Contacts of the helix formed by residues 136 - 141 (chain B) in PDB entry 1XV2
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.5 0.9 - - + -
14B LEU* 3.7 50.0 + - + +
15B MSE 3.2 32.2 + - - -
19B LEU* 4.4 7.0 - - + -
42B SER* 3.1 32.8 - - - +
126B MSE 4.0 19.3 - - + -
129B GLN* 4.4 3.4 - - - +
134B THR 3.1 6.4 + - - -
135B ARG* 1.3 70.3 - - - +
137B ILE* 1.3 60.9 + - - +
139B SER* 3.0 33.3 + - - +
140B ALA* 3.4 5.7 + - - +
233B ALA* 5.9 0.2 - - + -
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Residues in contact with ILE 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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15B MSE 4.7 4.7 + - + +
135B ARG* 2.8 18.5 + - + +
136B LEU* 1.3 79.0 - - - +
138B ASP* 1.3 72.8 + - - +
140B ALA* 3.3 3.1 + - + -
141B ARG* 3.2 36.3 + - + +
229B GLU* 3.2 46.0 - - + +
232B GLU* 2.9 36.3 - - + +
233B ALA* 3.5 28.3 - - + -
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Residues in contact with ASP 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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129B GLN* 5.1 1.3 - - - +
134B THR* 3.3 22.1 + - - +
135B ARG* 3.0 19.2 + - - +
137B ILE* 1.3 85.9 - - - +
139B SER* 1.3 62.2 + - - +
141B ARG* 3.3 30.3 + - - +
142B ARG* 3.7 15.2 - - - +
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Residues in contact with SER 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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42B SER* 5.6 0.2 - - - -
126B MSE 3.8 10.8 - - - -
127B PRO* 3.0 47.9 + - - +
128B ALA 5.0 0.7 + - - -
129B GLN* 3.3 30.3 + - - +
136B LEU* 3.0 19.4 + - - +
138B ASP* 1.3 75.0 - - - +
140B ALA* 1.3 64.5 + - - +
141B ARG 3.1 2.3 + - - -
142B ARG* 3.3 17.4 + - - +
143B GLN 3.4 1.0 + - - -
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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
----------------------------------------------------------
126B MSE 3.6 13.4 - - + -
136B LEU 3.4 2.9 + - - +
137B ILE* 3.3 8.4 + - + +
139B SER* 1.3 78.8 - - - +
141B ARG* 1.3 57.2 + - - +
142B ARG 3.1 2.6 + - - -
143B GLN* 3.0 42.6 - - - +
232B GLU* 6.0 0.7 - - + -
233B ALA* 3.5 37.5 - - + -
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Residues in contact with ARG 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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137B ILE* 3.2 31.1 + - + +
138B ASP* 3.6 23.9 + - - +
139B SER 3.1 1.6 - - - -
140B ALA* 1.3 77.0 - - - +
142B ARG* 1.3 63.0 + - - +
229B GLU* 5.8 0.4 + - - -
232B GLU* 3.2 40.7 + - + +
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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