Contacts of the strand formed by residues 57 - 64 (chain N) 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 ILE 57 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ILE* 5.6 0.9 - - - -
47N LYS* 5.7 5.4 - - - +
49N THR* 5.6 7.4 - - + -
50N SER 3.5 8.7 - - - +
51N ILE* 3.7 35.0 - - + -
55N GLY 3.6 7.8 + - - +
56N THR* 1.3 87.6 - - - +
58N MET* 1.3 66.4 + - - +
59N ASN* 4.6 8.7 - - - +
176N TYR* 3.6 53.2 - - + -
181N ALA* 5.7 0.7 - - - +
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Residues in contact with MET 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M PHE* 4.1 9.9 - - + +
132M ASN* 3.5 51.8 - - - +
135M SER* 3.7 20.2 - - - +
136M ILE* 4.1 14.8 - - + -
49N THR* 3.6 3.9 - - - -
50N SER 3.4 26.5 + - - +
57N ILE* 1.3 81.5 - - - +
59N ASN* 1.3 67.2 + - - +
60N LEU* 3.6 11.8 + - + +
176N TYR* 3.4 13.5 - - - +
177N SER 4.0 9.2 - - - +
178N SER 3.4 23.1 - - - +
179N GLY* 4.7 1.3 - - - -
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Residues in contact with ASN 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M PHE* 4.5 0.5 - - - -
47N LYS* 3.7 17.1 + - + +
48N LEU 3.6 5.6 - - - +
49N THR* 3.3 17.5 - - + +
57N ILE* 4.6 6.1 - - - +
58N MET* 1.3 76.5 - - - +
60N LEU* 1.3 65.6 + - - +
61N GLN* 3.3 7.1 + - - +
62N TYR* 3.6 14.3 + - + +
130N LYS* 4.7 1.0 + - - -
173N GLU* 3.5 38.4 + - - +
176N TYR* 2.9 19.4 + - - +
177N SER* 3.3 39.8 + - - +
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Residues in contact with LEU 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M LEU* 3.8 35.4 - - + +
131M PHE* 3.6 21.8 - - + -
132M ASN* 3.2 32.3 - - - +
48N LEU* 2.9 28.8 + - + +
50N SER* 4.7 2.5 - - - -
58N MET* 3.6 19.9 + - + +
59N ASN* 1.3 72.6 - - - +
61N GLN* 1.3 57.2 + - + +
83N TYR* 3.5 39.3 - - + -
130N LYS* 2.7 26.1 + - - +
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Residues in contact with GLN 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M LEU* 4.6 8.8 - - + +
47N LYS* 3.3 4.7 - - - +
48N LEU* 2.8 34.1 + - + +
59N ASN* 3.3 4.8 - - - +
60N LEU* 1.3 84.5 - - + +
62N TYR* 1.3 67.6 + - - +
63N TYR* 3.2 32.8 + - + -
123N GLN* 2.7 24.2 + - - +
126N TYR* 3.5 17.9 - - + -
127N SER* 4.6 2.8 + - - -
130N LYS* 3.7 7.0 - - - +
301N GSH 3.0 51.0 - - - +
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Residues in contact with TYR 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N ILE* 4.8 3.4 - - + -
46N THR 3.3 3.4 - - - +
47N LYS* 3.5 24.0 - - + -
59N ASN* 3.6 16.9 + - + -
61N GLN* 1.3 73.9 - - - +
63N TYR* 1.3 63.0 + - - +
64N LYS 4.0 0.2 + - - -
88N ILE* 3.5 30.6 - - + +
146N GLN* 3.8 14.8 - - - -
150N LEU* 4.1 16.6 - - + -
154N TYR* 3.1 22.0 + + - +
166N LEU* 5.1 9.4 - - + +
169N LEU* 4.5 11.6 - - + +
173N GLU* 3.8 15.2 + - - +
174N LEU* 5.6 0.6 - - + -
177N SER* 3.6 21.2 + - - -
301N GSH 2.7 58.4 + - - +
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Residues in contact with TYR 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M LEU* 5.0 3.5 - - - +
41N LEU* 3.7 5.1 - - + +
45N ILE* 3.6 0.9 - - - +
46N THR* 2.5 55.9 + - + +
48N LEU* 3.8 37.6 - - + +
61N GLN* 3.2 31.0 + - + -
62N TYR* 1.3 73.9 - - - +
64N LYS* 1.3 59.8 + - - +
67N PHE* 3.4 35.0 - + + -
68N VAL 4.3 1.6 - - - -
69N ILE* 3.7 34.3 - - + +
85N LEU* 4.3 11.7 - - + -
123N GLN* 2.2 31.4 + - - -
301N GSH 3.8 3.6 - - - -
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Residues in contact with LYS 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N LEU* 3.8 1.5 - - - +
44N GLY 3.3 5.4 - - - -
45N ILE* 3.6 24.2 - - + -
63N TYR* 1.3 76.4 - - - +
65N GLY* 1.3 73.3 + - - +
67N PHE* 4.4 1.6 - - - +
153N VAL* 2.2 61.7 + - + +
154N TYR* 3.5 20.4 - - + +
232N THR* 5.7 4.6 - - - +
301N GSH 3.1 46.2 + - + +
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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