Contacts of the helix formed by residues 130 - 142 (chain B) in PDB entry 6O81
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 SER 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PHE* 3.4 15.3 - - - -
129B ARG* 1.3 81.5 + - - +
131B LEU* 1.3 59.8 + - - +
132B GLY* 3.6 1.5 + - - -
133B ASP* 3.3 18.1 + - - +
134B VAL* 3.1 28.4 + - - +
267B GLN* 2.3 60.7 + - - +
268B THR* 4.4 2.7 - - - +
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Residues in contact with LEU 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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48B VAL* 3.8 24.2 - - + -
52B PHE* 3.7 11.9 - - + -
130B SER* 1.3 73.8 + - - +
132B GLY* 1.3 61.3 + - - +
134B VAL* 3.2 10.4 + - + +
135B LEU* 2.9 46.2 + - + +
150B LEU* 4.4 21.3 - - + -
152B TYR* 3.4 43.1 - - + +
260B PHE* 4.6 7.9 - - + -
267B GLN 3.8 4.0 + - - +
268B THR* 4.5 7.7 - - + +
269B ARG* 4.5 19.3 - - + +
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Residues in contact with GLY 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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130B SER* 4.4 0.2 - - - -
131B LEU* 1.3 74.5 - - - +
133B ASP* 1.3 60.7 + - - +
135B LEU* 3.4 2.1 + - - +
136B ARG* 2.9 42.3 + - - -
260B PHE* 3.6 33.9 - - - +
266B TYR 4.4 1.6 - - - -
267B GLN 3.2 14.4 + - - -
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Residues in contact with ASP 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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127B LEU 5.5 0.2 - - - +
128B TYR* 3.7 20.0 - - + -
129B ARG* 3.7 7.8 + - - +
130B SER* 3.3 31.9 + - - +
131B LEU 3.2 0.4 - - - -
132B GLY* 1.3 74.2 - - - +
134B VAL* 1.3 59.2 + - - +
136B ARG* 2.5 37.6 + - + +
137B ASP* 2.9 37.5 + - - +
267B GLN* 4.5 3.6 - - - +
430S THR* 5.9 0.9 - - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 5.6 3.4 - - + -
48B VAL* 4.4 18.2 - - + -
52B PHE* 4.5 7.2 - - + -
94B PHE* 3.5 38.9 - - + -
128B TYR* 3.7 28.9 - - + -
130B SER 3.1 16.3 + - - +
131B LEU* 3.2 13.4 + - + +
133B ASP* 1.3 75.7 - - - +
135B LEU* 1.3 60.7 + - + +
137B ASP* 3.3 9.7 + - - +
138B VAL* 2.9 29.5 + - + +
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Residues in contact with LEU 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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46B VAL* 4.4 12.8 - - + -
131B LEU* 2.9 32.8 + - + +
132B GLY 3.9 3.4 - - - +
134B VAL* 1.3 80.1 - - + +
136B ARG* 1.3 57.6 + - - +
138B VAL* 3.3 13.2 + - + +
139B ASP 2.9 22.0 + - - -
148B PHE* 3.9 30.5 - - + -
150B LEU* 4.7 13.2 - - + -
181B MET* 6.3 0.2 - - + -
256B VAL* 4.5 12.8 - - + -
257B ALA* 3.5 17.7 - - + +
260B PHE* 3.6 39.0 - - + -
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Residues in contact with ARG 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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132B GLY* 2.9 16.6 + - - +
133B ASP* 2.5 61.7 + - + +
135B LEU* 1.3 74.6 - - - +
137B ASP* 1.3 67.7 + - - +
139B ASP* 3.7 1.6 - - - +
140B ALA* 2.9 28.1 + - - +
257B ALA 4.8 0.7 - - - -
260B PHE* 2.5 37.4 + - - +
261B THR* 3.8 27.2 - - + +
263B ASN 3.5 11.7 + - - -
264B PHE* 3.7 32.3 + - - +
266B TYR 4.3 3.0 + - - -
267B GLN* 5.8 1.4 + - - -
430S THR* 4.6 17.7 - - - -
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Residues in contact with ASP 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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94B PHE* 4.6 9.9 - - + -
128B TYR* 3.6 30.8 - - - +
133B ASP* 2.9 23.2 + - - +
134B VAL* 3.3 5.4 + - - +
136B ARG* 1.3 79.6 - - - +
138B VAL* 1.3 60.0 + - - +
140B ALA* 3.8 7.3 - - - +
141B LYS* 2.9 53.3 + - - +
303S LYS* 6.3 1.6 - - - -
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Residues in contact with VAL 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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46B VAL* 4.2 14.4 - - + -
94B PHE* 3.6 28.5 - - + -
134B VAL* 2.9 21.2 + - + +
135B LEU* 3.4 18.8 - - + +
137B ASP* 1.3 75.7 - - - +
139B ASP* 1.3 57.7 + - - +
141B LYS* 3.4 0.5 + - - -
142B ALA* 2.8 29.1 + - - -
143B LEU* 3.5 14.2 + - + -
144B VAL* 4.2 37.2 - - + +
148B PHE* 5.2 1.3 - - + -
257B ALA* 4.9 7.0 - - + -
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Residues in contact with ASP 139 (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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135B LEU 2.9 15.8 + - - +
136B ARG 3.7 5.2 - - - +
137B ASP 3.3 0.4 - - - -
138B VAL* 1.3 77.4 - - - +
140B ALA* 1.3 59.9 + - - +
142B ALA* 3.5 9.0 + - - +
254B PRO 4.5 0.5 - - - +
257B ALA* 3.7 21.1 - - + +
258B GLN* 2.8 39.6 + - - +
261B THR* 3.5 26.6 + - + +
75S ARG* 4.1 4.7 + - - -
352S ARG* 3.0 35.0 + - - -
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Residues in contact with ALA 140 (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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136B ARG 2.9 18.3 + - - +
137B ASP* 3.9 9.2 - - - +
138B VAL 3.3 0.2 - - - -
139B ASP* 1.3 76.7 - - - +
141B LYS* 1.3 63.2 + - + +
142B ALA* 5.0 0.7 - - - +
261B THR* 5.5 0.6 - - + +
301S VAL 5.0 14.8 - - - +
352S ARG* 4.8 5.2 + - - +
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Residues in contact with LYS 141 (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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94B PHE* 5.5 2.0 - - + -
123B ILE* 4.4 27.0 - - + +
137B ASP* 2.9 37.5 + - - +
140B ALA* 1.3 78.3 - - + +
142B ALA* 1.3 70.6 + - - +
143B LEU* 3.7 36.3 + - + +
303S LYS* 4.3 34.8 + - - +
304S ALA* 5.3 3.8 - - - +
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Residues in contact with ALA 142 (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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138B VAL 2.8 12.0 + - - -
139B ASP* 3.5 10.3 + - - +
140B ALA 3.4 2.5 - - - +
141B LYS* 1.3 81.2 - - - +
143B LEU* 1.3 59.0 + - - +
144B VAL* 3.7 4.0 - - - -
145B ARG* 3.3 28.1 + - - +
352S ARG* 4.8 13.5 - - - +
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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