Contacts of the strand formed by residues 43 - 49 (chain E) in PDB entry 5LF4
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 HIS 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E LYS* 3.2 5.0 - - - +
40E SER* 2.9 34.8 + - - +
42E THR* 1.4 104.1 + - - +
44E ALA* 1.3 63.1 + - - +
142E PRO* 3.6 7.5 - - - +
183E ASN 5.7 0.2 - - - -
184E LEU* 3.8 51.9 + - + +
187E LEU* 3.8 6.7 - - + +
214E ILE* 4.2 5.8 - - + -
215E VAL 3.4 8.7 - - - +
216E GLY* 3.7 20.0 - - - -
218E ASP* 3.5 23.4 + - - -
219E LEU* 4.6 6.4 - - + +
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Residues in contact with ALA 44 (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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38E LEU 3.6 4.3 - - - -
39E LYS* 4.2 1.3 - - + -
43E HIS* 1.3 74.0 - - - +
45E VAL* 1.3 60.5 + - - +
135E ALA* 3.8 15.2 - - + +
136E GLY 3.8 15.5 - - - +
142E PRO* 4.0 6.0 - - + +
143E HIS 3.4 25.6 - - - +
144E ILE* 4.0 4.7 - - + -
213E GLY 4.0 0.2 - - - +
214E ILE* 3.6 2.4 - - - +
215E VAL* 2.8 37.3 + - + +
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Residues in contact with VAL 45 (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* 3.2 4.0 - - - -
38E LEU* 2.8 51.0 + - + +
44E ALA* 1.3 78.5 - - - +
46E LEU* 1.3 80.0 + - - +
47E VAL* 3.8 14.8 - - + -
144E ILE* 3.8 2.8 - - - +
184E LEU* 4.0 12.3 - - + -
187E LEU* 3.8 19.3 - - + -
188E VAL* 3.8 32.5 - - + -
212E ILE* 4.4 3.8 - - + -
213E GLY 3.3 5.8 - - - +
214E ILE* 4.1 6.5 - - + -
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Residues in contact with LEU 46 (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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36E VAL 3.3 3.4 - - - +
37E GLY* 4.0 10.1 - - - -
45E VAL* 1.3 81.4 - - - +
47E VAL* 1.3 70.6 + - - +
63E ILE* 4.3 14.1 - - + -
71E GLY 3.8 18.2 - - - +
72E ILE* 3.6 32.3 - - - +
73E SER* 3.6 7.9 - - - +
133E LEU* 3.9 30.5 - - + +
135E ALA* 3.7 19.5 - - + +
144E ILE* 4.4 3.4 - - + -
212E ILE* 3.4 1.7 - - - -
213E GLY 2.7 35.3 + - - +
221E PHE* 4.2 10.5 - - + -
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Residues in contact with VAL 47 (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* 2.8 5.1 + - - -
36E VAL* 2.7 41.9 + - + +
38E LEU* 5.3 0.4 - - + -
45E VAL* 3.8 15.9 - - + -
46E LEU* 1.3 81.2 - - - +
48E ALA* 1.3 63.7 + - - +
63E ILE* 4.6 0.4 - - - -
188E VAL* 4.5 4.3 - - + +
191E GLY* 4.1 25.6 - - - +
192E LEU* 3.5 26.2 - - + +
195E LEU* 3.3 27.9 - - + +
210E VAL* 4.4 1.8 - - + -
211E SER 3.4 9.0 - - - +
212E ILE* 4.4 7.9 - - + -
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Residues in contact with ALA 48 (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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34E ALA 3.9 3.6 - - - -
35E THR* 3.8 5.4 - - - +
47E VAL* 1.3 76.0 - - - +
49E LEU* 1.3 61.8 + - - +
50E LYS 3.7 0.5 + - - -
62E LYS* 3.6 31.2 - - + -
63E ILE* 4.0 10.3 - - + -
73E SER* 3.8 14.1 - - - +
195E LEU* 3.8 5.8 - - - +
209E ASN 3.5 2.4 - - - +
210E VAL* 3.5 3.1 - - - -
211E SER* 2.8 37.4 + - - +
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Residues in contact with LEU 49 (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 SER* 2.7 35.7 + - - -
34E ALA* 3.1 19.6 + - + +
48E ALA* 1.3 71.8 - - - +
50E LYS* 1.3 59.0 + - - +
62E LYS* 2.9 8.2 - - - +
164E ARG* 6.3 0.9 - - - +
195E LEU* 3.7 19.4 - - + +
198E THR* 3.4 25.6 - - - +
199E LEU* 3.7 23.6 - - + -
203E GLN* 5.8 0.2 - - - +
205E LEU* 4.1 20.0 - - + -
209E ASN* 3.3 33.0 - - + +
210E VAL* 4.6 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