Contacts of the helix formed by residues 149 - 153 (chain D) in PDB entry 1XPM
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 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D TYR* 3.3 29.0 - - - +
147D SER* 3.3 3.2 + - - -
148D GLY* 1.3 75.0 - - - +
150D GLU* 1.3 63.8 + - - +
151D PRO* 3.3 4.7 - - - -
152D THR* 2.7 24.1 + - - -
196D VAL* 5.3 5.2 - - - +
4402D CAA 3.7 23.8 - - - -
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.0 10.0 - - + +
26D ARG* 2.9 39.5 + - - +
42D MET* 2.9 20.8 - - - +
143D TYR* 3.7 0.2 - - - +
144D GLY 3.5 16.2 - - - +
145D LEU* 3.7 3.9 - - - +
146D ASN* 2.8 27.6 + - - -
147D SER* 3.2 15.1 + - - +
149D GLY* 1.3 75.4 - - - +
151D PRO* 1.3 67.4 - - + +
153D GLN* 3.0 23.3 + - - +
346D TYR* 2.7 32.9 + - - +
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Residues in contact with PRO 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D MET* 3.1 28.7 - - + +
22D LEU* 4.4 4.5 - - + -
26D ARG* 6.4 0.7 - - + -
33D PHE* 3.6 31.4 - - + -
37D ILE* 3.7 26.4 - - + +
39D GLN* 4.5 8.3 - - - +
42D MET* 3.6 10.4 - - + +
147D SER 4.2 2.9 - - - +
148D GLY 3.6 12.1 - - - +
149D GLY 3.3 5.4 - - - -
150D GLU* 1.3 95.7 - - + +
152D THR* 1.3 57.2 + - + +
153D GLN 3.4 0.6 - - - +
4402D CAA 4.6 6.3 - - - +
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Residues in contact with THR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE* 4.2 15.5 - - + -
39D GLN* 5.4 2.9 - - - -
143D TYR* 3.3 16.7 + - - -
149D GLY 2.7 17.2 + - - -
151D PRO* 1.3 79.5 - - + +
153D GLN* 1.3 66.3 + - - +
235D PRO 3.7 13.6 - - - +
236D PHE* 4.1 21.5 - - + -
274D GLY* 5.0 1.1 - - - -
275D ASN* 3.1 28.5 + - - +
4402D CAA 3.8 36.1 + - + +
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D MET* 3.5 27.5 - - + +
43D ALA 5.6 0.4 - - - +
141D ALA* 3.2 20.2 - - - +
143D TYR* 2.8 38.5 + - + +
144D GLY 3.1 14.7 + - - +
150D GLU* 3.0 23.2 + - - +
151D PRO 3.4 1.5 - - - +
152D THR* 1.3 83.5 + - - +
154D GLY* 1.3 59.9 + - - +
274D GLY* 3.4 12.5 - - - -
275D ASN 4.0 0.2 - - - -
346D TYR* 2.9 29.9 + - - -
350D PHE* 3.6 16.8 - - - -
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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