Contacts of the strand formed by residues 125 - 128 (chain B) in PDB entry 2PG0
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 THR 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 4.0 1.7 - - - +
94B HIS* 2.9 30.9 + - - +
98B VAL* 3.4 30.8 - - + +
99B THR* 3.8 8.3 - - + +
102B ILE* 4.6 4.9 - - + -
118B CYS* 3.8 25.1 - - - -
124B ILE* 1.3 79.1 - - - +
126B ALA* 1.3 61.6 + - - +
163B ASN* 3.0 27.7 + - - +
167B ALA* 4.0 1.6 - - - -
169B LEU* 3.3 23.3 - - + -
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Residues in contact with ALA 126 (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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93B LEU* 4.2 2.2 - - - -
98B VAL* 3.4 15.2 - - - +
125B THR* 1.3 75.1 - - - +
127B ILE* 1.3 60.9 + - - +
161B ILE* 3.9 13.9 - - + -
162B THR 3.4 23.8 - - - +
163B ASN 4.2 0.2 - - - +
167B ALA* 3.5 20.4 - - + -
169B LEU 3.0 5.5 + - - +
170B ILE* 3.4 10.2 - - + -
171B VAL 2.9 23.7 + - - -
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Residues in contact with ILE 127 (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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93B LEU* 4.4 10.8 - - + +
97B ILE* 4.4 11.4 - - + -
98B VAL* 3.7 20.2 - - + -
101B TYR* 3.5 44.9 - - + +
126B ALA* 1.3 76.1 - - - +
128B ALA* 1.3 64.9 + - - +
129B MET* 4.0 28.3 - - + -
161B ILE* 3.7 6.4 - - - +
162B THR 5.0 0.4 + - - -
170B ILE* 4.6 0.7 - - - -
171B VAL* 3.4 21.5 - - + +
189B LEU* 6.2 0.4 - - + -
241B LEU* 4.1 12.8 - - + -
248B GLU* 5.2 0.4 - - - +
401B FAD 3.0 31.4 + - + +
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Residues in contact with ALA 128 (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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127B ILE* 1.3 73.3 - - - +
129B MET* 1.3 61.5 + - - +
130B THR 4.0 0.2 - - - -
158B LYS* 3.5 31.5 - - + -
161B ILE* 3.6 17.7 - - + -
170B ILE* 3.9 19.7 - - + -
171B VAL 2.8 11.1 + - - +
172B VAL* 4.3 6.1 - - + -
173B ALA 3.0 26.0 + - - -
218B LEU* 4.2 3.4 - - + -
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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