Contacts of the strand formed by residues 84 - 91 (chain A) in PDB entry 2PRF
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 ALA 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL* 5.6 2.2 - - + -
67A TYR* 3.8 9.4 - - + +
80A LYS* 4.1 3.6 - - - +
81A LYS* 3.4 38.9 + - + +
82A GLY 4.3 0.9 + - - -
83A SER* 1.3 83.3 + - - +
85A GLY* 1.3 61.4 + - - +
100A TYR* 3.3 22.7 + - - +
101A ASN* 4.0 11.4 - - - -
102A GLU 4.7 0.4 - - - +
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Residues in contact with GLY 85 (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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67A TYR* 3.2 15.3 + - - -
79A GLY 3.9 7.0 - - - -
80A LYS* 4.3 0.9 - - - -
84A ALA* 1.3 81.6 - - - +
86A VAL* 1.3 59.8 + - - +
98A GLY 3.2 2.1 - - - +
99A VAL* 3.9 0.2 - - - -
100A TYR* 2.6 56.1 + - - -
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Residues in contact with VAL 86 (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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60A PHE* 4.3 11.2 - - + -
62A LEU* 5.7 6.1 - - + -
67A TYR* 3.2 43.1 - - + +
79A GLY* 3.4 26.0 + - - +
85A GLY* 1.3 74.5 - - - +
87A ILE* 1.3 60.5 + - - +
88A THR* 3.2 16.6 + - + +
97A VAL* 3.1 36.1 - - + -
98A GLY 3.2 3.6 - - - +
99A VAL* 4.1 9.6 - - + -
100A TYR* 3.6 0.4 - - - -
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Residues in contact with ILE 87 (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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16A VAL* 4.8 3.4 - - + -
78A TYR* 3.5 38.1 - - + +
79A GLY 5.8 0.7 - - - +
86A VAL* 1.3 69.4 - - - +
88A THR* 1.3 57.4 + - - +
89A VAL* 3.7 5.1 + - + -
96A LEU* 3.0 10.8 - - + +
97A VAL* 3.3 0.2 - - - -
98A GLY* 3.0 33.1 + - - +
100A TYR* 3.8 21.1 - - + +
106A PRO 5.6 1.1 - - - +
109A ALA* 3.4 40.2 - - + +
110A ALA* 4.2 6.1 - - + +
113A VAL* 3.4 38.8 - - + -
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Residues in contact with THR 88 (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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45A LEU* 5.2 15.1 - - + +
49A PHE* 5.0 3.6 - - - -
60A PHE* 6.1 2.5 - - + -
77A ILE* 2.5 61.0 + - - +
79A GLY 5.0 0.2 + - - -
86A VAL* 3.2 29.5 + - + +
87A ILE* 1.3 76.0 - - - +
89A VAL* 1.3 59.5 + - - +
95A ILE* 3.9 13.5 - - - +
96A LEU 3.2 6.3 - - - -
97A VAL* 3.8 17.7 - - + -
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Residues in contact with VAL 89 (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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2A TRP* 4.6 1.3 - - + -
75A ARG 4.9 0.7 - - - -
76A SER* 3.8 13.7 - - - +
77A ILE* 3.8 8.5 - - - +
78A TYR* 3.1 42.0 - - + -
87A ILE* 3.7 5.6 + - + -
88A THR* 1.3 79.9 - - - +
90A LYS* 1.3 63.8 + - - +
91A THR* 4.8 1.3 - - + -
95A ILE* 3.0 24.8 - - - -
96A LEU* 3.0 47.8 + - + +
113A VAL* 3.8 10.1 - - + +
117A ALA* 5.0 3.8 - - + -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.6 15.0 - - + +
49A PHE* 5.6 12.1 - - + -
75A ARG 4.5 15.9 + - - +
76A SER* 5.2 0.2 - - - +
77A ILE* 5.8 3.8 - - + -
89A VAL* 1.3 78.6 - - - +
91A THR* 1.3 70.0 + - - +
93A LYS 5.5 0.2 - - - -
94A SER 3.3 13.2 - - - +
95A ILE* 4.2 29.6 - - + -
117A ALA* 4.9 1.0 - - - +
121A ILE* 4.8 8.0 - - - +
125A PHE* 4.4 19.0 + - - +
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Residues in contact with THR 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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1A SER* 3.9 16.5 - - - -
2A TRP* 3.5 24.6 - - + -
90A LYS* 1.3 83.3 - - - +
92A SER* 1.3 58.2 + - - -
93A LYS 3.3 0.9 - - - +
94A SER* 3.0 22.2 + - - +
96A LEU* 3.2 13.9 - - + +
117A ALA* 4.1 24.2 - - + -
120A LEU* 4.0 15.0 - - + -
121A ILE* 5.0 1.8 - - + -
125A PHE* 2.6 41.6 + - - +
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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