Contacts of the strand formed by residues 54 - 59 (chain C) in PDB entry 1M5P
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 GLN 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B G 2.9 42.9 - - - +
40B C 4.0 4.3 - - - +
13C TYR* 2.3 40.2 + - + +
14C ILE 3.1 10.5 - - - +
15C ASN* 4.0 1.3 - - + -
17C LEU* 3.7 6.0 - - - +
26C LEU* 4.8 1.9 - - - +
45C VAL* 4.0 14.0 - - - +
46C SER 4.6 3.5 + - - +
50C LYS 2.5 30.7 + - - -
51C MET* 3.2 18.5 + - - +
52C ARG 3.0 9.7 + - - +
53C GLY* 1.3 88.5 + - - +
55C ALA* 1.3 65.9 + - - +
56C PHE* 5.7 4.0 - - + -
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE 3.8 0.5 - - - +
13C TYR* 3.9 1.2 - - - -
14C ILE* 2.9 37.6 + - + +
17C LEU* 3.9 6.1 - - + -
30C LEU* 3.9 19.7 - - + -
43C ILE* 4.9 1.6 - - + -
44C LEU 3.2 7.0 - - - +
45C VAL* 3.3 24.5 - - + -
54C GLN* 1.3 80.4 - - - +
56C PHE* 1.3 69.3 + - - +
57C VAL* 4.9 2.0 - - + -
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B C 3.7 22.4 - - - -
41B A 3.2 81.4 - + + -
11C THR* 3.6 19.3 - - + -
12C ILE 3.4 5.6 - - - -
13C TYR* 3.6 31.0 - + + -
43C ILE* 3.4 3.1 - - - +
44C LEU* 2.8 45.1 + - + +
51C MET* 4.8 9.2 - - - -
54C GLN* 5.7 2.0 - - + -
55C ALA* 1.3 78.1 - - - +
57C VAL* 1.3 61.4 + - - +
58C ILE* 4.0 3.0 + - + -
87C ALA* 4.6 1.3 - - + -
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C THR* 3.5 2.9 - - - -
12C ILE* 3.2 37.4 + - + +
14C ILE* 3.5 29.2 - - + -
30C LEU* 4.5 10.8 - - + -
34C PHE* 4.6 8.3 - - + -
40C ILE* 4.1 19.3 - - + -
42C ASP 3.9 2.2 - - - -
43C ILE* 3.8 28.9 - - + -
55C ALA* 4.7 2.2 - - + +
56C PHE* 1.3 77.8 - - - +
58C ILE* 1.3 61.4 + - - +
59C PHE* 3.6 22.4 + - + -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B C 5.4 0.4 - - - +
10C HIS* 4.2 1.1 - - + -
11C THR* 3.1 26.9 - - + +
40C ILE* 3.6 4.0 - - - +
41C LEU* 2.8 39.3 + - + -
42C ASP* 2.9 27.6 + - + +
44C LEU* 4.4 19.5 - - + -
56C PHE* 4.9 3.8 - - + +
57C VAL* 1.3 71.0 - - - +
59C PHE* 1.3 57.8 + - - +
91C SER* 4.0 20.2 - - - +
93C ILE* 4.1 25.4 - - + -
94C ILE* 3.7 31.2 - - + -
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C HIS* 3.0 39.6 + - - +
12C ILE* 3.5 26.9 - - + -
34C PHE* 4.0 31.4 - - + -
37C PHE* 4.0 10.3 - - + -
38C GLY 3.8 15.7 - - - -
39C GLN 3.3 17.5 - - - -
40C ILE* 4.0 6.3 - - + -
41C LEU* 4.0 6.5 - - - +
57C VAL* 3.8 20.4 - - + -
58C ILE* 1.3 74.8 - - - +
60C LYS* 1.3 64.1 + - - +
61C GLU 3.4 15.0 + - - +
64C SER* 3.4 17.9 - - - -
65C ALA* 3.9 11.7 - - + +
68C ALA* 4.1 16.6 - - + -
94C ILE* 4.2 0.5 - - - +
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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