Contacts of the strand formed by residues 144 - 148 (chain B) in PDB entry 1XR2
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 ALA 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 3.8 28.0 - - + -
56B ILE 2.7 9.0 + - - +
57B PRO* 3.3 6.4 - - - +
58B SER* 3.3 13.8 + - - -
143B THR* 1.3 72.3 - - - +
145B PRO* 1.3 70.3 - - - +
146B TRP 3.3 0.7 + - - -
195B GLU* 3.1 24.2 - - + +
197B LEU* 3.7 20.3 - - + +
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Residues in contact with PRO 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 3.3 19.0 - - - +
59B ASN* 4.6 3.4 - - + -
129B PRO* 4.3 18.8 - - + +
133B TYR* 4.3 4.5 - - + -
143B THR 3.5 10.1 - - - +
144B ALA* 1.3 80.0 - - - +
146B TRP* 1.3 57.1 + - - +
147B VAL* 4.4 2.7 - - + -
188B LEU* 3.7 39.3 - - + -
193B CYS* 3.5 9.6 - - - -
195B GLU 3.3 12.8 - - - +
196B ILE* 3.7 9.8 - - + +
197B LEU 2.8 33.1 + - - +
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Residues in contact with TRP 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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6B PHE* 3.8 24.8 - + + +
7B GLY 5.3 0.9 - - - -
57B PRO* 4.6 2.2 - - + -
58B SER 2.8 19.4 + - - +
59B ASN* 2.6 40.7 + - - +
60B GLU* 3.8 34.5 - - + -
66B PHE* 3.9 50.7 - + + -
105B PHE* 6.2 0.7 - + - -
144B ALA 3.3 3.1 + - - +
145B PRO* 1.3 70.2 - - - +
147B VAL* 1.3 58.1 + - - +
148B ILE* 4.1 12.8 - - + -
197B LEU* 3.5 16.8 - - + -
199B ASN* 2.8 41.6 + - + +
230B PHE* 6.0 0.9 - + - -
232B TYR* 4.1 7.9 - - - -
310B PRO* 4.9 5.8 - - + -
312B PHE* 4.6 13.5 - + - -
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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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59B ASN* 3.4 15.3 - - - +
73B MET* 5.7 6.5 - - + -
129B PRO* 4.1 17.9 - - + -
145B PRO* 4.4 6.3 - - + -
146B TRP* 1.3 87.9 - - - +
148B ILE* 1.3 63.3 + - - +
181B TYR* 4.7 5.4 - - + -
184B VAL* 6.1 0.7 - - + -
185B PHE* 4.4 19.7 - - + -
196B ILE* 4.5 4.0 - - + -
197B LEU 2.8 18.0 + - - +
198B VAL* 4.2 18.2 - - + -
199B ASN* 2.7 39.0 + - - +
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Residues in contact with ILE 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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66B PHE* 3.9 35.4 - - + +
67B VAL* 4.8 6.7 - - + -
70B THR* 3.8 26.3 + - + +
105B PHE* 5.0 8.5 - - + -
146B TRP* 4.1 12.6 - - + -
147B VAL* 1.3 74.4 - - - +
149B GLY* 1.3 65.8 + - - +
152B THR* 3.8 25.4 - - + -
153B PHE* 3.9 13.2 - - + +
156B LEU* 5.2 3.6 - - + -
181B TYR* 2.6 33.8 + - - -
199B ASN* 3.7 19.3 - - + +
201B PRO* 5.5 1.6 - - + -
232B TYR* 5.3 0.2 - - - +
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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