Contacts of the strand formed by residues 62 - 70 (chain C) in PDB entry 3MX0
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 MET 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ILE* 3.5 6.4 - - - +
59C MET 2.5 38.8 + - - +
60C ASN* 4.0 7.6 - - + +
61C ASP* 1.3 90.9 - - + +
63C PRO* 1.3 79.8 - - + +
64C ILE* 3.3 4.7 - - + +
104D ARG* 5.4 13.0 - - - +
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Residues in contact with PRO 63 (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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56C GLN* 5.0 4.7 - - - +
57C ASN 3.6 3.8 - - - +
58C ILE* 3.3 21.3 - - + -
62C MET* 1.3 91.7 - - + +
64C ILE* 1.3 69.3 + - - +
65C TYR* 4.1 21.7 - - + +
114D PHE* 5.0 10.8 - - + -
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Residues in contact with ILE 64 (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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56C GLN* 3.5 3.3 - - - -
57C ASN* 2.9 34.5 + - + +
59C MET* 3.3 51.6 - - + +
62C MET 3.3 13.5 - - - +
63C PRO* 1.3 82.2 - - - +
65C TYR* 1.3 65.7 + - - +
66C MET* 3.5 23.0 - - + +
192C LEU* 4.9 7.2 - - + -
126D LEU* 4.3 10.5 - - + -
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Residues in contact with TYR 65 (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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34C PHE* 3.2 21.4 - - + -
38C GLY* 3.6 25.8 - - - -
39C GLY* 3.8 22.0 - - - +
54C LEU* 3.4 30.3 - - + -
55C MET 3.5 2.9 - - - -
56C GLN* 3.0 45.3 + - + -
63C PRO* 4.1 20.1 - - + +
64C ILE* 1.3 84.1 - - - +
66C MET* 1.3 66.5 + - - +
192C LEU* 3.9 9.7 - - - +
113D LYS 4.6 6.4 + - - -
114D PHE* 5.3 1.4 - - - -
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Residues in contact with MET 66 (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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34C PHE* 4.2 1.8 - - - -
53C ASP 3.5 0.3 - - - +
54C LEU* 3.0 6.0 - - - -
55C MET 2.7 43.8 + - - +
57C ASN* 4.2 16.8 - - - +
64C ILE* 3.5 42.6 - - + +
65C TYR* 1.3 75.2 - - - +
67C TYR* 1.3 61.4 + - - +
68C SER 3.6 0.2 + - - -
191C LEU 3.7 11.0 - - - +
192C LEU* 3.5 28.0 - - + -
124D PHE* 3.1 54.7 - - + -
126D LEU* 4.5 3.1 - - + -
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Residues in contact with TYR 67 (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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34C PHE* 3.5 34.3 - + - -
42C GLY* 3.1 13.2 - - - -
43C TRP* 2.7 57.0 + + + -
45C THR* 4.3 9.2 - - + -
52C TRP* 3.4 12.5 - - + -
53C ASP* 3.6 12.6 - - - -
54C LEU* 4.0 26.6 - - + +
66C MET* 1.3 70.9 - - - +
68C SER* 1.3 58.4 + - - +
81C LEU* 2.9 45.8 - - + -
191C LEU* 3.3 33.9 + - + +
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Residues in contact with SER 68 (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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52C TRP* 3.2 5.6 - - - -
53C ASP 2.9 34.8 + - - -
55C MET* 4.2 12.8 - - - +
66C MET* 3.6 1.7 + - - -
67C TYR* 1.3 75.0 - - - +
69C VAL* 1.3 62.4 + - - +
70C CYS* 5.7 0.2 - - - +
189C VAL 3.3 15.5 - - - -
190C ALA* 4.6 0.2 - - - -
119D GLN* 4.9 3.8 + - - -
123D PRO* 4.4 4.6 - - - +
124D PHE* 3.0 40.5 - - - -
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Residues in contact with VAL 69 (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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51C GLY 3.2 28.3 - - - +
52C TRP* 3.6 15.8 - - + -
68C SER* 1.3 76.2 - - - +
70C CYS* 1.3 71.6 + - - +
71C ASN* 4.7 6.7 - - - +
79C ASN* 3.5 25.6 - - + +
184C ASP* 3.0 35.0 - - + +
187C ALA 3.5 4.5 - - - +
189C VAL* 3.2 35.2 + - + +
123D PRO* 4.0 2.1 - - - +
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Residues in contact with CYS 70 (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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68C SER* 5.7 0.2 - - - +
69C VAL* 1.3 82.3 - - - +
71C ASN* 1.3 66.0 + - - +
72C VAL* 4.3 10.7 - - - +
187C ALA 3.2 9.0 - - - -
188C CYS* 2.1 40.6 - - - -
119D GLN* 5.8 1.1 - - - +
121D PHE* 3.2 35.5 - - + +
123D PRO* 4.2 5.6 - - + -
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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