Contacts of the helix formed by residues 132 - 138 (chain B) in PDB entry 4LT6
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 PHE 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.2 9.0 - - + -
70B LEU* 4.1 8.3 - - + -
71B VAL* 3.7 42.6 - - + -
74B TRP* 3.4 49.3 - + + +
127B ASP 3.1 7.5 + - - -
128B PHE* 3.5 28.9 - + - +
131B SER* 1.3 72.4 - - - +
133B PHE* 1.3 67.9 + - - +
134B GLU 3.1 1.8 - - - -
135B LYS* 2.9 17.7 + - + +
136B LEU* 3.0 48.2 + - + +
156B ILE* 4.6 1.1 - - + -
167B LEU* 3.6 17.3 - - + -
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Residues in contact with PHE 133 (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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128B PHE 3.4 6.8 + - - +
129B PHE 3.5 20.2 - - - +
130B GLN* 2.9 9.1 + - - +
132B PHE* 1.3 78.4 - - - +
134B GLU* 1.3 68.5 + - + +
136B LEU* 3.2 7.6 + - - +
137B LYS* 3.0 28.8 + - + +
145B LEU* 3.5 44.0 - - + +
146B ARG* 4.7 0.4 - - - -
147B ALA* 3.5 41.3 - - + -
156B ILE* 4.2 17.3 - - + -
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Residues in contact with GLU 134 (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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130B GLN* 2.8 20.4 + - + +
131B SER* 4.0 9.2 - - - +
132B PHE 3.1 0.2 - - - -
133B PHE* 1.3 84.1 - - + +
135B LYS* 1.3 57.4 + - - +
137B LYS* 3.2 36.1 + - - +
138B HIS* 2.4 54.7 + - + -
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Residues in contact with LYS 135 (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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70B LEU* 4.5 28.5 - - + +
73B GLU* 3.0 32.5 + - - +
74B TRP* 4.5 11.0 - - + +
77B ASP* 3.6 23.8 + - - -
131B SER 3.4 13.1 + - - +
132B PHE* 2.9 16.3 + - + +
134B GLU* 1.3 75.7 - - - +
136B LEU* 1.3 64.6 + - - +
137B LYS 3.2 0.4 - - - -
138B HIS* 3.4 13.2 + - + +
139B GLN* 3.4 18.5 + - + +
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Residues in contact with LEU 136 (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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67B LEU* 4.7 2.5 - - + -
70B LEU* 3.9 24.9 - - + -
132B PHE* 3.0 44.9 + - + +
133B PHE* 3.2 8.5 + - - +
135B LYS* 1.3 76.5 - - - +
137B LYS* 1.3 64.8 + - - +
138B HIS 3.3 0.5 + - - -
139B GLN* 3.4 4.2 + - - -
142B ILE* 3.3 38.7 - - + +
145B LEU* 4.0 14.1 - - + -
156B ILE* 4.0 22.0 - - + -
158B PHE* 3.9 35.9 - - + -
160B PHE* 5.9 0.2 - - + -
167B LEU* 4.5 0.4 - - + -
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Residues in contact with LYS 137 (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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133B PHE* 3.0 19.8 + - + +
134B GLU* 3.2 42.0 + - - +
136B LEU* 1.3 79.7 - - - +
138B HIS* 1.3 76.3 + - + +
139B GLN 3.5 5.9 + - - +
142B ILE* 5.6 0.5 - - - +
145B LEU* 3.8 13.4 - - + +
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Residues in contact with HIS 138 (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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134B GLU* 2.4 54.6 + - + +
135B LYS* 3.4 8.8 + - + +
136B LEU 3.2 1.0 - - - -
137B LYS* 1.3 99.9 + - + +
139B GLN* 1.3 66.0 + - - +
140B ASP 4.2 0.3 + - - -
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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