Contacts of the helix formed by residues 148 - 152 (chain A) in PDB entry 1B39
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.5 32.5 + - + -
33A LYS* 4.8 3.4 - - + +
35A ILE* 5.3 0.2 - - + -
52A ILE* 3.7 26.9 - - + -
55A LEU* 3.9 13.9 - - + -
66A LEU* 5.7 0.9 - - + -
78A LEU* 3.9 27.4 - - + -
80A PHE* 4.4 8.7 - - + -
145A ASP* 3.4 41.4 + - - +
146A PHE 3.2 2.3 - - - +
147A GLY* 1.3 75.2 - - - +
149A ALA* 1.3 55.8 + - - +
151A ALA* 3.0 3.8 + - - +
152A PHE* 3.0 37.6 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.0 18.0 + - - +
125A HIS 3.8 21.4 + - - +
126A ARG* 3.9 11.0 - - + +
127A ASP* 4.9 5.8 - - + -
145A ASP 4.9 1.4 + - - -
147A GLY 3.3 1.0 + - - -
148A LEU* 1.3 73.9 - - - +
150A ARG* 1.3 58.4 + - - +
153A GLY* 2.9 31.1 + - - -
154A VAL* 3.4 29.1 + - + +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.9 34.7 + - + +
122A ARG 5.5 4.8 + - - -
124A LEU 5.8 3.7 + - - +
125A HIS 5.4 0.4 + - - -
126A ARG* 5.8 0.6 - - - +
147A GLY* 3.4 8.4 + - - +
148A LEU 3.3 0.4 - - - -
149A ALA* 1.3 80.2 - - - +
151A ALA* 1.4 65.5 + - - +
152A PHE 3.6 0.2 + - - -
153A GLY 4.6 1.4 + - - -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 5.4 2.1 - - - +
48A ALA* 3.5 22.9 + - - +
51A GLU* 3.5 33.0 - - + -
52A ILE* 3.6 29.8 - - + +
55A LEU* 5.2 0.4 - - + -
147A GLY 3.2 12.0 + - - +
148A LEU 3.0 4.5 + - - +
150A ARG* 1.4 82.1 - - - +
152A PHE* 1.3 57.1 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 4.5 17.3 - + + -
35A ILE* 4.1 33.0 - - + -
44A VAL* 5.1 2.7 - - + -
45A PRO* 5.5 6.1 - - + -
48A ALA* 4.0 18.2 - - + -
52A ILE* 3.3 32.5 - - + -
76A LEU* 3.5 31.0 - - + -
78A LEU* 4.5 2.0 - - + -
148A LEU* 3.0 35.8 + - + +
150A ARG 5.0 0.2 - - - -
151A ALA* 1.3 79.0 - - - +
153A GLY* 1.3 61.8 + - - +
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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