Contacts of the helix formed by residues 153 - 161 (chain B) in PDB entry 1H4O
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 LEU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B THR* 4.1 16.2 - - + +
51B HIS* 3.5 30.7 - - + -
55B PHE* 4.0 0.9 - - - -
149B LEU* 3.4 50.0 - - + +
150B THR* 3.3 19.3 + - - +
151B CYS 3.4 0.2 - - - -
152B SER* 1.3 84.9 - - - +
154B ALA* 1.3 69.0 + - - +
155B PRO* 3.4 12.3 - - + -
156B ASN* 3.1 14.9 + - - +
157B ILE* 3.5 8.3 + - - +
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Residues in contact with ALA 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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51B HIS* 5.0 1.0 + - - -
54B GLY* 3.8 32.6 - - - +
55B PHE* 3.5 34.7 - - + +
58B GLN* 4.2 13.2 - - + -
62B LEU* 5.3 1.6 - - + -
153B LEU* 1.3 72.4 - - - +
155B PRO* 1.3 71.3 - - + +
157B ILE* 3.2 4.3 + - - +
158B ILE* 3.1 26.0 + - + +
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Residues in contact with PRO 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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54B GLY* 5.8 2.9 - - - -
58B GLN* 5.3 9.4 - - + +
153B LEU* 3.4 14.4 - - + -
154B ALA* 1.3 94.1 - - + +
156B ASN* 1.3 60.3 + - - +
158B ILE* 3.3 18.3 + - + +
159B SER* 3.4 11.6 + - - -
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Residues in contact with ASN 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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141B ASN* 3.4 22.8 + - - +
150B THR 4.6 3.6 - - - +
151B CYS* 2.8 44.6 + - - +
153B LEU* 3.1 7.7 + - - +
155B PRO* 1.3 79.1 - - - +
157B ILE* 1.3 61.6 + - - +
159B SER* 2.4 33.8 + - - -
160B GLN* 3.4 15.7 + - - +
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Residues in contact with ILE 157 (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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35B VAL* 4.1 12.1 - - + -
55B PHE* 4.1 13.5 - - + -
62B LEU* 4.0 22.7 - - + -
129B SER* 3.3 33.4 - - - +
130B MET 3.8 26.5 - - - +
131B VAL* 3.6 13.9 - - + -
141B ASN* 4.1 3.8 - - - +
153B LEU 3.5 6.9 + - - +
154B ALA 3.2 11.7 + - - +
156B ASN* 1.3 78.2 - - - +
158B ILE* 1.3 63.8 + - - +
160B GLN* 2.8 35.7 + - - +
161B LEU* 3.1 17.6 + - + +
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Residues in contact with ILE 158 (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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58B GLN* 3.7 18.6 - - + +
61B ALA* 4.1 16.2 - - + +
62B LEU* 3.3 46.7 - - + +
65B LYS* 3.8 27.7 + - + +
154B ALA 3.1 14.8 + - - +
155B PRO* 3.5 9.6 - - + +
156B ASN 3.3 0.4 - - - -
157B ILE* 1.3 80.6 - - - +
159B SER* 1.3 62.9 + - - +
160B GLN 3.1 1.2 + - - -
161B LEU* 3.2 21.5 + - + +
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Residues in contact with SER 159 (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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65B LYS* 5.8 0.2 - - - +
155B PRO 3.4 7.4 + - - -
156B ASN* 2.4 35.8 + - - -
158B ILE* 1.3 80.5 - - - +
160B GLN* 1.3 61.1 + - - +
161B LEU* 3.4 4.2 - - - +
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Residues in contact with GLN 160 (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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131B VAL* 4.7 8.4 - - + +
139B ALA* 3.8 25.8 - - + +
141B ASN* 2.8 43.5 + - - -
156B ASN* 3.4 21.2 + - - +
157B ILE* 2.8 19.7 + - - +
159B SER* 1.3 81.1 - - - +
161B LEU* 1.3 64.1 + - - +
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Residues in contact with LEU 161 (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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33B LYS* 3.9 21.1 + - + -
35B VAL* 4.5 3.4 - - + -
62B LEU* 3.6 31.6 - - + -
65B LYS* 3.9 39.8 + - + +
67B VAL* 3.7 25.8 - - + -
131B VAL* 3.9 32.1 - - + -
157B ILE* 3.1 21.6 + - + +
158B ILE* 3.2 15.8 + - - +
159B SER 4.3 3.8 - - - +
160B GLN* 1.3 84.7 - - - +
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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