Contacts of the strand formed by residues 89 - 93 (chain A) in PDB entry 4P5E
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 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 3.5 0.2 + - - -
23A LEU* 3.6 37.3 - - + -
24A TYR 3.0 23.6 + - - -
87A ALA* 3.4 5.5 - - - +
88A ASP* 1.3 78.8 - - - +
90A VAL* 1.3 74.6 + - - +
91A VAL* 4.4 5.6 - - + -
113A LYS* 5.7 0.7 - - - -
114A ARG* 3.4 37.5 - - + +
157A TYR* 4.2 15.5 - - + +
158A PHE* 4.1 4.9 - - + -
163A LEU* 3.7 19.5 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.4 11.7 - - + +
26A CYS* 3.8 27.4 - - - -
84A LEU* 3.7 24.9 - - + -
87A ALA* 4.5 3.6 - - + -
89A VAL* 1.3 78.6 - - - +
91A VAL* 1.3 64.7 + - - +
104A GLU 5.5 0.7 - - - +
105A LEU* 4.4 16.8 - - + -
108A ALA* 4.1 9.0 - - + -
113A LYS* 4.0 23.8 - - + -
114A ARG 2.9 10.3 + - - +
115A ILE* 3.3 9.2 - - + +
116A LEU 2.9 25.6 + - - +
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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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23A LEU* 5.0 1.1 - - + -
24A TYR 2.8 8.4 + - - +
25A PHE* 3.2 17.0 - - + -
26A CYS* 2.9 23.7 + - - +
42A ILE* 4.6 1.8 - - + -
46A LEU* 4.1 33.9 - - + -
89A VAL* 4.4 17.7 - - + -
90A VAL* 1.3 79.3 - - - +
92A ALA* 1.3 63.3 + - - +
116A LEU* 3.2 20.0 - - + +
118A LEU* 4.1 23.3 - - + -
154A LEU* 4.4 8.3 - - + -
158A PHE* 4.6 9.4 - - + -
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Residues in contact with ALA 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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25A PHE* 4.6 1.6 - - - -
26A CYS* 3.4 23.1 - - + -
90A VAL 4.2 0.4 - - - -
91A VAL* 1.3 76.3 - - - +
93A GLU* 1.3 60.4 + - - +
94A VAL* 3.6 18.6 + - + +
101A VAL* 4.3 1.8 - - + -
105A LEU* 4.0 24.7 - - + -
116A LEU 2.9 8.1 + - - +
117A CYS* 3.3 5.2 - - - -
118A LEU* 2.8 28.4 + - - +
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Residues in contact with GLU 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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25A PHE* 4.0 13.8 - - + -
26A CYS 2.9 11.8 + - - +
27A GLY* 4.1 9.4 - - - -
28A SER 4.7 1.4 + - - -
35A ASP* 4.2 1.2 - - - +
38A LEU* 4.3 2.7 - - + -
39A TYR* 3.7 30.1 + - + -
42A ILE* 3.6 18.2 - - + -
92A ALA* 1.3 71.4 - - - +
94A VAL* 1.3 58.8 + - - +
95A THR* 2.8 34.8 + - - -
96A GLN 4.4 3.8 + - - +
101A VAL* 4.4 5.0 - - - +
118A LEU* 3.5 9.4 - - + +
120A ARG* 3.1 14.4 + - - -
145A TYR* 2.6 34.7 + - - +
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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