Contacts of the strand formed by residues 43 - 51 (chain L) in PDB entry 3E8E
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 PHE 43 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L ALA* 4.1 9.4 - - + -
39L HIS 3.4 27.8 - - - -
40L LEU* 3.3 15.7 + - + +
41L ASP* 3.0 5.9 - - - +
42L GLN* 1.3 80.5 - - + +
44L GLU* 1.3 60.9 + - - +
45L ARG* 3.9 10.6 + - + -
60L VAL* 3.4 29.8 - - + -
61L LYS 3.4 1.8 - - - -
62L HIS* 3.2 39.5 - + + -
63L MET* 4.4 6.8 - - - +
69L TYR* 4.3 3.8 - + - -
71L MET* 3.4 26.2 - - + -
108L PHE* 3.9 23.1 - + - -
110L PHE* 3.9 12.1 - + - -
119L VAL* 3.9 18.8 - - + -
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L PHE* 1.3 71.4 - - - +
45L ARG* 1.3 68.5 + - - +
46L ILE* 3.5 9.6 + - + +
60L VAL* 3.3 6.9 - - - -
61L LYS* 2.8 76.3 + - + +
63L MET* 3.5 28.6 - - + +
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Residues in contact with ARG 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L LEU* 4.6 24.2 - - + +
43L PHE* 4.4 10.8 - - + +
44L GLU* 1.3 76.6 - - - +
46L ILE* 1.3 63.1 + - - +
58L MET* 3.9 23.5 - - - +
59L LEU 4.2 0.4 - - - -
60L VAL* 4.1 17.7 - - + -
71L MET* 5.5 1.8 - - - -
73L ILE* 4.7 3.2 - - + +
333L GLU 5.0 1.0 + - - -
334L GLU* 4.0 16.8 + - - +
335L ILE* 3.3 54.0 + - - +
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Residues in contact with ILE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L GLU* 3.8 18.2 - - + +
45L ARG* 1.3 74.8 - - - +
47L LYS* 1.3 70.5 + - + +
58L MET* 5.7 0.2 - - - -
59L LEU* 3.1 29.3 + - + +
60L VAL 4.2 2.7 - - - -
61L LYS* 3.9 19.5 - - + -
68L HIS* 3.5 36.3 - - + +
322L GLY 5.6 0.9 - - - +
324L THR* 5.7 0.7 - - + -
332L GLU* 4.2 7.4 - - - +
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Residues in contact with LYS 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ARG 4.0 0.4 - - - -
46L ILE* 1.3 89.9 - - + +
48L THR* 1.3 71.2 + - - +
49L LEU* 5.1 2.0 - - + +
58L MET* 3.1 9.8 - - - +
59L LEU* 2.7 33.1 + - + +
324L THR* 3.4 37.2 + - + +
327L PHE* 4.6 4.2 + - - +
328L ASP 3.2 20.2 + - - -
329L ASP* 2.9 35.1 + - - +
330L TYR 4.6 1.0 - - - +
332L GLU* 3.7 15.4 + - - +
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Residues in contact with THR 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L LYS* 1.3 88.3 + - - +
49L LEU* 1.3 61.1 + - - +
50L GLY 3.5 21.5 - - - +
51L THR* 5.3 0.9 - - - -
56L ARG* 3.4 33.3 + - + +
57L VAL 3.6 7.2 - - - +
58L MET* 3.6 10.5 - - - +
328L ASP 4.1 0.3 - - - +
330L TYR* 3.6 36.7 + - + -
332L GLU* 2.7 29.2 + - - +
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Residues in contact with LEU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L LYS* 3.6 4.2 + - + +
48L THR* 1.3 75.1 - - - +
50L GLY* 1.3 58.0 + - - +
57L VAL* 2.8 13.3 + - + +
58L MET 3.8 5.2 - - - +
59L LEU* 3.4 31.4 - - + +
70L ALA* 4.6 1.8 - - + -
122L TYR* 3.3 31.6 - - + +
127L GLU* 5.6 0.7 - - - +
324L THR* 3.9 27.8 - - + -
327L PHE* 3.8 37.0 - - + +
328L ASP 5.2 0.2 + - - -
330L TYR* 3.2 18.3 + - - -
351L G98 3.5 30.8 - - + +
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Residues in contact with GLY 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L THR* 3.5 8.5 - - - +
49L LEU* 1.3 81.7 - - - +
51L THR* 1.3 59.9 + - - -
56L ARG* 3.3 8.0 - - - +
57L VAL* 3.0 31.4 + - - +
330L TYR* 3.8 13.0 - - - -
351L G98 4.0 16.5 - - - +
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Residues in contact with THR 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L THR* 5.5 0.7 - - - -
50L GLY* 1.3 74.8 - - - -
52L GLY* 1.3 68.6 + - - +
55L GLY 3.8 5.0 + - - -
56L ARG* 4.5 8.1 + - - +
330L TYR* 3.7 32.5 - - + -
351L G98 3.4 25.4 - - - +
20N ASN* 5.3 6.2 - - - +
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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