Contacts of the strand formed by residues 130 - 138 (chain E) in PDB entry 5LEZ
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 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.1 4.7 - - - -
75E ALA 3.5 16.6 - - - +
76E GLY 5.0 0.2 - - - -
77E LEU 4.2 5.4 - - - +
80E ASP* 4.1 18.8 - - + +
81E ALA* 3.7 33.2 - - + +
84E LEU* 3.7 30.7 - - + +
128E TYR* 3.3 12.3 + - + +
129E GLY* 1.3 78.6 - - - +
131E GLY* 1.3 69.6 + - - +
132E LEU* 4.1 7.0 - - + -
147E THR* 4.4 1.6 + - - +
148E 6V1 4.0 3.5 + - - +
149E PRO* 3.4 18.1 - - - +
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Residues in contact with GLY 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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29E VAL* 3.8 15.6 - - - +
74E ILE* 3.7 0.5 - - - -
75E ALA 2.9 34.8 + - - -
130E VAL* 1.3 75.3 - - - +
132E LEU* 1.3 67.1 + - - +
147E THR* 3.2 13.9 - - - -
148E 6V1 5.0 0.9 - - - -
149E PRO* 4.6 1.1 - - - -
161E ILE* 3.9 11.3 - - - +
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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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72E ILE* 4.0 12.1 - - + -
73E SER 3.3 4.5 - - - +
74E ILE* 3.6 28.3 - - + -
81E ALA* 5.1 3.6 - - + +
84E LEU* 4.1 21.3 - - + -
88E MET* 3.8 28.7 - - - -
112E ILE* 4.6 2.7 - - + -
130E VAL* 4.1 12.8 - - + -
131E GLY* 1.3 83.1 - - - +
133E LEU* 1.3 67.4 + - - +
134E ILE* 4.0 18.3 - - + +
146E GLN* 3.1 8.0 - - - +
147E THR* 2.9 45.9 + - - +
161E ILE* 4.2 1.6 - - - -
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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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35E THR* 3.7 29.2 - - + +
36E VAL 3.9 2.5 - - - -
37E GLY* 3.6 28.5 - - - +
46E LEU* 3.8 16.3 - - + +
72E ILE* 3.3 4.9 - - - +
73E SER* 2.8 36.8 + - - +
132E LEU* 1.3 80.6 - - - +
134E ILE* 1.3 60.1 + - - +
144E ILE* 5.1 3.6 - - + -
145E PHE 3.3 4.0 - - - +
146E GLN* 3.9 15.3 - - + -
159E MET* 3.8 33.7 - - + +
161E ILE* 4.0 15.9 - - + +
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Residues in contact with ILE 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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46E LEU* 4.6 2.0 - - - -
70E ILE* 3.9 25.6 - - + -
71E GLY 3.5 4.0 - - - +
72E ILE* 3.9 12.3 - - + -
88E MET* 3.9 7.0 - - + -
105E VAL* 4.3 18.8 - - + +
108E LEU* 5.5 1.3 - - + -
109E VAL* 4.0 13.7 - - + -
112E ILE* 3.8 20.9 - - + -
132E LEU* 4.0 10.1 - - + -
133E LEU* 1.3 76.1 - - - +
135E ALA* 1.3 60.4 + - - +
143E HIS 3.5 1.4 - - - +
144E ILE* 3.2 6.5 - - - -
145E PHE* 2.7 42.5 + - + +
147E THR* 3.7 28.7 - - + -
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Residues in contact with ALA 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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44E ALA* 3.8 23.1 - - + +
46E LEU* 3.7 27.8 - - + +
70E ILE* 3.3 4.9 - - - +
71E GLY 2.9 33.7 + - - +
133E LEU 4.1 1.2 + - - -
134E ILE* 1.3 75.7 - - - +
136E GLY* 1.3 58.8 + - - +
143E HIS 3.3 5.4 - - - -
144E ILE* 3.9 5.8 - - + -
215E VAL* 4.0 10.2 - - + +
221E PHE* 4.5 5.2 - - + -
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Residues in contact with GLY 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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44E ALA* 4.0 3.6 - - - +
69E HIS 3.1 12.1 - - - -
70E ILE* 4.4 0.7 - - - -
105E VAL* 3.9 19.4 - - - +
134E ILE 4.2 0.2 + - - -
135E ALA* 1.3 76.2 - - - +
137E TYR* 1.3 58.9 + - - +
142E PRO* 3.3 3.8 - - - +
143E HIS* 2.7 36.4 + - - +
215E VAL* 3.8 7.3 - - - +
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Residues in contact with TYR 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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41E LYS 5.1 1.9 + - - -
42E THR* 3.6 19.1 - - - -
69E HIS* 3.1 33.5 + - + +
105E VAL* 4.1 1.4 - - - +
136E GLY* 1.3 74.3 - - - +
138E ASP* 1.3 73.2 + - - +
141E GLY* 3.5 12.4 - - - -
142E PRO* 3.4 36.1 - - + -
215E VAL* 4.1 19.0 - - + +
216E GLY* 3.9 10.5 - - - +
217E LYS* 3.6 45.6 - - + +
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Residues in contact with ASP 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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69E HIS* 4.7 4.9 - - + -
102E PRO* 6.0 2.9 - - + -
104E PRO* 3.7 14.9 - - + +
105E VAL* 2.9 33.8 + - + +
106E SER* 4.5 2.1 + - - -
137E TYR* 1.3 89.7 - - - +
139E ASP* 1.3 61.5 + - - +
140E MET* 3.0 14.3 + - - +
141E GLY* 2.9 20.9 + - - -
143E HIS* 2.7 31.7 + - - -
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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