Contacts of the strand formed by residues 148 - 151 (chain B) in PDB entry 2PX7
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 GLN 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ARG* 5.9 0.7 - - - -
86B VAL 3.8 0.7 - - - +
87B LEU* 3.3 2.6 - - - -
88B VAL* 2.8 34.0 + - + +
104B VAL* 4.1 1.1 - - - -
114B ALA 3.7 4.3 - - - -
115B VAL* 3.4 17.8 - - + +
144B VAL* 3.3 8.9 - - - +
145B GLN 2.8 26.2 + - - +
146B THR* 4.0 10.3 + - - +
147B PRO* 1.3 76.5 - - - +
149B GLY* 1.3 59.5 + - - +
150B PHE* 3.5 19.8 - - + -
171B ASP* 3.0 29.4 + - - +
172B ASP* 3.4 12.7 + - + +
173B ALA 3.0 28.1 + - - -
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Residues in contact with GLY 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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86B VAL 3.2 8.3 - - - -
87B LEU* 3.8 14.4 - - - -
104B VAL* 3.5 7.5 - - - +
108B ALA* 3.6 12.5 - - - +
113B ALA* 3.3 1.0 - - - -
114B ALA 2.9 37.2 + - - -
148B GLN* 1.3 72.1 - - - +
150B PHE* 1.3 67.3 + - - -
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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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85B LEU* 3.5 10.5 - - - +
86B VAL* 2.9 40.7 + - + +
88B VAL* 4.8 1.1 - - + -
108B ALA* 3.9 2.4 - - - +
112B GLY 3.2 9.9 - - - +
113B ALA* 3.5 24.5 - - + -
114B ALA 4.6 2.2 - - - -
115B VAL* 4.5 1.6 - - + -
148B GLN* 3.5 39.9 - - + -
149B GLY* 1.3 81.5 - - - -
151B PHE* 1.3 70.7 + - - +
154B LEU* 5.0 1.3 - - + -
155B LEU* 4.0 24.5 - - + +
172B ASP* 3.7 17.3 - - + -
173B ALA* 3.8 29.8 - - + -
176B VAL* 3.7 24.5 - - + -
183B VAL* 4.9 1.8 - - + -
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Residues in contact with PHE 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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84B PRO 3.6 7.9 - - - +
85B LEU* 3.9 15.7 - - + -
108B ALA 3.6 11.2 - - - -
109B GLN* 3.7 26.2 - - - -
110B ARG 5.2 0.7 - - - -
111B SER 4.4 3.6 - - - -
112B GLY* 3.0 38.9 + - - +
150B PHE* 1.3 71.7 - - - +
152B THR* 1.3 66.5 + - - +
153B ALA* 3.3 3.8 - - + +
154B LEU* 3.0 26.7 + - + +
155B LEU 3.2 9.5 + - - -
181B TYR* 4.4 10.5 - + - -
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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