Contacts of the helix formed by residues 141 - 152 (chain B) in PDB entry 2XWU
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 CYS 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B TRP* 3.4 6.8 - - - -
140B PRO* 1.3 90.6 - - - +
142B ALA* 1.3 65.3 + - - +
143B VAL 3.3 2.2 - - - -
144B ALA* 3.7 22.7 - - + +
145B ASP* 3.1 29.3 + - - +
148B ARG* 5.8 0.4 - - - +
197B GLU* 3.5 7.4 - - - +
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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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131B ALA* 4.5 9.9 - - + +
135B MET* 5.5 7.2 - - - -
139B TRP* 3.5 36.8 + - + +
140B PRO 3.8 0.4 - - - -
141B CYS* 1.3 73.6 - - - +
143B VAL* 1.3 63.2 + - + +
145B ASP* 3.9 1.6 - - - +
146B MET* 2.9 43.0 + - + +
173B LEU* 5.6 4.3 - - + -
197B GLU* 2.9 17.6 + - + +
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Residues in contact with VAL 143 (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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141B CYS 3.3 0.4 - - - -
142B ALA* 1.3 74.4 - - + +
144B ALA* 1.3 64.5 + - - +
146B MET* 3.2 7.4 + - - +
147B VAL* 2.7 42.8 + - + +
170B LEU* 4.2 10.3 - - + -
173B LEU* 4.8 11.2 - - + -
197B GLU* 3.4 42.8 + - + +
200B ALA* 3.3 26.9 - - + -
201B VAL* 3.7 27.8 - - + +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B CYS* 3.4 26.2 + - + +
143B VAL* 1.3 78.9 - - - +
145B ASP* 1.3 59.0 + - - +
147B VAL* 3.9 4.8 - - - +
148B ARG* 3.0 47.8 + - - +
197B GLU* 4.6 0.8 + - - -
200B ALA* 4.5 9.0 - - + +
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Residues in contact with ASP 145 (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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102B LYS* 4.4 4.2 + - - -
106B PHE* 5.5 3.1 - - + -
139B TRP* 2.4 40.6 + - + -
141B CYS* 3.1 21.8 + - - +
144B ALA* 1.3 76.5 - - - +
146B MET* 1.3 63.1 + - - +
148B ARG* 3.0 43.6 + - - +
149B LEU* 3.1 11.3 + - - +
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Residues in contact with MET 146 (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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106B PHE* 4.5 10.1 - - + -
127B LEU* 4.3 10.3 - - + +
128B ALA* 5.3 1.8 - - - -
131B ALA* 4.1 26.2 - - + -
139B TRP* 4.1 18.2 - - + -
142B ALA* 2.9 31.5 + - + +
143B VAL* 3.7 7.2 - - - +
145B ASP* 1.3 79.5 - - - +
147B VAL* 1.3 64.2 + - + +
149B LEU* 3.3 1.5 + - - +
150B PHE* 3.0 30.7 + - + -
166B LEU* 3.9 14.4 - - + -
169B LEU* 4.1 35.2 - - + -
170B LEU* 4.7 11.4 - - + -
173B LEU* 5.0 12.1 - - + -
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Residues in contact with VAL 147 (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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143B VAL* 2.7 42.6 + - + +
144B ALA* 3.9 4.7 - - - +
146B MET* 1.3 78.9 - - + +
148B ARG* 1.3 62.5 + - - +
150B PHE* 3.3 7.1 + - - +
151B GLN* 3.2 41.7 + - - +
166B LEU* 3.7 15.2 - - + +
170B LEU* 4.8 2.2 - - + -
200B ALA* 5.2 4.5 - - + +
204B LEU* 3.5 37.5 - - + -
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Residues in contact with ARG 148 (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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141B CYS* 5.8 0.6 - - - +
144B ALA* 3.0 28.4 + - - +
145B ASP* 3.0 37.1 + - - +
147B VAL* 1.3 75.3 - - - +
149B LEU* 1.3 68.1 - - + +
151B GLN* 3.4 20.3 + - - +
152B ALA* 3.5 10.2 + - - +
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Residues in contact with LEU 149 (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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106B PHE* 3.4 46.9 - - + +
110B THR* 5.4 4.5 - - - +
145B ASP 3.1 13.7 + - - +
146B MET* 3.8 4.7 - - - +
147B VAL 3.3 0.2 - - - -
148B ARG* 1.3 85.3 - - + +
150B PHE* 1.3 68.5 + - + +
151B GLN 3.3 0.2 - - - -
152B ALA* 3.3 21.4 - - + +
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Residues in contact with PHE 150 (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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106B PHE* 4.9 14.4 - + - -
109B ILE* 3.9 26.7 - - + -
110B THR* 4.7 15.9 - - + -
146B MET* 3.0 30.3 + - - +
147B VAL 3.3 4.2 + - - +
149B LEU* 1.3 82.3 - - + +
151B GLN* 1.3 63.7 + - - +
152B ALA* 3.3 1.0 - - - -
162B ARG* 3.6 44.6 - - + +
163B CYS* 5.9 0.2 - - - -
165B ALA* 4.0 19.3 - - + -
166B LEU* 3.6 37.2 - - + -
169B LEU* 4.1 18.4 - - + -
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Residues in contact with GLN 151 (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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147B VAL* 3.2 38.7 - - + +
148B ARG* 3.4 10.7 + - - +
149B LEU 3.3 0.4 - - - -
150B PHE* 1.3 80.0 - - + +
152B ALA* 1.3 67.9 + - - +
166B LEU* 5.6 2.2 - - + -
204B LEU* 5.2 6.5 - - - +
207B GLN* 5.7 2.4 + - - -
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Residues in contact with ALA 152 (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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148B ARG 3.5 7.5 + - - +
149B LEU* 3.3 27.1 - - + +
150B PHE 3.3 1.3 - - - -
151B GLN* 1.3 84.8 - - - +
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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