Contacts of the strand formed by residues 70 - 75 (chain I) in PDB entry 2A3W
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 GLU 70 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LYS* 3.6 8.9 - - - +
66I GLU* 3.5 24.7 + - + +
67I ARG* 2.8 64.7 + - + +
68I VAL 4.8 0.9 - - - +
69I GLY* 1.3 82.7 - - - +
71I TYR* 1.3 62.8 + - - +
81I THR* 4.1 17.2 - - + +
82I SER 3.6 2.7 - - - -
83I LYS* 3.7 35.3 - - + +
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Residues in contact with TYR 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LEU* 4.5 8.5 - - + -
63I VAL* 5.4 1.6 - - + -
64I TYR 4.0 2.0 - - - -
65I LYS* 3.4 32.4 + - + -
70I GLU* 1.3 76.5 - - - +
72I SER* 1.3 63.0 + - - +
81I THR* 3.3 2.2 - - - +
82I SER 2.9 34.5 + - - +
84I VAL* 3.6 18.8 - - + -
86I GLU* 2.6 34.0 + - - -
92I VAL* 3.7 18.8 - - + +
94I ILE* 3.6 26.0 - - + -
107I PHE* 3.6 33.7 - + + -
109I ILE* 3.6 28.7 - - + -
114I LEU* 4.4 4.0 - - + -
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Residues in contact with SER 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I LEU 4.3 0.2 - - - -
63I VAL* 3.5 4.3 - - - -
64I TYR 2.8 36.7 + - - -
66I GLU* 2.7 33.4 + - - +
71I TYR* 1.3 73.2 - - - +
73I LEU* 1.3 60.5 + - - +
74I TYR* 4.0 15.9 - - - -
79I LYS* 4.0 2.0 - - - +
80I VAL 3.1 7.9 - - - -
81I THR* 2.6 23.2 + - - +
107I PHE* 3.6 7.5 - - - -
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I PHE* 4.2 5.6 - - + -
61I LEU* 3.8 20.4 - - + -
62I LEU 3.3 9.2 - - - +
63I VAL* 4.2 11.0 - - + -
72I SER* 1.3 73.7 - - - +
74I TYR* 1.3 77.9 + - - +
75I ILE* 4.0 21.8 - - + -
78I HIS 3.9 0.2 - - - +
79I LYS* 3.2 2.9 - - - +
80I VAL* 2.9 37.9 + - + +
96I VAL* 4.0 15.5 - - + -
98I TRP* 4.1 11.4 - - + -
105I ALA* 3.7 26.7 - - + -
107I PHE* 3.8 17.8 - - + -
119I LEU* 4.1 3.4 - - + +
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Residues in contact with TYR 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B CPJ 3.4 32.3 - - + +
59I ASN* 3.8 37.7 - - + +
61I LEU* 3.2 7.1 - - - -
62I LEU* 2.7 56.7 + - + +
64I TYR* 3.9 23.1 - - + -
66I GLU* 3.8 7.8 + - - -
72I SER* 4.0 10.1 - - - -
73I LEU* 1.3 78.9 - - - +
75I ILE* 1.3 68.4 + - - +
77I ARG 3.8 17.3 - - - -
78I HIS 3.0 3.8 - - - +
79I LYS* 3.6 40.2 + - + +
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I PHE* 3.7 34.8 - - + -
60I GLU 3.4 6.1 - - - +
61I LEU* 4.5 3.1 - - + -
73I LEU* 4.0 19.5 - - + -
74I TYR* 1.3 82.2 - - - +
76I GLY* 1.3 69.5 + - - +
77I ARG 3.2 0.2 - - - -
78I HIS 2.8 16.1 + - - +
98I TRP* 3.9 32.1 - - + -
119I LEU* 3.8 15.8 - - + +
120I ARG* 3.0 22.3 - - + +
123I TYR* 3.8 24.7 - - + -
125I VAL* 4.1 9.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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