Contacts of the strand formed by residues 86 - 93 (chain C) 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 ALA 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.9 4.3 - - + -
37C GLN 3.7 17.0 - - - +
38C TYR* 3.7 18.4 - - + -
84C ASP 3.3 7.4 + - - +
85C SER* 1.3 78.7 - - - +
87C VAL* 1.3 70.1 + - - +
88C TYR* 4.1 10.7 - - + -
111C LYS* 3.9 4.2 - - - +
112C VAL* 2.9 34.9 + - - +
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Residues in contact with VAL 87 (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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36C VAL* 3.3 24.6 - - - +
37C GLN* 3.1 28.2 + - + +
86C ALA* 1.3 81.8 - - - +
88C TYR* 1.3 64.6 + - - +
89C PHE* 4.1 22.0 + - + -
110C THR 3.5 6.7 - - - +
111C LYS* 4.3 22.9 - - + +
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Residues in contact with TYR 88 (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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5C GLN* 3.1 21.3 + - - -
18C LEU* 4.2 15.7 - - + +
20C LEU* 3.2 34.8 - - + -
34C TRP* 3.7 4.9 - + + -
35C TYR 3.6 1.8 - - - -
36C VAL* 3.2 24.0 - - + -
46C LEU* 5.2 0.7 - - + -
62C PHE* 4.3 24.0 - + - -
75C LEU* 3.8 16.8 - - + -
84C ASP* 3.8 16.4 + - - +
85C SER* 5.4 0.7 - - - -
86C ALA* 4.0 16.4 - - - -
87C VAL* 1.3 77.5 - - - +
89C PHE* 1.3 63.6 + - - +
109C GLY* 3.4 1.6 - - - -
110C THR* 2.9 23.6 + - + +
112C VAL* 3.7 37.1 - - + +
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Residues in contact with PHE 89 (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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5C GLN* 3.6 0.9 - - - -
33C PHE 3.8 0.3 - - - +
34C TRP* 3.1 6.9 - - - -
35C TYR* 2.7 48.4 + - + +
36C VAL* 5.7 1.1 - - - -
37C GLN* 5.8 3.1 - - + -
87C VAL* 4.4 24.7 - - + -
88C TYR* 1.3 79.2 - - - +
90C CYS* 1.3 60.2 + - - +
91C ALA 4.1 0.6 + - - -
106C PHE* 3.7 31.4 - + + -
107C GLY 3.4 19.3 - - - -
108C SER 2.9 28.0 - - - -
109C GLY* 4.7 2.9 - - - -
110C THR 5.6 0.4 - - - -
37D GLN* 3.6 29.4 - - + -
43D LEU* 4.1 16.8 - - + -
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Residues in contact with CYS 90 (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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3C VAL* 2.8 31.1 - - - +
5C GLN* 2.9 13.6 + - - +
22C CYS* 2.0 48.2 - - + -
32C LEU* 6.0 1.1 - - - -
33C PHE 3.2 10.3 - - - -
34C TRP* 3.4 31.2 - - + -
73C PHE* 4.2 10.1 - - - -
89C PHE* 1.3 73.1 - - - +
91C ALA* 1.3 59.9 + - - +
92C VAL* 5.8 3.1 - - - -
107C GLY 3.3 4.3 + - - -
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Residues in contact with ALA 91 (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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33C PHE* 3.0 42.2 + - + +
35C TYR* 5.9 0.6 - - + -
89C PHE 4.1 1.0 - - - -
90C CYS* 1.3 74.1 - - - +
92C VAL* 1.3 60.4 + - - +
104C LEU* 4.0 7.7 - - + +
105C THR 3.0 20.9 - - - +
106C PHE* 3.4 40.4 - - + -
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Residues in contact with VAL 92 (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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1C GLN* 3.4 41.9 + - - +
2C SER 3.7 5.6 - - - +
3C VAL* 4.6 9.6 - - + +
22C CYS* 6.1 0.2 - - - -
24C TYR* 3.8 21.1 - - + -
30C PRO* 4.6 5.6 - - + -
31C TYR 3.3 11.4 - - - +
32C LEU* 3.4 28.0 - - + +
90C CYS* 5.8 3.1 - - - -
91C ALA* 1.3 73.5 - - - +
93C SER* 1.3 61.5 + - - +
104C LEU* 3.1 28.2 - - - +
105C THR* 3.3 16.4 + - - +
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Residues in contact with SER 93 (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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1C GLN* 4.3 5.6 - - - +
30C PRO* 3.1 9.5 - - - +
31C TYR* 3.0 44.4 + - - +
33C PHE* 4.3 0.7 - - - -
92C VAL* 1.3 79.4 - - - +
99C GLY* 1.4 58.5 + - - +
101C ALA 3.4 6.1 + - - -
102C SER* 4.9 0.4 - - - -
103C ALA 4.4 2.9 - - - -
104C LEU* 3.4 20.4 - - - -
97D GLY 4.5 4.1 + - - -
4Q LYS* 2.7 26.5 + - - -
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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