Contacts of the helix formed by residues 128 - 136 (chain B) in PDB entry 1B0P
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 GLN 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 4.5 6.6 + - + -
135A GLN* 5.4 1.6 - - - +
225A TYR* 3.2 22.1 + - - -
229A ARG* 2.9 40.3 - - - +
115B ALA* 3.6 1.7 - - - +
116B ILE* 3.7 28.6 - - + +
126B ASP* 3.0 34.5 + - - +
127B HIS* 1.3 78.1 - - - +
129B ASP* 1.3 60.7 + - - +
131B TYR* 3.7 2.8 + - - +
132B ALA* 3.3 19.1 + - - +
330B THR* 3.3 28.2 + - - +
331B LYS 4.2 7.8 + - - +
365B LEU* 4.4 5.1 - - + +
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 3.8 3.8 - - - -
87B SER* 2.9 39.4 + - - +
90B LEU* 3.3 22.3 - - + +
91B LEU* 5.5 0.8 - - + +
111B VAL* 4.2 3.3 - - - +
113B ALA* 3.4 24.9 - - - +
114B ARG 2.9 30.0 + - - +
116B ILE* 3.7 12.5 - - + +
126B ASP 3.7 2.8 - - - +
127B HIS 4.0 0.5 - - - -
128B GLN* 1.3 75.7 - - - +
130B ILE* 1.3 79.4 + - - -
131B TYR 3.1 1.8 - - - -
132B ALA* 3.0 19.2 + - - +
133B ALA 3.4 2.4 + - - -
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Residues in contact with ILE 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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90B LEU* 4.1 5.2 - - + -
111B VAL* 3.6 31.6 - - + -
113B ALA* 4.0 2.2 - - + -
127B HIS* 3.6 26.2 - - + +
129B ASP* 1.3 86.4 + - - +
131B TYR* 1.3 84.6 + - + +
133B ALA* 3.1 12.5 + - - +
134B ARG 3.4 2.4 + - - -
140B MET* 3.1 33.2 - - + +
168B MET* 4.1 7.9 - - + -
170B PHE* 3.6 49.8 - - + -
276B MET* 4.5 1.8 - - + -
305B TYR* 5.0 0.2 - - + -
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Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 4.8 1.1 - - - +
127B HIS* 3.1 36.0 + - + +
128B GLN 4.0 4.0 - - - +
129B ASP 3.1 0.8 - - - -
130B ILE* 1.3 82.5 - - + +
132B ALA* 1.3 57.5 + - - +
133B ALA 3.2 0.2 - - - -
134B ARG* 3.0 37.3 + - + +
135B GLN* 4.3 1.4 - - - +
276B MET* 3.5 27.4 - - + +
305B TYR* 3.4 31.2 - + - -
328B ASP* 2.8 32.1 + - - -
329B ARG 4.7 2.5 - - - -
330B THR* 3.6 26.9 - - + +
332B GLU* 4.1 8.5 - - - +
339B PRO* 3.4 29.6 - - + -
340B LEU* 3.5 10.7 - - - +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.7 19.3 - - - +
132A ALA 5.1 0.2 - - - +
135A GLN* 4.3 17.9 + - - +
91B LEU* 3.9 22.7 - - + -
94B ILE* 3.9 9.7 - - + +
116B ILE* 5.6 0.2 - - + -
128B GLN 3.3 14.1 + - - +
129B ASP* 3.0 14.2 + - - +
131B TYR* 1.3 79.1 - - - +
133B ALA* 1.3 55.0 + - - +
134B ARG 3.3 0.9 - - - -
135B GLN* 3.0 23.9 + - - +
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Residues in contact with ALA 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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90B LEU* 4.4 6.7 - - + -
94B ILE* 4.3 7.6 - - + -
97B MET* 3.7 33.4 - - + +
129B ASP 3.4 5.7 + - - +
130B ILE 3.1 10.2 + - - +
132B ALA* 1.3 77.0 - - - +
134B ARG* 1.3 60.1 + - - +
135B GLN 3.3 2.9 - - - -
136B THR* 2.7 33.6 + - + -
137B GLY 4.7 0.2 + - - -
138B PHE* 4.9 1.9 + - - +
140B MET* 4.5 6.3 - - - +
168B MET* 4.0 9.8 - - + +
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Residues in contact with ARG 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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134A ARG* 3.4 40.2 - - - +
135A GLN* 4.3 9.5 + - - +
332A GLU* 4.9 5.8 - - - +
333A PRO 4.8 4.7 - - - +
342A LEU* 5.8 3.6 - - - +
130B ILE 3.4 1.6 + - - -
131B TYR* 3.0 23.5 + - - +
132B ALA 3.3 0.6 - - - -
133B ALA* 1.3 77.7 - - - +
135B GLN* 1.3 64.5 + - + +
136B THR 3.6 0.5 + - - -
137B GLY 4.3 4.7 + - - -
138B PHE 5.0 2.9 - - - +
140B MET* 4.0 12.4 - - - +
305B TYR* 3.8 35.4 - - + -
306B ARG* 4.2 33.1 + - - +
332B GLU* 2.9 37.5 + - - -
339B PRO* 3.6 24.7 + - - +
342B LEU* 5.0 6.5 - - - +
343B ASP* 5.8 1.0 + - - -
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Residues in contact with GLN 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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94A ILE* 6.2 0.4 - - - +
128A GLN 5.4 2.0 - - - +
131A TYR 4.9 0.2 - - - +
132A ALA* 4.2 23.8 + - + +
134A ARG* 4.6 6.2 + - - +
135A GLN* 4.3 9.2 - - - +
331A LYS 4.7 2.1 - - - +
332A GLU* 3.3 41.9 - - + +
333A PRO* 3.9 13.4 - - - +
94B ILE* 4.4 6.9 - - - +
98B TYR* 3.0 35.2 + - + +
131B TYR 4.3 1.2 - - - +
132B ALA 3.0 28.3 + - - +
134B ARG* 1.3 81.6 + - - +
136B THR* 1.3 76.0 + - - +
137B GLY 3.3 4.6 + - - -
229B ARG* 5.0 0.7 + - - -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PRO* 4.9 0.7 - - - -
94B ILE* 4.2 7.9 - - + -
97B MET* 3.4 39.5 - - + +
98B TYR* 3.6 31.1 - - + -
101B SER* 2.6 28.1 + - - -
133B ALA* 2.7 31.4 + - + +
135B GLN* 1.3 92.2 - - - +
137B GLY* 1.3 51.1 + - - +
138B PHE* 3.7 6.8 + - - +
229B ARG* 6.1 0.4 - - - -
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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