Contacts of the strand formed by residues 128 - 132 (chain E) in PDB entry 4LOU
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 128 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E PRO 4.0 2.0 + - - -
127E PRO* 1.3 73.4 - - - +
129E VAL* 1.3 60.8 + - - +
130E TYR* 3.5 31.5 + - - -
149E LEU 3.7 1.0 - - - +
150E VAL* 3.6 2.4 - - - -
151E LYS* 2.9 40.1 + - - +
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Residues in contact with VAL 129 (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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127E PRO 4.1 4.9 + - - +
128E SER* 1.3 78.6 - - - +
130E TYR* 1.3 70.9 + - - +
131E PRO* 4.1 0.2 - - - +
148E CYS* 4.5 2.5 - - + -
149E LEU 3.3 6.3 - - - +
150E VAL* 4.3 7.6 - - + -
203E CYS* 4.0 9.9 - - - -
205E VAL* 3.7 44.4 - - + -
214E VAL* 3.9 28.8 - - + +
216E LYS* 3.2 45.2 + - + +
122F GLU* 5.5 0.3 - - - +
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Residues in contact with TYR 130 (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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128E SER* 3.5 28.4 + - - -
129E VAL* 1.3 79.2 - - - +
131E PRO* 1.3 67.4 - - - +
132E LEU* 4.9 1.6 - - + -
148E CYS* 3.2 6.3 - - - +
149E LEU* 2.7 71.2 + - + +
151E LYS* 4.3 20.4 - - + +
120F SER* 3.4 17.0 - - - +
122F GLU* 4.1 13.5 - - + -
123F GLN* 3.7 47.6 - - + +
126F SER* 4.2 18.5 + - - -
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Residues in contact with PRO 131 (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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129E VAL 4.1 0.9 - - - +
130E TYR* 1.3 84.9 - - + +
132E LEU* 1.3 68.6 + - - +
133E ALA* 4.0 2.7 + - + -
148E CYS* 4.2 1.6 - - - -
216E LYS* 4.1 19.7 - - + -
217E LYS 4.4 9.2 - - - +
218E ILE* 3.9 28.5 - - + -
219E VAL* 5.2 3.4 - - + +
221E ARG* 5.1 1.6 + - - -
120F SER* 3.4 20.8 - - - +
122F GLU* 3.7 33.9 - - - +
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Residues in contact with LEU 132 (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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130E TYR* 4.3 7.9 - - + +
131E PRO* 1.3 84.1 - - - +
133E ALA* 1.3 59.0 + - - +
146E LEU* 3.6 5.4 - - - -
147E GLY 2.7 41.2 + - - +
148E CYS 4.2 6.7 - - - +
149E LEU* 3.9 28.5 - - + +
186E SER* 4.7 0.9 - - - +
218E ILE* 3.4 10.2 - - - +
221E ARG* 5.4 0.9 - - - +
117F PHE* 3.8 24.5 - - + -
118F PRO 4.9 9.0 - - - +
120F SER* 4.9 4.9 - - - +
123F GLN* 6.0 0.7 - - - +
130F SER 5.8 2.5 - - - +
132F VAL* 4.0 38.6 - - + -
134F PHE* 4.5 10.5 - - + -
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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