Contacts of the strand formed by residues 147 - 154 (chain B) in PDB entry 2XSX
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 VAL 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B PRO* 1.3 71.4 - - - +
148B PRO* 1.4 81.6 - - + +
149B ALA* 3.9 0.9 + - - +
171B LEU* 3.9 24.2 - - + +
172B PRO 4.0 10.8 - - - -
173B VAL* 4.0 11.7 - - + +
391B GLY 2.8 13.0 + - - +
392B GLN* 3.5 4.6 - - + +
393B ILE 3.2 22.7 + - - +
423B PHE* 3.7 10.8 - - + -
424B ALA* 4.5 0.2 - - - +
425B GLY* 3.3 44.0 - - - +
428B PHE* 3.8 12.8 - - + -
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Residues in contact with PRO 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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146B PRO 3.6 7.4 - - - +
147B VAL* 1.4 91.4 - - + +
149B ALA* 1.3 59.1 + - - +
150B PHE* 3.6 26.6 - - + -
170B ILE 3.7 1.0 - - - +
171B LEU* 3.6 5.5 - - - -
172B PRO* 3.3 18.6 - - + +
178B PHE* 3.7 20.2 - - + -
181B ALA* 3.9 23.8 - - + -
182B MET* 4.6 0.7 - - - -
393B ILE* 3.5 9.0 - - + +
407B TYR* 3.7 27.1 - - + -
423B PHE* 4.4 0.2 - - + -
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Residues in contact with ALA 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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147B VAL 5.1 0.9 - - - +
148B PRO* 1.3 71.2 - - - +
150B PHE* 1.3 61.5 + - - +
151B ASN 3.8 2.3 + - - -
169B MET* 3.9 18.6 - - - +
170B ILE 3.6 4.9 - - - -
171B LEU* 3.7 24.0 - - + -
368B MET* 4.3 13.9 - - + -
392B GLN* 6.3 0.2 - - + -
393B ILE 2.8 15.6 + - - +
394B LYS* 3.6 24.7 - - + +
395B THR 4.1 1.0 + - - -
396B GLY 4.1 1.2 + - - +
407B TYR* 3.7 6.5 + - - -
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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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148B PRO* 3.6 31.4 - - + -
149B ALA* 1.3 72.5 - - - +
151B ASN* 1.3 59.4 + - - +
152B VAL* 3.1 21.6 + - + +
169B MET* 3.0 5.3 - - - -
170B ILE* 3.0 50.2 + - + +
172B PRO* 4.0 10.3 - - + -
181B ALA 4.1 4.3 - - - -
182B MET* 3.7 27.8 - - + -
185B GLY* 3.7 22.9 - - - -
396B GLY 3.4 19.1 - - - +
398B PRO* 3.7 22.2 - - + -
407B TYR* 3.6 26.5 - + - -
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Residues in contact with ASN 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 ALA 3.8 3.6 + - - -
150B PHE* 1.3 65.9 - - - +
152B VAL* 1.3 58.6 + - - +
153B ILE 3.1 12.3 - - - +
154B ASN* 2.9 34.3 + - - +
166B GLN 4.8 1.2 + - - -
167B GLU* 3.4 25.8 - - + +
168B PHE 3.4 10.1 + - - -
169B MET* 3.7 15.0 - - + +
210B GLU* 2.9 34.8 + - + +
212B GLY* 3.6 12.0 + - - -
371B HIS* 5.7 0.7 - - + +
394B LYS* 6.6 0.2 - - + -
396B GLY* 3.9 9.2 + - - +
397B ALA* 3.6 11.9 + - - +
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Residues in contact with VAL 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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150B PHE* 3.1 29.6 + - + +
151B ASN* 1.3 76.7 - - - +
153B ILE* 1.3 65.4 + - - +
168B PHE 3.2 5.1 + - - +
170B ILE* 4.2 19.5 - - + -
188B VAL* 6.0 1.3 - - + -
189B TYR* 4.0 22.9 - - + -
192B LEU* 3.7 17.3 - - + -
212B GLY* 3.6 4.4 - - - -
213B PHE* 3.0 28.4 + - - -
227B LEU* 3.3 33.2 - - + -
397B ALA* 4.4 0.7 - - + -
398B PRO* 4.4 4.9 - - + -
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Residues in contact with ILE 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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151B ASN* 3.1 4.2 - - - +
152B VAL* 1.3 85.7 - - - +
154B ASN* 1.3 64.4 + - - +
163B LEU* 4.1 22.0 - - + -
167B GLU 3.8 0.3 - - - -
168B PHE* 2.9 43.4 + - + +
192B LEU* 3.9 17.7 - - + -
196B ILE* 3.8 28.5 - - + -
213B PHE 3.4 3.4 - - - +
215B PRO* 3.9 23.3 - - + -
217B ILE* 5.1 0.7 - - + -
223B ALA* 4.1 17.3 - - + +
226B LEU* 4.2 11.9 - - + -
227B LEU* 4.1 13.2 - - + -
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Residues in contact with ASN 154 (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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151B ASN* 2.9 47.9 + - - +
153B ILE* 1.3 78.4 - - - +
155B GLY* 1.3 59.3 + - - +
159B ALA* 4.0 6.2 - - + +
161B ASN* 3.0 22.0 + - - -
163B LEU* 3.7 7.2 - - - +
166B GLN 3.5 5.6 - - - +
208B GLY* 4.4 10.4 - - - -
210B GLU* 5.6 3.2 + - - +
212B GLY* 3.2 27.7 + - - +
213B PHE 2.9 14.3 + - - +
214B ALA* 3.9 11.9 - - + +
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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