Contacts of the strand formed by residues 153 - 157 (chain B) in PDB entry 2ANL
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 LEU 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.4 7.7 - - - +
151B GLN* 3.1 25.9 + - + +
152B ALA* 1.3 76.1 - - - +
154B PHE* 1.3 63.3 + - - +
155B THR* 4.4 10.1 - - + -
169B THR 5.0 0.2 - - - +
170B ILE* 3.5 8.1 - - - +
171B GLY 3.1 24.2 + - - +
172B GLY* 3.5 34.1 - - - +
173B ILE* 3.9 20.4 - - + -
312B VAL* 4.6 4.3 - - + -
313B PHE 2.7 21.5 - - - +
314B ASP* 3.2 26.9 - - + +
315B TYR* 4.4 3.1 - - - +
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 3.5 29.8 - - + -
126B LEU* 3.5 40.4 - - + -
140B VAL* 4.1 17.3 - - + -
153B LEU* 1.3 75.3 - - - +
155B THR* 1.3 65.4 + - - +
156B PHE* 4.0 13.0 - + - -
168B LEU* 3.9 11.2 - - + -
169B THR 3.2 9.2 - - - +
170B ILE* 4.4 9.2 - - + -
193B TRP* 3.8 15.7 - + - -
313B PHE* 3.0 62.0 + + + +
315B TYR* 4.1 8.7 - + - -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.4 5.6 - - + -
154B PHE* 1.3 80.6 - - - +
156B PHE* 1.3 64.2 + - - +
157B TYR 3.9 0.2 - - - -
167B TYR 3.3 1.4 + - - +
168B LEU* 3.2 9.2 - - - +
169B THR* 2.6 62.6 + - - +
172B GLY 4.0 17.4 + - - +
173B ILE* 4.7 1.8 - - - -
177B PHE* 4.6 2.6 - - - -
310B PHE* 3.2 35.8 - - + -
311B THR 3.5 2.9 - - - -
312B VAL* 3.9 20.4 - - + -
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.7 32.8 - - + -
16B PHE* 3.9 13.0 - + - -
33B PHE* 3.8 21.8 - - + -
35B THR* 4.0 3.4 - - + -
126B LEU* 3.7 21.3 - - + -
154B PHE* 4.0 18.3 + + - -
155B THR* 1.3 73.5 - - - +
157B TYR* 1.4 61.2 + - - +
158B LEU* 4.0 4.5 + - + -
167B TYR 3.9 0.2 - - - -
168B LEU* 4.5 9.6 - - + -
215B SER* 3.4 33.9 - - - -
306B MET* 3.7 21.8 - - + +
309B TYR 4.5 1.4 - - - +
310B PHE* 3.5 5.4 - - - -
311B THR* 3.0 41.9 + - - +
313B PHE* 4.1 5.1 - + + -
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Residues in contact with TYR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.5 0.7 - - - +
155B THR 3.9 0.2 + - - -
156B PHE* 1.4 72.7 - - - +
158B LEU* 1.3 86.5 + - - +
159B PRO* 4.5 8.6 - - + +
164B HIS* 5.7 2.9 - - + +
165B SER 4.2 8.5 - - - -
166B GLY* 3.4 4.7 - - - -
167B TYR* 2.8 68.3 + + + +
176B LYS 5.7 0.4 - - - -
177B PHE* 3.4 50.0 - + + -
310B PHE* 3.8 14.4 - + + -
325B ALA* 3.8 24.5 - - + -
326B LYS* 3.0 23.6 + - + +
327B ASN 4.2 3.6 + - - -
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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