Contacts of the helix formed by residues 150 - 156 (chain B) in PDB entry 2XI4
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 VAL 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B CYS* 4.6 11.0 - - + +
68B GLN 3.8 17.7 - - - +
69B GLN* 4.0 4.9 - - + +
116B TYR* 4.2 6.1 - - + +
120B PHE* 3.3 14.8 - - - +
121B TYR 3.6 18.2 - - - +
122B SER* 3.6 27.1 - - - +
123B GLY 5.1 0.4 - - - +
148B TYR* 3.5 30.5 - - + +
149B ARG* 1.3 78.4 - - - +
151B GLY* 1.3 69.2 + - - +
153B PHE* 3.6 15.8 + - - +
154B GLY 3.4 5.7 + - - -
155B PHE* 4.2 2.0 - - - -
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Residues in contact with GLY 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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120B PHE 2.7 18.9 + - - -
121B TYR* 3.6 12.1 - - - +
150B VAL* 1.3 70.3 - - - +
152B ALA* 1.3 67.7 + - - -
153B PHE* 5.0 1.8 - - - -
154B GLY 2.9 3.1 + - - -
155B PHE* 2.8 19.9 + - - +
278B GLU* 4.4 14.8 - - - -
292B PHE* 3.5 15.8 - - - +
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Residues in contact with ALA 152 (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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45B PHE* 3.5 14.3 - - + -
151B GLY* 1.3 69.0 - - - -
153B PHE* 1.3 67.1 + - + +
155B PHE 3.1 0.2 + - - -
156B LEU* 2.8 32.6 + - + +
248B LEU* 4.0 19.1 - - + -
274B LEU* 4.6 15.7 - - + -
278B GLU* 5.0 3.0 + - + -
292B PHE* 3.4 35.8 - - + -
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Residues in contact with PHE 153 (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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44B ARG* 3.8 20.4 - - + -
45B PHE* 4.0 16.0 + - - -
68B GLN* 3.9 24.2 - - + -
92B GLU* 3.6 25.6 - - + +
149B ARG* 3.7 27.1 + - + -
150B VAL 3.7 14.1 - - - +
151B GLY* 3.1 1.3 + - - -
152B ALA* 1.3 79.5 - - + +
154B GLY* 1.3 59.0 + - - +
168B VAL* 3.6 13.3 - - - +
271B PRO* 3.6 41.1 - - + -
274B LEU* 3.7 25.6 - - + -
275B ILE* 4.0 17.9 - - + -
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Residues in contact with GLY 154 (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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149B ARG* 3.4 30.7 - - - +
150B VAL 3.4 2.8 + - - -
151B GLY 2.9 6.3 + - - -
153B PHE* 1.3 79.6 - - - +
155B PHE* 1.3 71.1 + - - +
168B VAL* 3.4 15.1 + - - +
169B GLY 2.9 22.4 + - - -
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Residues in contact with PHE 155 (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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120B PHE* 3.7 38.6 - + + -
148B TYR* 4.4 5.4 - + - -
149B ARG 3.4 19.1 - - - -
150B VAL* 4.2 0.9 - - - -
151B GLY 2.8 8.3 + - - +
154B GLY* 1.3 96.7 - - - +
156B LEU* 1.3 68.9 + - - +
157B ALA* 3.0 12.5 + - - +
166B GLY* 4.5 1.8 - - - -
167B ASN* 4.0 16.6 + - - +
169B GLY* 3.6 16.8 - - - -
170B LEU* 3.8 21.5 - - + -
292B PHE* 3.4 44.6 - - - +
293B VAL 3.5 11.1 + - - +
294B PRO* 3.7 27.6 - - + -
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Residues in contact with LEU 156 (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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45B PHE* 3.8 24.7 - - + +
152B ALA* 2.8 26.6 + - + +
154B GLY 4.0 0.2 - - - -
155B PHE* 1.3 70.9 - - - +
157B ALA* 1.3 61.0 + - - +
158B LEU* 4.1 11.4 - - + -
164B ALA* 3.6 31.0 - - + +
166B GLY* 3.4 15.4 + - - -
168B VAL* 6.0 1.6 - - - +
245B ALA* 3.6 29.4 - - + -
248B LEU* 3.8 26.0 - - + -
263B ILE* 5.0 1.3 - - + -
266B LEU* 4.0 21.3 - - + -
292B PHE* 3.8 13.9 - - + -
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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