Contacts of the strand formed by residues 134 - 143 (chain E) in PDB entry 3SKU
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 ARG 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E VAL* 2.7 38.3 + - - +
33E VAL* 3.6 7.9 - - + +
53E PHE* 3.5 47.0 - - + -
54E ALA* 3.1 35.6 - - - +
55E ASN 4.2 1.4 + - - +
125E GLU* 3.1 24.4 - - - +
126E PHE 3.3 13.5 + - - +
128E THR* 5.6 0.8 + - - +
132E GLY* 3.1 20.0 - - - +
133E ASN* 1.3 71.9 - - - +
135E GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 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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32E VAL* 5.4 2.8 - - - +
33E VAL* 3.0 18.8 + - - +
68E GLN* 5.8 0.2 - - - +
123E ILE* 4.0 22.9 - - + +
124E CYS 3.1 11.9 - - - +
125E GLU* 3.9 13.1 - - + +
133E ASN 5.1 4.3 - - - +
134E ARG* 1.3 77.5 - - - +
136E SER* 1.3 65.0 + - - +
137E GLN* 4.9 12.7 + - - +
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Residues in contact with SER 136 (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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32E VAL* 5.3 4.7 - - - -
33E VAL* 3.4 18.7 + - - +
35E VAL* 3.5 30.3 + - - +
123E ILE* 3.8 0.8 - - - -
124E CYS* 2.9 32.4 + - - +
135E GLU* 1.3 78.2 - - - +
137E GLN* 1.3 67.6 + - - +
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Residues in contact with GLN 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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35E VAL* 4.5 2.7 - - - +
36E ASN 3.7 7.4 - - - +
37E ASP* 4.1 4.3 - - - +
67E TRP* 6.4 0.2 - - - -
70E SER* 5.5 2.0 - - - -
121E VAL* 3.8 27.4 - - + +
122E TYR 3.0 13.7 - - - +
123E ILE* 4.0 23.8 - - + +
135E GLU* 4.9 10.8 + - - +
136E SER* 1.3 85.8 + - - +
138E LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 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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35E VAL* 4.0 15.7 - - + -
36E ASN* 3.0 32.8 - - + +
37E ASP 3.1 10.8 - - - +
39E MET* 3.6 29.2 - - + -
49E LEU* 3.8 28.9 - - + -
50E HIS 5.3 0.4 - - - +
67E TRP* 4.5 5.6 - - + -
121E VAL* 3.1 7.8 - - - -
122E TYR* 2.7 63.2 + - + +
137E GLN* 1.3 71.0 - - - +
139E ASN* 1.3 64.2 + - - +
140E LEU 4.3 1.6 - - - +
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Residues in contact with ASN 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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37E ASP 3.2 4.8 + - - -
38E SER* 4.2 12.3 - - - -
39E MET* 2.4 38.5 + - - +
40E TYR* 5.9 0.9 - - + -
120E GLY 3.6 4.7 - - - -
121E VAL* 2.8 26.8 - - - +
138E LEU* 1.3 74.4 - - - +
140E LEU* 1.3 60.4 + - - +
141E THR* 4.8 8.3 + - - +
1H NAG 1.4 68.2 + - - +
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Residues in contact with LEU 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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39E MET* 3.6 25.8 - - + +
40E TYR* 4.7 1.3 - - - +
41E GLY 5.0 2.5 - - - +
47E VAL* 4.7 15.7 - - + -
49E LEU* 4.7 14.1 - - + -
111E LEU* 4.1 11.4 - - + -
114E LEU* 4.0 17.5 - - + -
118E ASP* 3.4 38.4 - - + +
119E GLU* 3.1 3.7 - - - +
120E GLY 2.5 45.9 + - - +
122E TYR* 4.3 9.6 - - + -
138E LEU* 3.7 3.6 + - + +
139E ASN* 1.3 72.5 - - - +
141E THR* 1.3 68.5 + - - +
142E VAL* 4.0 4.3 - - + -
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Residues in contact with THR 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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39E MET 2.9 13.1 + - - +
40E TYR* 3.5 42.5 - - + +
41E GLY 3.5 4.2 + - - -
119E GLU* 4.0 8.3 - - + -
139E ASN* 3.8 8.7 + - - +
140E LEU* 1.3 76.4 - - - +
142E VAL* 1.3 75.2 + - - +
143E MET* 4.6 7.4 - - + +
178E LYS* 3.6 12.3 - - - +
179E PRO* 6.0 4.3 - - + -
231F HIS* 5.9 2.9 - - - +
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Residues in contact with VAL 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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41E GLY 3.6 3.6 - - - +
43E ILE* 3.9 15.5 - - + -
114E LEU* 3.5 26.9 - - + -
115E GLU 3.2 17.5 - - - +
116E LEU* 3.0 35.0 - - + +
118E ASP* 4.0 7.4 - - + -
119E GLU* 3.6 16.9 - - - +
140E LEU* 4.6 2.2 - - + -
141E THR* 1.3 80.4 - - - +
143E MET* 1.3 71.2 + - - +
178E LYS* 2.7 29.7 + - - +
179E PRO* 5.1 0.3 - - - +
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Residues in contact with MET 143 (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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40E TYR* 4.2 21.3 - - + -
41E GLY 3.2 7.9 + - - +
42E PHE* 3.2 63.2 - - + -
43E ILE* 3.3 13.3 + - - +
141E THR* 4.6 12.3 - - + +
142E VAL* 1.3 79.8 - - - +
144E ALA* 1.3 58.3 + - - +
178E LYS* 3.6 5.6 - - - -
179E PRO* 4.0 16.6 - - + -
230E TYR* 3.8 6.5 - - - +
231E HIS* 4.1 20.9 - - + +
40F TYR* 4.1 8.5 - - + +
231F HIS* 3.9 25.1 - - - -
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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