Contacts of the strand formed by residues 90 - 93 (chain A) in PDB entry 4R54
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP 2.9 17.0 + - - +
67A ILE* 3.3 9.8 - - + +
68A ALA 3.0 22.3 + - - +
88A GLY 4.9 0.2 - - - +
89A VAL* 1.3 76.0 - - - +
91A VAL* 1.3 63.3 + - - +
119A HIS* 3.9 14.4 - - + +
121A GLY* 3.7 4.7 - - - +
123A ILE* 3.7 27.1 - - + -
341A LEU* 4.0 17.7 - - + -
346A LEU 4.1 6.3 - - - +
347A VAL* 4.1 7.9 - - + -
348A ARG 3.4 39.7 - - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 3.3 3.1 - - - +
70A PHE* 3.6 28.9 - - + -
81A ALA* 4.0 21.8 - - + +
84A ALA* 3.8 29.4 - - + -
85A VAL* 4.1 6.1 - - + -
89A VAL* 4.2 5.4 - - + -
90A VAL* 1.3 74.2 - - - +
92A VAL* 1.3 71.5 + - - +
93A ASP* 3.9 10.5 - - + +
121A GLY 2.7 17.5 + - - +
122A ILE* 3.4 10.0 - - + -
123A ILE* 2.8 30.5 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 5.7 0.2 - - - +
67A ILE* 4.8 7.4 - - + -
68A ALA 2.8 8.9 + - - +
69A LEU* 3.4 22.4 - - + +
70A PHE 2.9 24.8 + - - +
90A VAL 5.0 0.9 - - - +
91A VAL* 1.3 75.9 - - - +
93A ASP* 1.3 61.4 + - - +
94A ASN* 3.8 0.9 + - - +
123A ILE* 3.3 9.2 - - + +
125A CYS* 4.9 2.7 - - + -
334A SER* 3.9 40.3 + - - +
337A ILE* 4.0 32.3 - - + -
338A ALA* 4.6 2.5 - - - +
341A LEU* 4.0 16.4 - - + -
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.3 10.1 - - - +
77A SER* 2.5 33.6 + - - -
81A ALA* 5.6 0.4 - - - -
91A VAL* 3.8 12.0 - - + -
92A VAL* 1.3 71.6 - - - +
94A ASN* 1.3 67.4 + - - +
95A THR* 2.7 33.9 + - - +
98A PHE* 3.4 18.4 + - + +
122A ILE* 4.2 11.4 - - + -
123A ILE 2.8 13.1 + - - +
124A ALA* 3.4 6.0 - - + +
125A CYS* 2.8 28.9 + - - +
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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