Contacts of the strand formed by residues 72 - 75 (chain E) in PDB entry 5IY7
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 MET 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E LEU* 4.9 0.4 - - + -
21E CYS* 3.5 33.2 - - + -
24E ARG* 3.7 25.8 - - - +
26E TYR* 3.4 41.5 - - + +
61E LEU* 3.1 6.1 - - - +
62E VAL* 2.6 49.6 + - + +
64E HIS* 5.2 0.2 + - - -
71E GLN* 1.3 73.4 - - - +
73E PHE* 1.3 68.1 + - - +
74E VAL* 4.6 5.6 - - + -
99E ILE* 4.6 0.4 - - - -
101E ARG* 3.4 34.5 - - + +
102E ALA 5.9 0.2 - - - -
103E LEU* 4.8 12.3 - - + +
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Residues in contact with PHE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR* 3.3 31.2 - - + -
60E VAL 3.7 15.0 - - - -
61E LEU* 3.3 29.4 - - + -
72E MET* 1.3 76.5 - - - +
74E VAL* 1.3 65.9 + - - +
75E PHE* 5.0 0.2 - + - -
90E TYR* 2.9 43.9 + + - +
93E ARG* 4.5 24.9 - - + -
94E MET* 5.6 2.9 - - + -
97E GLU* 6.3 1.1 - - + -
99E ILE* 3.6 33.2 - - + -
101E ARG 2.9 8.0 + - - +
102E ALA* 3.5 2.8 - - - -
103E LEU* 2.9 26.3 + - - +
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ILE* 4.3 14.1 - - + -
21E CYS* 4.2 24.7 - - - -
59E THR* 3.4 6.0 - - - +
60E VAL* 3.1 41.8 + - + +
62E VAL* 4.3 14.8 - - + -
72E MET* 4.6 3.4 - - + -
73E PHE* 1.3 78.9 - - - +
75E PHE* 1.3 63.4 + - - +
76E PHE* 3.6 30.7 - - + -
103E LEU* 3.6 26.9 - - + +
105E VAL* 4.7 0.9 - - + -
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Residues in contact with PHE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ARG 4.6 1.6 - - - -
56E THR* 5.0 10.1 - - + -
59E THR* 3.6 21.1 - - + -
73E PHE* 4.4 1.1 - - + -
74E VAL* 1.3 73.6 - - - +
76E PHE* 1.3 81.0 + - - +
77E PRO* 3.4 39.1 - - + +
86E THR* 5.0 12.8 - - + -
90E TYR* 3.3 57.2 - + + +
93E ARG* 5.5 7.6 - - - -
103E LEU 3.0 10.8 + - - +
104E ILE* 4.2 12.8 - - + -
105E VAL* 3.1 25.6 + - - +
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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