Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 1XL4
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 MET 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ARG* 1.3 72.8 - - - +
149B VAL* 1.3 70.6 + - - +
159B LEU* 3.8 25.8 - - + -
160B MET 3.1 13.9 - - - +
161B MET* 3.8 14.4 - - + -
178B LEU* 4.5 9.9 - - - -
239B PHE* 3.3 38.4 - - + -
260B TYR* 3.3 46.6 - - + -
264B GLU 2.9 10.1 + - - +
265B ILE* 3.9 16.4 - - + -
266B ILE* 2.8 25.6 + - - +
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Residues in contact with VAL 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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148B MET* 1.3 81.8 - - - +
150B ILE* 1.3 65.8 + - - +
151B SER* 4.4 2.5 - - - +
159B LEU* 3.3 5.2 - - - +
160B MET* 2.8 62.8 + - + +
266B ILE* 3.3 13.0 - - + +
269B GLY 3.7 27.1 - - - +
270B HIS* 4.4 2.0 - - - +
271B PHE* 3.9 13.5 - - + -
293B ILE* 3.5 34.8 - - + -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 1.3 80.7 - - - +
151B SER* 1.3 60.3 + - - +
157B PRO* 4.4 9.0 - - + -
158B THR 3.0 9.6 - - - +
159B LEU* 3.7 21.5 - - + -
218B ILE* 3.8 29.8 - - + -
224B ILE* 4.7 6.7 - - + -
232B LEU* 5.3 1.8 - - + -
265B ILE* 3.7 15.9 - - + -
266B ILE 3.2 6.5 + - - -
267B TRP* 3.6 52.0 - - + +
268B GLY* 2.9 25.7 + - - -
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Residues in contact with SER 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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149B VAL* 4.0 1.6 - - - +
150B ILE* 1.3 74.4 - - - +
152B ASP* 1.3 68.0 + - - +
157B PRO* 4.2 1.6 - - - -
158B THR 2.9 26.7 + - - +
160B MET* 3.5 21.5 - - - +
268B GLY* 4.1 4.3 - - - -
269B GLY 2.8 28.1 + - - -
270B HIS* 3.7 27.7 - - - -
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Residues in contact with ASP 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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188A GLU* 3.5 28.7 - - + +
151B SER* 1.3 80.8 + - - +
153B PHE* 1.3 60.4 + - - +
155B GLY* 4.6 7.8 - - - +
156B LYS 3.2 13.9 - - - +
157B PRO* 3.6 20.8 - - - +
160B MET* 4.6 1.6 - - - +
270B HIS* 5.0 8.9 + - - +
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Residues in contact with PHE 153 (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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186A SER* 4.2 9.0 - - - -
188A GLU* 3.3 6.7 - - - -
190A MET* 5.4 9.2 - - - -
192A PHE* 3.5 48.0 - + - -
194A ARG* 3.9 7.4 - - - -
151B SER 3.5 0.2 + - - -
152B ASP* 1.3 75.5 - - - +
154B GLU* 1.3 99.5 + - + +
155B GLY 3.0 2.3 + - - -
156B LYS* 2.8 19.6 + - - +
158B THR* 3.7 17.5 + - + +
160B MET* 4.1 14.8 - - + -
201B THR* 5.1 9.2 - - + -
215B MET* 3.7 36.8 - - + -
217B PRO* 5.9 2.2 - - + -
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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