161A GLU* 3.8 15.3 - - + +
162A LEU* 3.7 4.8 - - + +
165A TYR* 3.6 47.3 - - + +
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Residues in contact with ILE 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 ILE* 3.0 22.4 + - + +
150A GLU* 4.0 7.6 - - + +
151A GLU 3.5 0.2 - - - -
152A VAL* 1.3 76.0 - - + +
154A SER* 1.3 59.2 + - - +
156A SER 4.6 2.1 - - - +
157A ARG* 4.9 1.0 + - - -
162A LEU* 3.7 41.9 - - + +
165A TYR* 4.2 10.5 - - + -
166A TRP* 4.5 4.3 - - + +
257A HIS* 5.0 9.1 - - + +
260A GLY* 3.4 14.5 + - - +
261A ASN* 3.5 26.9 - - - +
262A MET* 3.6 49.6 - - + +
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Residues in contact with SER 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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150A GLU 2.7 22.5 + - - -
151A GLU* 3.1 12.0 + - - -
153A ILE* 1.3 77.6 - - - +
155A LYS* 1.3 68.5 + - - +
157A ARG* 3.2 17.8 + - - -
260A GLY 3.7 11.2 - - - -
269A GLU* 3.5 45.2 - - - +
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Residues in contact with LYS 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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151A GLU* 3.1 51.2 + - + +
152A VAL* 3.1 2.4 + - - -
154A SER* 1.3 88.1 - - - +
156A SER* 1.3 67.1 + - - +
157A ARG* 3.6 16.6 + - - +
269A GLU* 5.4 3.1 - - - +
290A GLU* 5.9 0.6 + - - -
358A THR* 6.1 2.8 - - - +
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Residues in contact with SER 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 VAL* 2.8 34.5 + - - +
153A ILE 4.6 1.2 - - - +
155A LYS* 1.3 72.9 - - - +
157A ARG* 1.3 74.4 + - - +
158A ASP* 3.1 16.1 + - - +
161A GLU* 2.6 29.3 + - - +
162A LEU* 3.5 21.5 - - - +
243A TYR* 4.3 0.2 + - - -
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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