Contacts of the strand formed by residues 235 - 240 (chain B) in PDB entry 1XU2
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU 4.8 1.6 - - - -
185A PHE* 3.7 21.5 - + + -
204A SER* 3.8 11.2 - - - -
205A ALA 3.2 27.8 - - - -
206A GLY* 4.7 0.7 - - - -
208A PHE* 5.6 0.4 - + - -
110B HIS* 3.6 26.0 - + + +
111B LEU 3.3 15.3 - - - +
129B TRP* 3.7 9.2 - - - -
157B TYR* 3.8 16.6 - + - -
158B SER* 3.4 3.1 + - - -
159B GLN* 2.8 69.8 + - + +
203B TYR* 4.4 2.5 - + - -
231B PRO 3.7 18.2 - - - +
232B HIS* 4.0 3.1 - - - -
233B GLY 4.3 0.2 - - - -
234B THR* 1.3 82.5 - - - +
236B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 236 (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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110B HIS* 3.7 1.0 - - - -
111B LEU* 2.8 51.3 + - + +
129B TRP* 3.8 39.7 - - + +
146B VAL* 4.1 15.0 - - + -
156B LEU* 5.4 3.1 - - + -
157B TYR* 3.4 23.3 - - - +
158B SER* 4.3 7.4 - - - -
173B VAL* 5.3 6.1 - - + -
185B PHE* 6.2 0.4 - - + -
216B ILE* 5.4 2.0 - - + +
218B VAL* 3.9 24.2 - - + -
235B PHE* 1.3 78.9 - - - +
237B GLY* 1.3 61.2 + - - +
238B PHE* 3.9 20.4 - - + -
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Residues in contact with GLY 237 (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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109B LEU 3.0 11.0 - - - -
156B LEU* 3.5 5.2 - - - +
157B TYR* 2.9 58.8 + - - +
236B LEU* 1.3 76.4 - - - +
238B PHE* 1.3 69.5 + - - -
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Residues in contact with PHE 238 (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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207A VAL* 5.8 0.7 - - - +
107B SER 4.6 0.2 - - - -
108B VAL* 3.3 5.6 - - - +
109B LEU* 2.9 33.8 + - + +
111B LEU* 3.8 24.2 - - + -
139B LEU* 3.2 38.6 - - + -
146B VAL* 3.9 28.0 - - + -
154B TYR* 4.4 4.0 - + + -
155B LEU 3.1 6.7 - - - +
156B LEU* 3.3 38.4 - - + -
157B TYR* 4.0 1.9 - - - -
210B LEU* 4.4 4.7 - - + -
216B ILE* 4.0 24.5 - - + -
236B LEU* 3.9 18.2 - - + -
237B GLY* 1.3 78.5 - - - -
239B VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 239 (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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155A LEU* 6.1 0.2 - - + -
207A VAL* 3.7 29.2 - - + -
241A LEU* 3.9 26.5 - - + -
106B HIS* 4.2 7.6 - - + -
107B SER 3.5 8.3 - - - +
108B VAL* 4.2 8.3 - - + -
154B TYR* 3.1 5.4 - - - -
155B LEU* 2.7 57.8 + - + -
157B TYR* 4.9 1.6 - - + -
238B PHE* 1.3 79.7 - - - +
240B LYS* 1.3 72.6 + - - +
241B LEU* 3.4 14.3 + - + +
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Residues in contact with LYS 240 (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 HIS* 2.5 35.7 + - - +
107B SER* 2.9 37.3 + - - +
137B ARG 5.5 0.7 - - - +
150B ASP* 4.3 13.1 + - + +
151B THR 3.0 28.9 + - - -
152B GLY* 3.4 14.6 - - - -
153B ILE 3.7 8.2 - - - +
154B TYR* 3.6 34.1 + - + +
239B VAL* 1.3 71.7 - - - +
241B LEU* 1.3 62.1 + - - +
105D LYS* 5.9 7.4 - - - +
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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