Contacts of the strand formed by residues 55 - 62 (chain M) in PDB entry 1I5L
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 ARG 55 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L ARG* 3.0 36.5 - - - +
26L GLU* 5.0 5.9 + - - -
69L PHE* 5.8 0.8 - - - -
25M ARG* 5.1 0.4 - - - +
46M GLU* 3.5 16.6 - - - +
47M GLU* 2.8 49.2 + - + +
53M VAL* 4.3 1.2 - - - +
54M VAL* 1.3 98.1 - - + +
56M LYS* 1.3 77.0 + - - +
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Residues in contact with LYS 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L ALA* 5.2 2.3 - - - +
45M ALA 3.4 8.1 - - - +
46M GLU* 2.4 42.1 + - + +
47M GLU 5.0 0.2 - - - +
53M VAL* 4.7 7.0 - - + -
54M VAL 5.3 0.4 - - - +
55M ARG* 1.3 90.2 - - - +
57M VAL* 1.3 73.6 + - - +
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Residues in contact with VAL 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ILE* 6.2 1.3 - - + -
69L PHE* 5.9 4.3 - - + -
71L SER* 3.0 27.8 - - - +
73L ALA* 4.1 18.2 - - + +
74L PRO* 6.2 0.4 - - - -
27M PHE* 4.6 7.9 - - + -
44M ASP* 3.8 0.9 - - - -
45M ALA* 3.0 37.8 + - + +
46M GLU 6.2 0.2 - - - -
56M LYS* 1.3 84.7 - - - +
58M GLY* 1.3 65.1 + - - +
59M SER* 3.1 2.6 + - - +
60M VAL* 3.3 28.3 - - + -
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Residues in contact with GLY 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L PRO* 6.3 0.4 - - - -
73L ALA* 4.9 11.6 - - - +
74L PRO* 5.7 1.8 - - - +
43M LEU* 3.4 4.0 - - - +
44M ASP* 2.6 33.9 + - - +
57M VAL* 1.3 72.7 - - - +
59M SER* 1.3 62.7 + - - +
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Residues in contact with SER 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L VAL* 4.9 12.7 - - - +
71L SER* 2.4 31.2 + - - -
72L PRO* 3.1 32.4 - - - +
41M VAL* 5.3 1.1 - - - -
42M LEU 3.1 14.8 - - - -
43M LEU* 3.9 14.6 - - - -
45M ALA 5.5 0.4 - - - +
57M VAL* 3.0 3.6 - - - +
58M GLY* 1.3 80.4 - - - +
60M VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L PHE* 4.4 12.3 - - + -
70L VAL 3.7 5.6 - - - -
71L SER* 3.4 13.0 - - - +
27M PHE* 3.9 30.1 - - + -
40M LEU 3.8 0.2 - - - +
41M VAL* 3.2 8.9 - - - +
42M LEU* 3.1 54.4 + - + +
45M ALA* 4.4 4.5 - - + -
57M VAL* 3.3 22.7 - - + -
59M SER* 1.3 80.2 - - - +
61M VAL* 1.3 65.5 + - - +
62M ILE* 4.0 11.3 - - + +
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Residues in contact with VAL 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L PRO* 4.2 20.4 - - + +
8L VAL* 4.0 29.2 - - + -
9L LEU* 3.8 30.7 - - + -
38L MET* 4.6 22.0 - - + +
67L VAL* 5.6 0.3 - - - +
69L PHE* 3.0 24.4 - - - -
70L VAL* 3.1 18.5 + - + +
39M ASN* 5.5 0.2 - - + -
40M LEU 3.2 8.1 - - - +
41M VAL* 4.6 5.2 - - + -
60M VAL* 1.3 77.5 - - - +
62M ILE* 1.3 62.6 + - - +
63M ARG 4.0 0.5 + - - -
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Residues in contact with ILE 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L VAL 3.5 7.2 - - - +
69L PHE* 4.2 12.3 - - + -
19M VAL* 4.5 17.0 - - + -
21M LEU* 3.7 30.5 - - + -
27M PHE* 4.6 13.9 - - + -
39M ASN* 3.1 3.9 - - - -
40M LEU* 2.7 47.4 + - + +
42M LEU* 4.3 25.8 - - + -
60M VAL* 4.5 13.7 - - + -
61M VAL* 1.3 75.3 - - - +
63M ARG* 1.3 75.3 + - - +
64M GLY* 3.1 1.4 + - - -
66M THR* 4.5 0.9 - - + -
67M VAL* 3.7 11.2 - - + -
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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