Contacts of the strand formed by residues 116 - 122 (chain E) in PDB entry 3W13
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 SER 116 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASN* 3.2 17.9 + - - +
91E TYR* 3.2 13.4 - - - +
92E ALA* 2.9 21.4 + - - -
93E LEU 3.5 2.8 + - - -
115E GLY* 1.3 74.0 - - - -
117E VAL* 1.3 65.3 + - - +
137E LEU* 3.5 7.2 - - - -
139E SER* 3.6 13.4 + - - -
142E ASP* 3.5 36.1 + - - +
143E ASN* 3.6 9.2 - - - -
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Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 3.8 2.4 - - - -
93E LEU* 3.6 26.5 - - + +
112E ILE* 3.9 13.9 - - + -
116E SER* 1.3 76.2 - - - +
118E ARG* 1.3 62.6 + - - +
119E ILE* 3.3 34.8 - - + -
133E TRP* 4.0 13.5 - - + -
137E LEU* 3.8 20.9 - - + -
143E ASN* 2.8 23.7 + - - +
144E HIS 2.9 24.4 + - - -
145E ILE* 3.5 12.3 - - + +
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Residues in contact with ARG 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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89E PHE* 5.5 2.4 - - - -
91E TYR* 2.9 54.7 + - + -
93E LEU 3.0 10.3 + - - +
94E VAL* 3.4 9.8 - - + +
95E ILE 3.0 24.3 + - - +
96E PHE* 5.3 1.1 - - + +
117E VAL* 1.3 71.8 - - - +
119E ILE* 1.3 61.2 + - - +
120E GLU* 2.9 33.7 + - + +
144E HIS* 3.4 43.6 + - - +
705F PHE* 3.3 50.3 - - + +
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Residues in contact with ILE 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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93E LEU* 4.5 3.1 - - + -
95E ILE* 3.2 28.5 - - + +
104E LEU* 4.0 26.2 - - + -
117E VAL* 3.3 26.0 - - + -
118E ARG* 1.3 75.4 - - - +
120E GLU* 1.3 60.0 + - - +
122E ASN* 3.2 18.4 - - - +
125E LEU* 3.6 20.6 - - + -
128E LEU* 4.5 5.4 - - + -
133E TRP* 4.2 8.1 - - + +
144E HIS 3.2 6.0 + - - -
145E ILE* 3.2 35.4 - - + +
146E VAL 3.3 0.2 + - - -
148E ASN* 3.2 14.3 + - - +
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Residues in contact with GLU 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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95E ILE 2.9 7.1 + - - -
96E PHE* 3.3 28.9 - - + -
97E GLU 3.2 16.3 + - - -
118E ARG* 2.9 43.1 + - + -
119E ILE* 1.3 75.4 - - - +
121E LYS* 1.3 81.8 + - + +
122E ASN* 2.9 13.7 + - - +
144E HIS* 3.8 6.5 + - - +
146E VAL* 3.3 31.7 - - + +
147E LEU* 3.6 12.0 - - + +
705F PHE* 4.5 0.9 - - - -
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Residues in contact with LYS 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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9B SER* 5.8 3.0 - - - -
96E PHE* 3.8 16.6 - - + -
97E GLU* 3.3 41.6 - - + +
99E VAL* 5.0 2.1 - - - +
120E GLU* 1.3 97.0 + - + +
122E ASN* 1.3 58.9 + - - +
123E ASN* 3.6 9.3 + - - +
146E VAL 3.3 1.6 + - - -
147E LEU* 3.2 38.1 + - + +
706F GLU* 3.2 24.4 + - - +
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Residues in contact with ASN 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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95E ILE* 3.1 16.9 + - - +
97E GLU 3.4 1.9 + - - -
98E MET* 2.8 45.7 + - + +
119E ILE* 3.2 9.9 - - - +
120E GLU 2.9 31.9 + - - +
121E LYS* 1.3 74.4 - - - +
123E ASN* 1.3 67.6 + - - +
125E LEU* 3.1 32.1 + - + +
147E LEU 3.2 1.0 + - - -
148E ASN* 2.9 36.9 + - - +
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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