Contacts of the helix formed by residues 150 - 156 (chain B) in PDB entry 6TXA
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B LYS* 3.3 1.6 - - - +
149B GLN* 1.3 89.7 - - + +
151B GLY* 1.3 55.8 + - - +
152B GLY 3.1 0.7 + - - -
153B GLY* 2.7 38.7 + - - -
154B TYR 5.0 0.4 - - - +
160B ALA* 4.0 13.1 + - + +
162B HIS* 3.7 26.1 + - + +
164B ARG* 5.8 0.4 - - - +
214B SER* 5.5 0.2 - - - -
319B ASP* 3.5 22.7 - - - +
323B LEU* 3.7 33.4 - - + -
373B ALA* 5.6 0.2 - - + -
374B TYR* 3.5 27.4 - - + -
383B ASP* 5.2 2.1 - - - +
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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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148B LYS* 3.6 16.8 + - - +
149B GLN 3.4 4.9 + - - -
150B LEU* 1.3 74.4 - - - +
152B GLY* 1.3 62.6 + - - -
153B GLY 3.3 0.5 + - - -
154B TYR* 3.5 17.5 + - - +
155B TYR* 4.7 0.9 - - - -
213B PHE* 3.7 47.5 + - - -
383B ASP* 4.7 1.3 - - - -
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Residues in contact with GLY 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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150B LEU 3.1 1.2 + - - -
151B GLY* 1.3 68.2 - - - -
153B GLY* 1.3 58.7 + - - +
154B TYR 3.1 2.5 - - - -
155B TYR* 2.9 40.3 + - - +
156B VAL* 3.9 1.4 + - - +
213B PHE* 4.1 4.6 - - - -
379B GLY* 4.5 10.7 - - - -
382B ILE* 4.3 12.1 - - - +
383B ASP* 3.0 27.9 + - - -
386B ILE* 4.9 1.6 - - - -
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Residues in contact with GLY 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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150B LEU* 2.7 27.1 + - - -
152B GLY* 1.3 71.0 - - - +
154B TYR* 1.3 51.8 + - - +
156B VAL* 2.9 9.6 + - - +
157B PHE* 2.7 41.2 + - - +
160B ALA* 4.6 5.8 - - - -
373B ALA 5.6 5.4 - - - -
379B GLY* 4.9 6.6 + - - -
383B ASP* 5.3 1.2 + - - -
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Residues in contact with TYR 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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145A ARG* 2.9 67.1 + - + +
146A TYR* 5.5 0.9 - + - -
163A ASN* 2.9 24.7 + - - +
165A PHE* 4.1 0.4 - + - +
166A GLU* 2.8 24.8 + - - -
148B LYS* 3.8 26.0 - - + -
150B LEU 4.2 1.6 + - - -
151B GLY 3.5 13.6 + - - +
152B GLY 3.1 1.0 - - - -
153B GLY* 1.3 75.8 - - - +
155B TYR* 1.3 69.3 + + + +
156B VAL 3.2 3.6 + - - -
157B PHE 3.3 16.3 - - - +
158B PRO* 3.3 28.4 - - + +
160B ALA* 3.7 29.9 + - - +
161B SER* 4.1 4.9 - - - -
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Residues in contact with TYR 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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142A GLN* 4.6 5.8 - - - -
145A ARG* 3.6 39.0 + - - +
146A TYR* 2.8 41.6 + + - -
148B LYS* 5.1 3.3 + - - -
151B GLY 4.8 0.7 - - - -
152B GLY* 2.9 27.1 + - - +
154B TYR* 1.3 89.4 - + + +
156B VAL* 1.3 54.0 + - - +
213B PHE* 4.4 21.0 - + - -
382B ILE* 3.5 27.4 - - + -
386B ILE* 4.7 5.8 - - + -
427B PHE* 3.7 18.6 - + - -
448B ILE* 4.6 13.7 - - + -
451B ARG* 2.8 38.9 + - - +
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Residues in contact with VAL 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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118A ILE* 4.6 8.0 - - - +
119A ASN* 5.3 2.1 + - - +
152B GLY 4.7 0.9 - - - +
153B GLY* 2.9 7.6 + - - +
155B TYR* 1.3 84.8 - - - +
157B PHE* 1.3 80.8 + - + +
158B PRO* 3.4 10.4 - - - +
376B HIS* 3.5 30.7 - - + +
378B VAL* 3.9 14.1 - - + -
379B GLY* 3.5 35.2 - - - +
382B ILE* 4.7 1.1 - - + -
451B ARG* 4.5 3.1 - - - +
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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