Contacts of the strand formed by residues 58 - 64 (chain E) in PDB entry 5X6E
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 MET 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E THR* 3.5 3.6 - - - -
50E SER* 2.9 41.7 + - - +
56E THR 4.6 1.8 - - - +
57E ILE* 1.3 77.2 - - - +
59E ASN* 1.3 76.3 + - - +
60E LEU* 3.7 13.4 + - + -
175E GLY 5.4 0.2 - - - +
176E TYR* 3.7 3.1 - - - +
178E SER 3.4 28.5 - - - +
179E GLY* 4.6 2.9 - - - -
131F PHE* 4.3 23.3 - - + +
132F ASN* 3.2 29.2 - - - +
135F SER* 3.6 32.3 - - - +
136F ILE* 4.4 14.6 - - + -
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Residues in contact with ASN 59 (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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47E LYS* 3.3 41.0 + - + +
48E LEU 4.0 4.5 - - - +
49E THR* 4.2 7.6 - - - +
57E ILE* 3.7 11.3 - - - +
58E MET* 1.3 80.4 - - - +
60E LEU* 1.3 65.2 + - - +
61E GLN 3.6 1.1 - - - +
62E TYR* 4.0 15.8 + - + -
173E GLU* 4.0 7.5 + - - +
176E TYR* 2.8 49.0 + - - +
177E SER* 3.5 22.6 + - - +
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Residues in contact with LEU 60 (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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48E LEU* 3.0 34.2 + - + +
50E SER* 4.7 4.9 - - - -
58E MET* 3.8 26.5 - - + +
59E ASN* 1.3 72.5 - - - +
61E GLN* 1.3 56.6 + - - +
83E TYR* 3.5 40.6 - - + +
130E LYS* 2.7 29.6 + - - +
128F LEU* 3.9 27.1 - - + +
131F PHE* 3.4 24.9 - - + -
132F ASN* 4.0 17.3 - - + -
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Residues in contact with GLN 61 (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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47E LYS* 3.4 1.4 - - - +
48E LEU* 2.7 35.6 + - + +
59E ASN* 3.6 2.4 - - - +
60E LEU* 1.3 85.9 - - + +
62E TYR* 1.3 78.7 + - - +
63E TYR* 2.6 28.9 + - + +
123E GLN* 2.5 27.3 + - - +
126E TYR* 3.2 21.3 - - + -
130E LYS* 4.1 3.8 - - - +
146E GLN* 6.2 0.2 - - - +
301E GSH 3.1 50.1 - - - +
128F LEU* 4.9 4.7 - - + +
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Residues in contact with TYR 62 (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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45E ILE* 4.7 3.4 - - + -
46E THR 3.4 4.3 - - - +
47E LYS* 3.5 25.8 - - + -
59E ASN* 4.0 12.2 + - + -
61E GLN* 1.3 85.5 - - - +
63E TYR* 1.3 62.6 + - - +
88E ILE* 3.7 18.2 - - + -
146E GLN* 5.0 4.0 - - - +
150E LEU* 4.1 14.8 - - + -
154E TYR* 3.5 29.2 - + - +
166E LEU* 4.3 15.7 - - + -
169E LEU* 4.2 11.8 - - + +
173E GLU* 2.8 24.3 + - - -
177E SER* 3.5 24.9 + - - -
301E GSH 2.9 49.0 + - - +
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Residues in contact with TYR 63 (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 LEU* 3.8 12.6 - - + +
45E ILE* 3.3 5.5 - - - +
46E THR* 2.4 62.6 + - + +
48E LEU* 3.6 35.4 - - + +
61E GLN* 2.6 35.0 + - + -
62E TYR* 1.3 72.1 - - - +
64E LYS* 1.3 60.5 + - - +
67E PHE* 3.8 23.6 - + + -
68E VAL 4.7 0.4 - - - -
69E ILE* 3.6 37.1 - - + +
85E LEU* 4.0 15.0 - - + -
123E GLN* 3.1 25.6 + - - -
154E TYR* 4.6 0.7 - - - -
301E GSH 3.6 5.2 - - - -
128F LEU* 5.1 1.6 - - - +
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Residues in contact with LYS 64 (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 LEU* 4.2 1.3 - - - +
44E GLY 3.7 3.4 - - - -
45E ILE* 4.4 11.2 - - + +
63E TYR* 1.3 76.2 - - - +
65E GLY* 1.3 73.8 + - - +
66E ALA 4.1 1.2 - - - -
67E PHE* 4.2 1.6 - - - +
153E VAL* 3.1 41.9 + - + +
154E TYR* 3.5 39.4 - - + +
165E THR* 6.0 0.2 + - - -
301E GSH 2.9 43.0 + - + +
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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