Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 3SKJ
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 ASN 140 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E LEU 3.7 0.3 - - - +
75E LYS* 3.1 9.2 - - - +
76E PHE* 2.9 67.8 + - + +
77E THR* 4.4 3.4 - - - +
78E VAL 4.6 0.6 - - - +
123E PRO* 3.5 20.0 - - + +
124E ASP* 3.2 10.6 + - + +
125E GLU* 2.9 49.3 + - - +
138E LYS 3.8 5.9 + - - -
139E LEU* 1.3 75.6 - - - +
141E VAL* 1.3 62.7 + - - +
142E GLU* 4.3 3.1 - - - +
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E GLU* 3.8 28.3 - - + +
74E LEU 3.3 9.2 - - - +
75E LYS* 4.1 24.7 - - + +
124E ASP* 5.1 2.3 - - - +
139E LEU* 5.3 5.6 - - + +
140E ASN* 1.3 77.9 - - - +
142E GLU* 1.3 79.1 + - - +
143E GLU* 5.2 1.3 - - + +
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ILE 3.7 1.2 - - - +
73E GLU* 3.5 1.1 - - - -
74E LEU* 2.8 36.5 + - + +
76E PHE* 3.5 26.8 - - + -
121E ILE* 3.7 20.0 - - + -
122E ALA 3.4 17.2 - - - +
124E ASP* 3.6 22.2 + - - +
140E ASN* 5.0 1.7 - - - +
141E VAL* 1.3 86.8 + - - +
143E GLU* 1.3 59.9 + - - +
144E ARG* 3.3 30.1 + - - +
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Residues in contact with GLU 143 (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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71E PHE* 3.9 15.9 - - - +
72E ILE 3.2 15.0 - - - +
73E GLU* 4.6 11.7 - - + +
141E VAL* 5.2 1.5 - - + +
142E GLU* 1.3 74.7 - - - +
144E ARG* 1.3 95.4 + - - +
173E TYR* 2.3 38.8 + - - -
175E LYS* 5.2 2.1 + - - -
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Residues in contact with ARG 144 (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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71E PHE* 3.5 2.5 - - - -
72E ILE* 2.9 33.6 + - + +
97E LEU* 4.3 14.1 - - + -
118E ILE* 4.0 20.0 - - + -
119E ASP* 2.9 34.3 + - + +
120E THR 3.8 12.7 + - - -
121E ILE* 4.0 25.1 - - + +
122E ALA 5.1 1.2 - - - +
142E GLU* 3.3 29.3 + - - +
143E GLU* 1.3 110.2 + - - +
145E SER* 1.3 63.4 + - - +
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Residues in contact with SER 145 (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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69E ARG* 2.8 35.8 + - - -
70E ILE 3.0 17.0 - - - -
71E PHE* 3.9 23.1 - - - -
72E ILE* 4.8 2.2 - - - -
118E ILE* 4.4 4.2 - - - +
144E ARG* 1.3 78.7 - - - +
146E VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 146 (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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69E ARG* 3.7 8.0 - - - +
70E ILE* 3.1 50.9 + - + +
72E ILE* 4.5 2.0 - - + +
99E TYR* 4.1 36.1 - - + +
118E ILE* 3.6 40.8 - - + -
145E SER* 1.3 82.9 - - - +
147E GLY* 1.3 69.8 - - - +
149E LEU* 4.6 2.4 - - + +
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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