Contacts of the strand formed by residues 130 - 135 (chain E) in PDB entry 4PJ7
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 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E GLN* 4.0 20.2 - - - -
123E ASP* 4.2 11.4 - - - -
128E ASP 5.2 0.9 - - - -
129E LYS* 1.3 72.3 - - - +
131E VAL* 1.3 62.2 + - - +
174E TRP* 3.2 26.2 - - - +
175E SER 2.8 19.2 + - - -
176E ASN* 5.2 0.3 - - - -
177E LYS 5.0 1.9 + - - -
180E PHE* 3.2 31.9 + - - +
126F PHE* 5.9 0.2 - - - -
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Residues in contact with VAL 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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120E GLN* 3.7 8.8 - - - +
121E LEU* 3.0 39.0 + - + +
123E ASP* 5.2 0.2 + - - -
129E LYS* 4.6 0.9 - - + -
130E SER* 1.3 81.8 - - - +
132E CYS* 1.3 66.8 + - - +
172E VAL* 3.8 26.5 - - + -
173E ALA 3.5 3.4 - - - +
174E TRP* 4.0 2.9 - - + -
126F PHE* 3.6 47.5 - - + -
142F VAL* 4.0 20.6 - - + -
144F LEU* 3.8 12.8 - - + -
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Residues in contact with CYS 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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118E VAL* 4.4 1.1 - - + -
119E TYR 3.3 4.9 - - - +
120E GLN* 4.8 2.5 - - - -
131E VAL* 1.3 76.5 - - - +
133E LEU* 1.3 60.6 + - - +
172E VAL* 3.6 4.2 - - - +
173E ALA* 2.8 35.8 + - + +
180E PHE* 3.5 24.9 - - - -
181E ALA 4.2 0.2 - - - -
182E CYS* 2.0 56.1 - - + -
185E ALA* 4.1 14.4 - - + -
186E PHE* 3.8 8.4 - - + -
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Residues in contact with LEU 133 (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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117E ALA 3.5 2.1 - - - +
118E VAL* 3.2 4.0 - - - -
119E TYR* 2.8 44.6 + - + +
121E LEU* 3.6 23.7 - - + +
132E CYS* 1.3 73.4 - - - +
134E PHE* 1.3 58.4 + - - +
135E THR* 3.9 22.3 + - + +
170E SER* 4.1 18.8 - - - -
171E ALA 3.7 7.4 - - - +
172E VAL* 3.8 24.9 - - + -
186E PHE* 4.4 1.1 - - - -
132F GLU* 4.5 7.4 - - - +
140F THR* 3.8 31.2 - - + +
142F VAL* 4.3 9.4 - - + -
191F ARG* 4.4 6.3 - - + -
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Residues in contact with PHE 134 (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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116E PRO* 4.2 7.0 - - + -
117E ALA 3.4 12.1 - - - -
118E VAL* 3.6 13.0 - - + -
133E LEU* 1.3 69.1 - - - +
135E THR* 1.3 60.6 + - - +
137E PHE* 3.4 47.3 - + + -
141E THR* 4.8 4.0 - - - -
142E ASN 5.6 1.3 - - - -
143E VAL* 4.2 17.5 - - + -
170E SER* 3.3 4.2 - - - -
171E ALA* 2.9 34.9 + - + +
186E PHE* 3.6 34.4 - + + -
189E SER* 5.8 0.7 - - - -
191E ILE* 3.7 30.1 - - + -
192E PRO* 3.9 15.0 - - + -
195E THR* 4.1 20.4 - - + -
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Residues in contact with THR 135 (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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116E PRO* 3.4 1.2 - - - +
117E ALA* 2.9 32.4 + - + +
119E TYR* 3.5 38.1 - - + -
133E LEU* 4.1 18.5 - - + +
134E PHE* 1.3 76.2 - - - +
136E ASP* 1.3 82.3 + - - +
137E PHE* 3.2 13.5 + - - -
168E SER* 4.4 1.6 + - - -
169E ASN 3.4 13.0 + - - -
170E SER* 3.9 6.6 - - - -
132F GLU* 5.3 0.2 - - - +
140F THR* 5.3 0.9 + - - +
193F ARG* 3.9 13.4 + - - +
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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