Contacts of the helix formed by residues 5 - 14 (chain B) in PDB entry 1XH8
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 THR 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B THR* 1.3 65.6 + - - +
7B TYR* 3.7 9.5 + - - +
8B ALA* 3.1 31.2 + - + +
9B ASP* 3.0 30.3 + - - +
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Residues in contact with THR 6 (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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229A TYR* 5.4 1.8 - - - +
235A TYR* 3.5 36.6 - - + -
239A PHE* 3.7 19.5 - - + -
256A ARG* 4.7 12.3 + - - -
5B THR* 1.3 74.3 - - - +
7B TYR* 1.3 62.5 + - - +
9B ASP* 3.1 12.7 + - - +
10B PHE* 3.0 18.9 + - - +
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Residues in contact with TYR 7 (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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136A GLY* 6.4 2.2 - - - -
234A GLY 5.9 2.7 - - - -
235A TYR* 4.0 29.1 + + + -
5B THR* 3.3 9.4 + - - +
6B THR* 1.3 76.9 - - - +
8B ALA* 1.3 66.2 + - + +
10B PHE* 3.1 12.0 + + - +
11B ILE* 3.0 55.3 + - + +
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Residues in contact with ALA 8 (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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5B THR* 3.1 29.4 + - - +
7B TYR* 1.3 81.2 - - + +
9B ASP* 1.3 65.4 + - - +
11B ILE* 3.3 7.0 + - - +
12B ALA* 3.0 24.3 + - - +
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Residues in contact with ASP 9 (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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239A PHE* 3.5 20.4 - - + -
5B THR 3.0 22.6 + - - +
6B THR* 3.4 15.9 + - - +
8B ALA* 1.3 76.5 - - - +
10B PHE* 1.3 62.2 + - - +
12B ALA* 3.2 7.6 + - - +
13B SER* 3.0 20.1 + - - -
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Residues in contact with PHE 10 (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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133A ARG* 3.8 31.4 - - - -
203A GLU* 5.9 0.4 - - - -
234A GLY 3.8 17.0 - - - -
235A TYR* 3.5 22.4 - + + -
236A PRO* 3.6 22.0 - - + -
239A PHE* 3.4 31.6 - + + -
6B THR 3.0 11.7 + - - +
7B TYR* 3.1 16.6 + + - +
9B ASP* 1.3 74.4 - - - +
11B ILE* 1.3 73.1 + - + +
13B SER* 2.7 24.8 + - - -
15B ARG* 3.5 24.0 - - + -
16B THR* 3.5 24.1 - - + +
19B ARG* 5.3 0.7 - - - -
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Residues in contact with ILE 11 (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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7B TYR* 3.0 54.8 + - + +
8B ALA* 3.3 8.5 + - - +
10B PHE* 1.3 81.4 - - + +
12B ALA* 1.3 62.1 + - - +
13B SER 3.3 0.7 + - - -
14B GLY* 3.5 10.0 + - - -
16B THR* 3.8 24.8 + - + +
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Residues in contact with ALA 12 (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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241A ASP* 3.9 7.4 - - - +
8B ALA 3.0 18.1 + - - +
9B ASP* 3.2 8.9 + - - +
11B ILE* 1.3 75.7 - - - +
13B SER* 1.3 62.4 + - - +
14B GLY* 3.2 1.6 + - - -
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Residues in contact with SER 13 (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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239A PHE* 4.0 15.3 - - - -
240A ALA* 3.9 18.8 - - - -
241A ASP* 3.4 33.3 - - - +
9B ASP 3.0 12.2 + - - -
10B PHE* 2.7 25.3 + - - -
12B ALA* 1.3 78.6 - - - +
14B GLY* 1.3 57.7 + - - +
15B ARG* 3.1 22.0 + - - +
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Residues in contact with GLY 14 (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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11B ILE 3.5 10.1 + - - -
12B ALA 3.2 5.4 + - - -
13B SER* 1.3 78.8 + - - +
15B ARG* 1.3 60.2 + - - +
16B THR* 3.4 9.0 + - - -
17B GLY 4.8 2.1 + - - -
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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