Contacts of the helix formed by residues 127 - 135 (chain B) in PDB entry 1B3U
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.0 27.5 - - + +
111B LEU* 3.6 32.8 - - + -
115B SER* 3.8 17.9 - - - -
118B HIS* 4.3 13.7 - + + -
122B ASP 3.2 2.2 + - - -
123B LEU* 3.2 27.6 + - + +
126B HIS* 1.3 76.2 - - - +
128B VAL* 1.3 63.9 + - - +
130B LEU* 3.0 20.4 + - + +
131B VAL* 3.0 33.8 + - + +
149B LEU* 3.9 33.7 - - + -
152B VAL* 4.5 3.8 - - + -
153B CYS* 3.8 24.2 - - + -
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Residues in contact with VAL 128 (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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123B LEU 2.8 24.8 + - - +
124B GLU* 4.4 5.2 - - - +
127B PHE* 1.3 71.6 - - + +
129B PRO* 1.3 70.8 - - + +
131B VAL* 3.0 10.9 + - - +
132B LYS* 2.8 48.6 + - + +
153B CYS* 4.6 12.6 - - + -
157B VAL* 4.7 6.3 - - + -
161B VAL* 3.9 29.8 - - + -
164B GLU* 5.9 0.4 - - + -
165B LEU* 4.5 20.9 - - + -
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Residues in contact with PRO 129 (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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124B GLU 3.4 16.4 - - - +
125B ALA 3.6 17.5 - - - +
126B HIS* 3.1 16.6 - - - +
128B VAL* 1.3 97.4 - - + +
130B LEU* 1.3 59.9 + - - +
132B LYS* 3.2 11.6 + - + +
133B ARG* 3.0 40.7 + - - +
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Residues in contact with LEU 130 (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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89B LEU* 3.8 35.0 - - + +
93B GLU* 3.4 45.3 - - + +
111B LEU* 3.9 22.7 - - + -
126B HIS 3.2 11.3 + - - +
127B PHE* 3.0 20.7 + - + +
129B PRO* 1.3 73.6 - - - +
131B VAL* 1.3 68.6 + - + +
132B LYS 3.1 0.2 + - - -
133B ARG* 3.1 16.8 + - - +
134B LEU* 3.0 34.2 + - + +
149B LEU* 5.0 3.4 - - + -
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Residues in contact with VAL 131 (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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127B PHE* 3.5 35.7 - - + +
128B VAL* 3.0 11.2 + - - +
130B LEU* 1.3 78.4 - - + +
132B LYS* 1.3 60.4 + - + +
134B LEU* 3.5 8.2 + - - +
135B ALA* 2.9 28.1 + - + +
146B ALA* 4.2 4.8 - - + +
149B LEU* 4.0 21.3 - - + +
150B PHE* 3.8 40.4 - - + -
153B CYS* 4.6 4.7 - - - -
165B LEU* 4.3 10.5 - - + -
168B TYR* 5.8 0.7 - - + -
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Residues in contact with LYS 132 (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 VAL* 2.8 35.6 + - + +
129B PRO* 3.2 15.8 - - + +
130B LEU 3.1 0.2 - - - -
131B VAL* 1.3 78.1 - - + +
133B ARG* 1.3 66.8 + - + +
135B ALA* 3.3 3.3 + - - +
136B GLY* 3.0 20.6 + - - -
164B GLU* 2.8 37.3 + - - -
165B LEU* 5.1 3.6 - - + +
168B TYR* 3.2 62.9 + - + +
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Residues in contact with ARG 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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89B LEU* 5.5 5.5 - - - +
90B PRO* 6.2 1.6 - - - +
93B GLU* 3.1 38.6 + - - +
126B HIS 5.0 1.8 + - - -
129B PRO* 3.0 31.5 + - - +
130B LEU* 3.5 28.0 - - - +
132B LYS* 1.3 75.5 - - + +
134B LEU* 1.3 64.2 + - - +
136B GLY* 3.3 2.8 + - - -
137B GLY* 3.0 22.2 + - - -
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Residues in contact with LEU 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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93B GLU* 4.0 26.7 - - + +
96B ALA* 4.8 13.2 - - + -
97B THR* 4.3 10.5 - - - +
111B LEU* 5.1 2.0 - - + -
130B LEU* 3.0 34.8 + - + +
131B VAL 3.7 3.8 - - - +
133B ARG* 1.3 77.1 - - - +
135B ALA* 1.3 64.2 + - - +
137B GLY 3.2 9.9 + - - -
142B SER* 3.3 52.1 - - - +
143B ARG 3.4 1.2 + - - -
145B SER* 4.8 4.0 - - - -
146B ALA* 3.8 9.4 - - + +
149B LEU* 4.0 25.4 - - + -
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Residues in contact with ALA 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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131B VAL 2.9 18.9 + - - +
132B LYS 3.3 4.2 + - - +
134B LEU* 1.3 75.8 - - - +
136B GLY* 1.3 57.6 + - - +
143B ARG* 3.3 20.1 - - - +
146B ALA* 3.6 15.8 - - + +
150B PHE* 4.8 4.3 - - + -
168B TYR* 3.8 22.2 - - + -
172B LEU* 3.8 27.4 - - + +
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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