Contacts of the strand formed by residues 141 - 147 (chain E) in PDB entry 5LF0
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 GLY 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E LYS 5.0 0.4 - - - -
137E TYR* 3.5 17.4 - - - -
138E ASP 2.9 30.4 + - - -
139E ASP 3.3 2.6 + - - -
140E MET* 1.3 76.9 - - - +
142E PRO* 1.4 71.7 - - - +
143E HIS* 3.2 12.3 - - - -
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Residues in contact with PRO 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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39E LYS* 3.5 20.9 + - + +
40E SER 3.4 15.3 - - - +
41E LYS* 3.2 29.4 - - - +
42E THR 3.5 4.0 - - - -
43E HIS 3.5 37.0 - - - +
44E ALA* 4.0 4.3 - - + +
136E GLY 3.4 6.5 - - - +
137E TYR* 3.8 9.0 - - + -
140E MET 4.6 1.9 - - - +
141E GLY* 1.4 85.0 - - - +
143E HIS* 1.3 69.6 + - - +
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Residues in contact with HIS 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LYS* 4.2 7.0 + - - +
44E ALA* 3.4 6.9 - - - +
105E VAL* 3.9 17.9 - - + +
106E SER* 5.6 3.8 + - - -
134E ILE 4.0 0.7 - - - -
135E ALA* 3.4 6.4 - - - -
136E GLY 2.8 32.8 + - - +
138E ASP* 2.8 36.7 + - - -
140E MET* 3.8 23.3 - - + +
141E GLY 3.2 18.9 + - - -
142E PRO* 1.3 81.1 + - - +
144E ILE* 1.3 64.3 + - - +
145E PHE* 3.5 32.4 - + + -
155E ASP* 4.9 6.8 + - - +
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Residues in contact with ILE 144 (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 GLY* 4.0 20.9 - - - +
38E LEU* 3.5 43.1 - - - +
39E LYS* 4.0 11.3 - - + +
44E ALA* 3.9 9.2 - - + -
45E VAL 3.7 9.4 - - - +
46E LEU* 4.5 2.5 - - + -
133E LEU* 5.3 3.4 - - + -
134E ILE 3.3 4.5 - - - +
135E ALA* 4.3 10.1 - - + -
143E HIS* 1.3 81.5 - - - +
145E PHE* 1.3 68.7 + - - +
155E ASP* 3.8 3.9 + - - +
156E CYS* 2.8 54.6 + - + +
157E ARG 4.7 0.4 - - - +
159E MET* 4.7 7.2 - - + +
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Residues in contact with PHE 145 (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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105E VAL* 3.7 26.2 - - + -
106E SER* 4.1 24.9 - - - -
109E VAL* 3.6 36.8 - - + -
132E LEU 3.7 0.2 - - - +
133E LEU* 3.2 6.9 - - - +
134E ILE* 2.7 44.9 + - + -
143E HIS* 3.5 30.7 - + + -
144E ILE* 1.3 79.3 - - - +
146E GLN* 1.3 61.8 + - - +
153E TYR* 4.8 7.2 - + - -
154E PHE 3.2 20.9 - - - -
155E ASP* 3.5 33.9 - - + -
156E CYS* 4.6 0.4 - - - -
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Residues in contact with GLN 146 (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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132E LEU 3.2 5.2 - - - +
133E LEU* 3.8 17.5 - - + -
145E PHE* 1.3 74.5 - - - +
147E THR* 1.3 71.7 + - - +
148E 6V1 3.4 32.7 + - - -
153E TYR* 3.1 6.6 - - - +
154E PHE* 2.8 42.2 + - + +
156E CYS* 4.0 11.0 - - - -
159E MET* 3.5 24.8 - - + +
161E ILE* 3.3 24.6 - - + +
58F TYR* 3.7 21.8 + - - -
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Residues in contact with THR 147 (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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84E LEU* 5.0 2.4 - - - +
109E VAL* 4.5 6.1 - - + +
112E ILE* 4.1 26.4 - - + +
130E VAL 4.9 0.9 + - - -
131E GLY* 3.2 6.2 - - - -
132E LEU* 2.9 51.4 + - - +
134E ILE* 3.6 26.7 - - + -
146E GLN* 1.3 82.3 - - - +
148E 6V1 1.3 66.9 + - - +
152E ASN 3.7 6.3 - - - -
153E TYR* 4.1 12.1 - - + -
161E ILE* 5.5 0.2 - - - +
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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