Contacts of the strand formed by residues 134 - 142 (chain E) in PDB entry 3U8M
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 ALA 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124E ASP 3.8 6.7 - - - +
125E VAL* 3.4 22.9 - - - +
126E SER 3.2 22.0 - - - +
127E GLY 3.5 2.2 + - - -
128E VAL* 3.6 11.8 - - + +
133E GLY* 1.3 74.0 - - - -
135E THR* 1.3 58.2 + - - +
136E CYS 4.0 0.4 - - - -
199E LEU 3.6 0.7 - - - +
200E ASN* 2.7 22.6 + - - -
201E PHE* 2.9 33.7 + - + -
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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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124E ASP* 3.4 24.0 + - - +
126E SER 4.7 0.4 + - - -
133E GLY 5.0 0.5 + - - -
134E ALA* 1.3 71.0 - - - +
136E CYS* 1.3 61.9 + - - +
137E ARG* 3.8 5.9 + - + +
198E SER* 3.9 28.5 - - - +
199E LEU 3.3 8.1 - - - +
200E ASN* 3.1 25.3 + - + +
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Residues in contact with CYS 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E VAL* 3.9 14.4 - - + -
50E VAL* 6.0 0.2 - - - -
121E PHE* 5.0 0.2 - - - -
123E CYS* 2.0 47.8 - - - -
124E ASP 4.0 5.8 - - - +
134E ALA 4.0 0.4 - - - -
135E THR* 1.3 70.7 - - - +
137E ARG* 1.3 63.2 + - - +
138E ILE* 3.8 14.4 + - - +
197E VAL 3.4 2.6 - - - +
198E SER* 4.5 0.7 - - - -
199E LEU* 2.7 49.0 + - + +
201E PHE* 4.0 18.8 - - + -
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Residues in contact with ARG 137 (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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167A GLN* 3.8 10.5 + - - -
168A TYR* 3.2 40.5 + - + -
90E ASN* 2.9 22.0 + - - -
123E CYS* 3.9 9.0 - - + +
124E ASP* 5.2 0.8 - - - +
135E THR* 3.8 6.4 + - + +
136E CYS* 1.3 73.1 - - - +
138E ILE* 1.3 63.2 + - - +
139E LYS* 4.2 2.2 - - + +
196E GLU* 3.3 47.2 + - + -
197E VAL 3.4 3.8 - - - +
198E SER* 3.8 20.0 - - - +
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Residues in contact with ILE 138 (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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33E LEU* 4.3 15.5 - - + -
35E PHE* 4.3 28.5 - - + -
50E VAL* 5.2 3.6 - - + -
52E PHE* 5.6 0.7 - - + -
88E ALA* 4.5 1.3 - - + -
90E ASN* 3.8 3.6 - - - +
121E PHE* 3.7 57.2 - - + -
136E CYS* 4.5 14.6 - - - +
137E ARG* 1.3 77.4 - - - +
139E LYS* 1.3 60.8 + - - +
140E ILE* 3.9 20.5 + - + -
195E VAL 3.5 1.9 - - - +
196E GLU* 3.4 3.8 - - - -
197E VAL* 2.9 43.9 + - - +
199E LEU* 5.6 2.0 - - + -
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Residues in contact with LYS 139 (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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88E ALA* 3.2 4.5 - - - -
89E TYR* 2.7 68.1 + - + -
90E ASN* 3.2 11.3 + - - +
137E ARG* 4.2 2.6 + - + +
138E ILE* 1.3 70.6 - - - +
140E ILE* 1.3 61.3 + - - +
183E VAL* 4.8 5.6 - - - +
185E TYR* 2.8 36.2 + - - -
194E ASP* 3.4 34.2 + - - +
195E VAL 3.5 4.0 - - - -
196E GLU* 4.1 18.6 - - + +
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Residues in contact with ILE 140 (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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31E VAL* 4.4 15.8 - - + +
33E LEU* 3.9 39.3 - - + -
52E PHE* 5.3 2.0 - - + -
54E GLN* 4.0 15.9 - - - +
86E LEU* 4.1 28.5 - - + -
87E ALA 3.3 10.5 - - - +
88E ALA* 4.2 11.2 - - + -
89E TYR* 4.6 0.2 - - - -
121E PHE* 6.4 0.2 - - + -
138E ILE* 4.0 13.7 - - + +
139E LYS* 1.3 80.0 - - - +
141E GLY* 1.3 60.3 + - - +
152E VAL* 4.6 2.1 - - - +
194E ASP* 3.1 4.3 - - - -
195E VAL* 2.7 44.2 + - + +
197E VAL* 5.3 3.8 - - + -
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Residues in contact with GLY 141 (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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86E LEU* 3.3 10.7 - - - -
87E ALA* 3.0 29.1 + - - +
89E TYR* 3.9 12.2 - - - -
140E ILE* 1.3 77.2 - - - +
142E SER* 1.3 68.5 + - - -
143E TRP* 3.4 0.7 + - - -
152E VAL* 4.6 3.6 - - - -
193E GLU 3.5 15.9 - - - -
194E ASP* 4.1 1.8 - - - -
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Residues in contact with SER 142 (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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85E ASP* 2.7 27.6 + - - -
86E LEU* 3.8 7.6 - - - +
89E TYR* 3.5 14.6 + - - -
141E GLY* 1.3 73.4 - - - -
143E TRP* 1.3 61.8 + - - +
145E HIS* 3.0 38.5 + - - +
150E ILE* 4.2 21.1 - - - -
152E VAL* 4.6 3.2 - - - +
192E TYR* 4.4 10.3 - - - +
193E GLU 3.8 7.7 + - - +
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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