Contacts of the strand formed by residues 116 - 123 (chain E) in PDB entry 3J7Y
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 LYS 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3150A U 3.3 24.8 + - - -
3151A A 4.5 12.6 - - + -
3165A C 5.4 3.6 + - - -
108E PRO* 3.7 17.6 - - + +
109E LEU 3.7 4.3 - - - -
110E TRP* 3.3 20.6 - - + +
115E GLN* 1.3 72.4 + - - +
117E HIS* 1.3 70.8 + - - +
118E VAL* 3.6 18.9 - - + +
95L ARG* 4.8 9.4 - - + -
165Q GLU* 3.2 33.9 - - - +
168Q ASN* 4.7 0.4 - - - +
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Residues in contact with HIS 117 (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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3165A C 5.5 11.0 + - - -
108E PRO* 4.6 1.1 - - - -
109E LEU* 2.8 39.1 + - + +
111E THR* 3.5 30.9 + - + +
115E GLN* 3.8 27.1 + - - +
116E LYS* 1.3 79.5 + - - +
118E VAL* 1.3 66.2 + - - +
119E VAL* 3.3 5.2 - - - +
274E TRP* 3.6 34.4 + + + +
286E ASN* 5.3 8.5 + - + +
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Residues in contact with VAL 118 (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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3150A U 3.5 41.3 - - + +
3164A C 3.8 21.9 + - - +
3165A C 5.8 4.4 - - - +
106E MET* 3.5 38.1 - - + -
107E MET 3.7 6.1 - - - +
108E PRO* 4.3 1.3 - - + -
116E LYS* 3.6 17.1 + - + +
117E HIS* 1.3 72.1 - - - +
119E VAL* 1.3 63.4 + - - +
286E ASN* 3.6 5.5 - - - +
287E GLY* 2.8 30.0 + - - +
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Residues in contact with VAL 119 (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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106E MET* 3.2 5.5 - - - +
107E MET* 2.8 37.8 + - + +
109E LEU* 3.4 23.6 - - + -
117E HIS 3.3 17.7 - - - +
118E VAL* 1.3 76.0 - - - +
120E THR* 1.3 60.6 + - - +
121E LEU* 4.0 4.6 - - + +
274E TRP* 3.6 18.2 - - + -
284E TYR* 3.4 27.8 - - + +
285E VAL 3.1 36.6 - - - +
286E ASN 4.2 0.2 - - - +
287E GLY 4.1 0.9 - - - +
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Residues in contact with THR 120 (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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103E LYS* 4.1 11.2 - - - +
105E GLY 3.4 8.6 + - - -
106E MET* 3.6 18.2 - - - +
119E VAL* 1.3 74.5 - - - +
121E LEU* 1.3 63.6 + - - +
122E LEU* 3.8 20.4 + - - +
285E VAL* 2.8 34.6 + - - +
286E ASN 5.0 0.2 - - - -
287E GLY 3.0 29.2 - - - +
288E SER* 3.7 7.9 - - - -
289E VAL* 3.8 18.9 - - + +
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Residues in contact with LEU 121 (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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103E LYS* 3.7 2.6 - - - -
104E LEU* 2.8 41.1 + - + +
105E GLY 2.8 18.3 + - - +
107E MET* 3.5 32.1 - - + -
119E VAL* 4.0 5.6 - - + +
120E THR* 1.3 75.9 + - - +
122E LEU* 1.3 58.7 + - - +
123E GLN 4.0 0.7 - - - -
282E ILE* 3.8 13.9 - - + -
283E ILE 3.5 4.3 - - - -
284E TYR* 3.2 38.1 - - + -
91Q LYS* 3.7 26.7 - - + -
94Q ILE* 4.3 16.6 - - + -
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Residues in contact with LEU 122 (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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101E ALA* 3.8 11.4 - - + -
102E LEU 3.3 2.0 - - - -
103E LYS* 3.7 26.2 - - + +
120E THR* 3.8 15.3 - - - +
121E LEU* 1.3 71.9 - - - +
123E GLN* 1.3 62.0 + - - +
124E VAL* 3.6 2.1 + - - +
206E VAL* 4.1 14.1 - - + -
281E ASN 3.7 0.2 - - - +
282E ILE* 3.5 2.0 - - - -
283E ILE* 2.8 47.3 + - + +
285E VAL* 3.6 28.0 - - + -
289E VAL* 4.3 8.3 - - + -
297E VAL* 3.7 17.9 - - + -
299E VAL* 3.7 26.9 - - + -
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Residues in contact with GLN 123 (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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101E ALA* 3.7 1.3 - - - -
102E LEU* 2.8 39.3 + - + +
104E LEU* 3.9 21.9 - - + +
121E LEU 4.0 1.6 + - - -
122E LEU* 1.3 70.5 - - - +
124E VAL* 1.3 60.0 + - - +
125E GLN* 2.7 47.6 + - + +
280E HIS 4.0 12.3 + - - +
281E ASN* 3.6 3.6 - - + -
282E ILE* 3.5 19.0 - - + +
88Q ASP* 5.3 1.4 - - - +
90Q LEU* 3.2 45.7 - - - +
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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