Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 2X2D
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PHE* 4.8 3.1 - - + -
29B VAL* 3.8 9.5 - - - +
87B ASN 5.2 0.4 + - - +
88B PHE* 6.0 1.2 - - - +
90B LEU* 3.8 47.7 + - + +
91B LYS 4.1 7.6 - - - +
92B HIS* 3.4 44.2 - - + +
97B ILE* 3.7 22.0 - - + -
98B LEU 3.5 11.9 - - - +
99B SER* 4.0 1.6 - - - +
126B HIS 3.3 2.0 + - - +
127B VAL* 1.3 80.6 - - - +
129B PHE* 1.3 61.9 + - - +
130B GLY 4.2 8.7 - - - +
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Residues in contact with PHE 129 (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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24B LEU* 3.5 5.9 - - + +
25B PHE* 2.9 29.9 + - - -
29B VAL* 3.5 21.9 - - + +
32B THR* 3.6 31.4 - - + -
33B ALA* 4.3 7.5 - - - +
36B PHE* 3.4 46.7 - + + -
98B LEU* 3.0 30.2 + - + -
99B SER* 3.6 20.6 - - - -
100B MET* 3.6 23.6 - - + -
112B PHE* 4.4 2.0 - - + -
127B VAL* 3.4 13.7 - - + -
128B VAL* 1.3 75.3 - - - +
130B GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 130 (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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23B GLU 3.0 14.1 - - - -
24B LEU* 4.2 0.9 - - - -
25B PHE* 3.4 17.9 - - - -
97B ILE* 3.8 3.6 - - - +
98B LEU* 2.9 35.4 + - - +
128B VAL* 4.2 3.5 - - - +
129B PHE* 1.3 80.8 - - - +
131B LYS* 1.3 62.4 + - - +
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Residues in contact with LYS 131 (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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22B PHE* 3.3 6.5 - - - -
23B GLU* 2.8 49.9 + - + +
25B PHE* 3.8 20.2 - - + -
96B GLY 3.2 13.9 - - - +
97B ILE* 4.7 9.4 - - + -
98B LEU* 4.2 2.5 - - - +
130B GLY* 1.3 76.1 - - - +
132B VAL* 1.3 89.7 + - - +
133B LYS* 3.7 14.6 + - - +
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Residues in contact with VAL 132 (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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20B VAL* 4.1 7.6 - - + -
21B SER 3.4 6.1 - - - +
22B PHE* 3.8 23.8 - - + -
96B GLY* 2.8 36.5 + - - +
114B ILE* 3.9 11.2 - - + -
131B LYS* 1.3 97.3 + - - +
133B LYS* 1.3 58.5 + - - +
134B GLU 3.5 22.4 - - - +
135B GLY 4.2 0.9 - - - -
136B MET* 3.8 33.0 - - + +
139B VAL* 4.4 2.0 - - + -
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Residues in contact with LYS 133 (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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5B THR* 4.1 23.4 + - + +
21B SER* 2.6 21.9 + - - +
22B PHE 4.5 0.7 - - - -
23B GLU* 3.7 41.8 + - + +
131B LYS* 3.4 16.8 + - - +
132B VAL* 1.3 77.0 - - - +
134B GLU* 1.3 77.4 + - - +
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Residues in contact with GLU 134 (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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19B ARG* 4.4 2.2 - - + +
20B VAL* 3.4 2.6 - - - -
21B SER* 2.8 43.6 + - - +
132B VAL* 3.5 4.2 - - - +
133B LYS* 1.3 95.6 - - + +
135B GLY* 1.3 63.9 + - - +
136B MET 3.5 2.0 - - - +
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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