Contacts of the strand formed by residues 27 - 30 (chain B) in PDB entry 1XRG
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 PHE 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.1 19.3 - + - -
22B ILE 3.9 0.3 - - - +
23B VAL* 3.4 5.5 - - - +
24B THR* 2.9 34.6 + - + +
25B GLY 3.4 0.2 - - - -
26B SER* 1.3 86.8 - - - +
28B VAL* 1.3 63.3 + - - +
29B TYR* 3.9 21.5 - + + -
74B VAL* 5.3 0.4 - - + -
123B VAL* 4.3 13.9 - - + -
124B ALA 3.4 12.3 - - - -
125B ILE* 4.0 15.9 - - + -
1C MSE 3.5 24.9 - - + -
24C THR* 4.0 15.3 - - + -
25C GLY* 5.5 0.4 - - - -
27C PHE* 3.7 32.3 - + - -
29C TYR* 4.1 15.7 - + - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 4.1 15.9 - - + -
22B ILE 3.4 9.6 - - - +
23B VAL* 4.2 12.8 - - + -
27B PHE* 1.3 77.2 - - - +
29B TYR* 1.3 65.2 + - - +
30B THR* 4.1 0.8 - - + +
63B LEU* 4.2 15.7 - - + -
66B ALA* 3.9 20.6 - - + -
68B SER* 3.8 23.3 - - - +
122B ALA 3.9 0.7 - - - +
123B VAL* 3.3 7.1 - - - +
124B ALA* 2.8 49.4 + - + +
125B ILE 4.3 0.9 - - - -
126B LYS* 4.3 14.6 - - + -
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Residues in contact with TYR 29 (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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27A PHE* 3.9 12.4 - + - -
74A VAL* 4.1 20.9 - - + +
75A LYS* 3.7 35.4 - - + -
103A ALA* 3.4 7.5 - - + +
123A VAL* 3.7 28.7 - - + +
503A UNX 2.6 28.7 - - - -
21B ALA* 3.1 3.1 - - - -
22B ILE* 2.9 41.8 + - + +
24B THR* 4.3 12.8 - - + -
27B PHE* 3.9 24.2 - - + +
28B VAL* 1.3 75.4 - - - +
30B THR* 1.3 61.4 + - - +
122B ALA 3.9 3.1 - - - -
123B VAL* 4.0 26.9 - - + -
27C PHE* 6.1 0.2 - - - -
29C TYR* 4.1 1.0 + - - -
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Residues in contact with THR 30 (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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75A LYS* 3.6 20.3 - - - -
103A ALA* 3.7 2.4 - - - +
20B GLN 3.6 9.0 - - - -
21B ALA* 3.8 3.8 - - + -
28B VAL* 4.6 1.8 - - + -
29B TYR* 1.3 76.1 - - - +
31B SER* 1.3 80.2 + - - +
33B GLN* 4.3 3.1 - - - -
59B LEU* 3.5 21.1 - - + +
62B VAL* 4.2 12.6 - - + -
63B LEU* 3.7 29.6 - - + -
121B GLU* 4.1 3.6 - - - +
122B ALA* 2.9 35.4 + - + +
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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