Contacts of the strand formed by residues 115 - 121 (chain E) in PDB entry 3IT8
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 GLY 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E GLU* 4.2 2.5 - - - -
112E THR* 2.8 33.4 + - - -
113E ALA 3.3 1.0 + - - -
114E ASN* 1.3 81.7 - - - +
116E PRO* 1.3 79.7 - - - +
117E LEU* 3.4 0.7 + - - +
243E TYR* 5.0 0.7 - - - -
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Residues in contact with PRO 116 (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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111E GLU* 3.9 9.0 - - + -
115E GLY* 1.3 85.5 - - - +
117E LEU* 1.3 62.4 + - - +
130E MET* 3.6 28.0 - - + -
131E THR* 3.7 20.3 + - - +
242E ASN* 4.0 28.0 - - + +
243E TYR* 3.2 37.4 - - + +
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Residues in contact with LEU 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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80E ILE* 4.1 20.9 - - + -
86E THR* 5.8 4.7 - - + -
110E VAL* 2.9 29.0 + - + +
111E GLU* 4.4 3.6 - - - -
112E THR* 4.1 17.9 - - - +
115E GLY 3.4 2.6 + - - +
116E PRO* 1.3 75.5 - - - +
118E ALA* 1.3 60.2 + - - +
129E LYS* 4.0 3.5 - - - -
130E MET* 3.1 23.6 + - - +
131E THR* 4.4 2.5 + - - -
134E GLY 4.2 10.7 - - - +
135E PHE* 3.7 28.0 - - + +
136E PRO* 4.2 12.8 - - + -
141E LEU* 4.0 23.6 - - + -
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Residues in contact with ALA 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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109E TYR* 3.2 2.1 - - - -
110E VAL* 2.7 35.3 + - + -
117E LEU* 1.3 79.8 - - + +
119E ARG* 1.3 59.1 + - - +
127E PHE* 3.8 22.7 - - + -
128E THR 3.5 6.7 - - - +
130E MET* 3.3 6.7 - - - +
135E PHE* 3.6 31.2 - - + -
141E LEU* 4.2 10.8 - - + -
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Residues in contact with ARG 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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108E GLY 4.4 4.9 - - - +
109E TYR* 3.8 5.8 - - + -
118E ALA* 1.3 73.6 - - - +
120E TYR* 1.3 67.5 + - - +
121E HIS* 3.5 34.2 + - + +
127E PHE* 3.3 2.6 - - - -
128E THR* 2.7 39.5 + - - +
129E LYS 4.4 3.6 + - - -
130E MET* 3.4 38.2 - - + +
242E ASN 2.9 24.7 + - - -
243E TYR* 3.7 0.6 - - - +
244E GLU* 3.3 27.7 + - - +
247E GLU* 2.8 42.5 + - - +
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Residues in contact with TYR 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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108E GLY 2.8 20.3 + - - +
119E ARG* 1.3 74.6 - - - +
121E HIS* 1.3 74.8 + - - +
122E THR* 4.2 8.5 - - - -
125E LYS* 3.6 24.5 - - - +
126E ARG 3.7 27.4 - - - -
127E PHE* 3.7 28.6 - + + -
148E TRP* 4.1 15.3 - + - -
151E VAL* 5.2 1.3 - - + -
152E LYS* 3.8 24.9 + - + +
155E LEU* 3.9 14.1 - - + -
156E GLY* 3.4 29.6 - - - -
159E GLU* 3.2 37.3 - - - +
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Residues in contact with HIS 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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119E ARG* 3.5 33.1 + - - -
120E TYR* 1.3 77.2 + - - +
122E THR* 1.3 60.8 + - - +
123E GLY 4.4 1.8 - - - +
124E ASP* 3.6 24.9 - - + +
125E LYS* 2.9 31.5 + - - -
126E ARG 3.0 14.0 + - - +
128E THR* 3.0 37.2 + - + +
244E GLU* 4.8 8.3 - - - -
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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