Contacts of the strand formed by residues 134 - 142 (chain E) in PDB entry 3SDI
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 VAL 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E ILE* 3.8 5.6 - - - -
78E LEU* 4.2 2.5 - - + -
79E ALA 3.7 21.5 - - - +
80E GLY* 4.1 1.1 - - - +
81E LEU 3.3 24.2 - - - +
84E ASP* 3.8 18.2 - - + -
85E ALA* 4.0 17.3 - - + +
88E LEU* 3.8 28.0 - - + -
132E TYR* 3.5 3.2 - - + -
133E GLY* 1.3 77.0 - - - +
135E GLY* 1.3 69.8 + - - +
136E LEU* 4.2 6.7 - - + -
151E PHE* 3.5 8.3 - - - -
153E PRO* 3.1 20.7 - - - +
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Residues in contact with GLY 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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31E ILE* 3.5 14.0 - - - +
78E LEU* 3.4 3.8 - - - -
79E ALA 2.7 39.5 + - - -
134E VAL* 1.3 74.9 - - - +
136E LEU* 1.3 63.0 + - - +
151E PHE 3.4 12.1 - - - -
152E GLN* 5.2 0.2 - - - -
165E ILE* 3.5 13.2 - - - +
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Residues in contact with LEU 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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76E LEU* 3.9 32.8 - - + -
77E SER 3.2 11.4 - - - +
78E LEU* 4.0 15.5 - - + -
85E ALA* 4.1 17.7 - - + -
88E LEU* 3.9 25.8 - - + -
116E LEU* 4.5 10.8 - - + -
134E VAL* 4.2 8.1 - - + -
135E GLY* 1.3 83.9 - - - +
137E LEU* 1.3 68.4 + - - +
138E ILE* 4.1 4.8 + - + +
151E PHE* 2.8 60.2 + - + +
165E ILE* 3.8 0.4 - - - +
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Residues in contact with LEU 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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37E THR 3.8 15.0 - - - +
38E VAL 3.7 7.9 - - - -
39E GLY* 3.5 28.9 - - - +
48E LEU* 3.7 11.8 - - + +
76E LEU* 3.0 3.3 - - - -
77E SER* 2.8 50.6 + - - +
136E LEU* 1.3 80.8 - - - +
138E ILE* 1.3 61.6 + - - +
148E LEU* 4.3 3.4 - - + -
149E LEU 3.3 3.8 - - - +
150E GLU* 3.7 25.6 - - + -
163E THR* 3.7 21.5 - - + +
164E ALA* 4.5 0.2 - - - -
165E ILE* 3.8 20.6 - - + -
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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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74E MET* 4.0 26.9 - - + -
75E GLY 3.4 14.4 - - - +
76E LEU* 3.9 15.7 - - + -
92E LEU* 4.7 6.3 - - + -
109E VAL* 4.5 10.6 - - + +
112E ALA* 5.6 1.8 - - + -
113E GLY* 5.3 2.5 - - - +
116E LEU* 3.6 30.1 - - + -
136E LEU* 4.6 3.4 - - + +
137E LEU* 1.3 76.8 - - - +
139E ILE* 1.3 64.1 + - - +
147E HIS 3.8 0.5 - - - +
148E LEU* 3.2 5.8 - - - +
149E LEU* 2.7 62.9 + - + +
151E PHE* 4.4 17.7 - - + -
157E VAL* 5.4 0.9 - - + -
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Residues in contact with ILE 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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40E LEU 5.0 0.4 - - - +
46E ALA* 3.5 40.2 - - + +
47E VAL 4.2 7.9 - - - +
48E LEU* 3.7 28.7 - - + -
74E MET* 3.3 6.7 - - - +
75E GLY 2.9 40.4 + - - +
109E VAL* 4.8 1.3 - - - -
138E ILE* 1.3 79.9 - - - +
140E GLY* 1.3 58.7 - - - +
147E HIS 3.3 4.3 - - - +
148E LEU* 3.8 19.5 - - + -
213E ALA 4.2 9.4 - - - +
215E VAL* 3.8 9.3 - - + +
221E PHE* 3.6 27.6 - - + -
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Residues in contact with GLY 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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46E ALA* 4.7 0.3 - - - +
73E HIS 3.0 14.1 - - - -
74E MET* 4.2 0.7 - - - -
109E VAL* 3.8 16.5 - - - +
139E ILE* 1.3 78.2 - - - +
141E TYR* 1.3 61.5 + - - -
142E ASP 4.0 0.7 - - - -
145E GLY 3.6 1.0 - - - +
146E ALA* 3.5 3.3 - - - +
147E HIS* 2.9 32.8 + - - +
215E VAL* 3.7 10.7 - - - +
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Residues in contact with TYR 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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43E ASN 4.1 10.1 + - - -
44E THR* 3.6 20.8 - - - -
73E HIS* 3.1 29.9 + - + +
106E LYS* 5.7 1.2 - - - +
140E GLY* 1.3 73.0 - - - -
142E ASP* 1.3 70.7 + - - +
145E GLY* 3.4 31.5 - - - -
146E ALA* 3.5 9.6 - - + -
215E VAL* 3.9 6.3 - - + +
216E GLY* 3.7 24.5 - - - +
217E LYS* 3.6 50.3 + - + +
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Residues in contact with ASP 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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73E HIS* 4.4 9.2 - - + +
106E LYS* 5.5 7.0 - - + +
107E LEU 4.4 1.3 - - - +
108E ALA* 3.5 17.7 - - - +
109E VAL* 2.9 31.5 + - + +
110E GLU* 4.5 0.9 + - - +
140E GLY 4.0 0.4 - - - -
141E TYR* 1.3 88.4 - - - +
143E LYS* 1.3 60.4 + - - +
144E SER* 3.0 20.0 + - - -
145E GLY 3.1 13.0 + - - +
147E HIS* 2.9 34.7 + - - -
76M GLU* 4.4 4.5 - - - +
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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