Contacts of the strand formed by residues 74 - 79 (chain B) 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 ASN 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 6.0 2.0 - - - -
23B CYS 2.7 20.2 - - - +
24B ASN* 3.5 12.9 + - - +
32B MET* 4.1 0.9 - - - -
69B ARG* 3.6 6.3 + - - -
70B PRO* 3.4 34.7 - - - +
71B SER* 3.1 32.2 + - - +
72B GLN 3.3 1.2 + - - -
73B GLU* 1.3 83.3 - - - +
75B PHE* 1.3 58.8 + - - +
76B SER* 4.3 7.8 + - - +
808B NAG 4.2 22.3 + - + +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B CYS* 3.2 19.1 + - + +
32B MET* 3.6 44.3 - - + +
33B TYR 4.0 3.1 - - - -
34B TRP* 2.8 39.8 + + - -
47B HIS* 3.3 26.0 - - + -
48B TYR* 3.6 20.0 - - - -
49B SER* 3.9 10.3 - - - -
55B THR* 4.0 9.6 - - - -
67B ALA* 3.6 28.3 - - + -
68B SER 3.6 11.4 - - - -
69B ARG* 3.6 20.9 - - - -
74B ASN* 1.3 76.6 - - - +
76B SER* 1.3 60.7 + - - +
92B CYS* 5.4 0.9 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.5 8.3 - - - +
21B LEU 3.5 12.3 - - - -
22B SER* 4.1 13.0 - - - +
34B TRP* 3.8 2.7 - - - -
67B ALA* 3.0 30.3 - - - +
68B SER* 3.1 15.5 + - - -
70B PRO* 5.1 3.3 - - - +
74B ASN* 4.3 10.4 + - - -
75B PHE* 1.3 74.4 - - - +
77B LEU* 1.3 60.3 + - - +
78B ILE* 3.8 16.2 - - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 3.9 0.5 - - - +
20B THR* 3.9 1.6 - - - -
21B LEU* 3.1 46.4 + - + +
34B TRP* 3.6 35.6 - - + +
46B ILE* 3.7 29.6 - - + -
47B HIS* 4.3 7.0 - - + -
65B TYR* 3.6 32.1 - - + -
66B LYS 3.3 8.5 - - - +
67B ALA* 4.7 0.4 - - + -
76B SER* 1.3 73.0 - - - +
78B ILE* 1.3 60.7 + - - +
79B LEU* 3.9 4.9 + - + +
90B TYR* 3.7 27.8 - - + -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LYS* 3.6 21.8 - - - +
19B VAL 3.8 3.4 - - - +
20B THR* 4.1 14.8 - - + +
63B GLY 4.3 0.2 - - - +
65B TYR* 3.6 7.1 - - - +
66B LYS* 2.7 48.0 + - + +
67B ALA* 4.4 1.8 - - - -
68B SER* 4.4 17.3 - - - +
76B SER* 3.8 27.6 - - - +
77B LEU* 1.3 76.8 - - - +
79B LEU* 1.3 63.4 + - - +
80B GLU* 3.5 27.5 + - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 3.4 11.4 - - - +
19B VAL* 2.8 43.4 + - + +
21B LEU* 5.6 1.8 - - + -
63B GLY 3.3 9.6 - - - +
65B TYR* 3.3 29.4 - - + -
77B LEU* 5.1 6.5 - - + +
78B ILE* 1.3 73.0 - - - +
80B GLU* 1.3 65.3 + - - +
81B LEU 2.8 6.3 + - - +
82B ALA* 3.7 8.6 + - + -
86B GLN* 3.0 45.8 - - + +
90B TYR* 5.1 0.7 - - + -
114B LEU* 3.6 31.4 - - + -
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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