Contacts of the strand formed by residues 62 - 70 (chain L) in PDB entry 1MWA
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 62 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H THR* 3.8 25.6 - - + -
94H THR* 4.2 2.9 - - + -
96H GLN* 3.3 24.2 - - + -
29L GLN 3.5 17.7 + - - -
30L PHE* 2.9 38.0 + - + +
31L HIS* 3.2 33.2 - + - -
33L PRO* 3.8 32.5 - - + -
54L MET* 3.8 27.4 - - + -
55L SER 3.2 17.0 - - - +
56L PHE* 3.6 10.5 - + + +
60L TRP 3.8 0.9 - - - -
61L SER* 1.3 73.7 - - - +
63L TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 63 (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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27H TYR* 4.3 12.8 + - - -
26L TYR* 4.1 21.5 - + + -
27L VAL 3.3 12.3 - - - +
28L THR* 3.9 16.4 - - + -
30L PHE* 4.1 0.7 - - - -
53L ASP 4.6 0.3 - - - +
54L MET* 3.1 14.3 - - - +
55L SER* 2.9 50.8 + - - -
56L PHE* 3.7 13.2 + - - -
57L SER* 3.3 27.6 - - - -
62L PHE* 1.3 76.9 - - - +
64L ILE* 1.3 72.2 + - - +
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Residues in contact with ILE 64 (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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25L CYS 4.0 1.4 - - - +
26L TYR* 3.7 7.8 - - - -
27L VAL* 3.1 29.6 + - + +
30L PHE* 3.6 28.3 - - + -
35L ILE* 4.9 2.2 - - + -
37L ILE* 3.9 16.4 - - + -
51L MET* 3.5 28.9 - - + -
52L SER* 3.9 25.8 - - - +
53L ASP 4.5 2.0 - - - +
54L MET* 3.9 24.7 - - + -
63L TYR* 1.3 85.7 - - - +
65L LEU* 1.3 70.0 + - - +
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Residues in contact with LEU 65 (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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235H PRO* 4.1 13.5 - - + +
237H GLY* 4.2 25.4 - - - -
10L TYR* 4.0 11.0 - - - +
24L ASN* 4.3 12.8 - - - +
25L CYS 4.1 2.2 - - - +
26L TYR* 3.9 36.6 - - + +
50L GLU 3.8 0.5 - - - +
51L MET* 3.4 2.4 - - - -
52L SER* 2.8 50.3 + - - +
64L ILE* 1.3 77.1 - - - +
66L ALA* 1.3 72.6 + - - +
67L HIS* 4.9 12.0 - - + -
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Residues in contact with ALA 66 (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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24L ASN* 3.5 1.9 - - - +
25L CYS* 2.7 41.6 + - + +
37L ILE* 3.9 18.6 - - + -
39L MET* 3.9 7.3 - - - +
49L VAL* 3.8 10.8 - - + -
50L GLU 3.2 5.2 - - - -
51L MET* 3.4 26.2 - - + -
65L LEU* 1.3 73.8 - - - +
67L HIS* 1.3 62.2 + - - +
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Residues in contact with HIS 67 (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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237H GLY* 6.3 0.2 - - - -
12L ARG* 4.9 12.2 + - - -
22L ILE* 3.7 20.9 - - + +
23L LEU 3.1 7.6 - - - +
24L ASN* 3.0 27.6 - - - +
39L MET* 4.0 1.1 - - - -
49L VAL* 3.7 0.8 - - - +
50L GLU* 2.8 76.8 + - + +
52L SER* 5.6 3.6 - - - -
65L LEU* 4.9 13.9 - - + -
66L ALA* 1.3 72.7 - - - +
68L THR* 1.3 70.1 + - - +
69L GLU 5.2 0.2 + - - -
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Residues in contact with THR 68 (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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22L ILE* 3.3 6.9 - - - -
23L LEU* 2.7 45.8 + - - +
39L MET* 3.9 4.6 - - - +
46L ILE* 3.6 30.5 - - + +
48L LYS 3.8 7.0 - - - +
49L VAL* 3.3 37.7 - - + -
50L GLU* 4.8 4.3 - - - -
67L HIS* 1.3 84.0 - - - +
69L GLU* 1.3 66.9 + - - +
70L PHE* 4.8 1.2 - - - +
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Residues in contact with GLU 69 (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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21L ASN 3.4 7.4 - - - +
22L ILE* 4.0 14.4 - - + +
46L ILE* 5.8 1.4 - - - +
48L LYS* 5.2 12.6 - - - -
50L GLU* 5.3 6.0 + - - +
67L HIS* 5.2 0.2 + - - -
68L THR* 1.3 77.3 - - - +
70L PHE* 1.3 63.4 + - - +
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Residues in contact with PHE 70 (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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11L SER* 4.0 11.7 - - - -
20L PRO* 3.4 1.1 - - - +
21L ASN* 2.5 77.6 + - + +
22L ILE 3.5 14.8 - - - -
23L LEU* 3.5 33.0 - - + -
46L ILE* 6.0 0.9 - - + -
68L THR* 4.6 3.8 - - - +
69L GLU* 1.3 76.3 - - - +
71L THR* 1.3 59.5 + - - +
72L PRO* 4.0 23.8 - - + -
78L TYR* 3.4 47.8 - + + +
95L TRP* 4.4 16.2 - + - -
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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