Contacts of the strand formed by residues 76 - 81 (chain C) in PDB entry 1M6X
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 SER 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C PHE* 3.2 2.8 - - - +
71C ASP* 2.7 53.5 + - - +
74C ASN* 4.2 11.8 + - - +
75C LYS* 1.3 77.0 - - - +
77C LEU* 1.3 60.9 + - - +
100C TRP* 3.3 1.7 - - - -
101C GLU* 3.3 17.5 - - - -
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Residues in contact with LEU 77 (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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19C PHE* 6.0 0.2 - - + -
23C PHE* 3.8 22.0 - - + -
31C ILE* 3.7 29.2 - - + -
34C CYS* 4.4 6.5 - - - -
38C LEU* 4.5 2.0 - - + -
68C LEU* 3.8 14.8 - - + -
69C SER 3.5 12.6 - - - +
70C PHE* 3.8 4.9 - - + +
76C SER* 1.3 75.9 - - - +
78C GLN* 1.3 62.9 + - - +
79C PHE* 3.4 33.2 - - + -
100C TRP* 4.0 10.0 - - + -
101C GLU 2.9 8.0 + - - +
102C PHE* 3.3 22.0 - - + +
103C THR* 3.2 20.8 + - - -
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Residues in contact with GLN 78 (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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67C SER 5.3 2.8 + - - +
68C LEU* 3.6 2.8 - - - +
69C SER* 3.1 49.9 + - - +
77C LEU* 1.3 76.9 - - - +
79C PHE* 1.3 70.5 + - - +
103C THR* 3.1 33.2 - - - +
105C ILE* 3.4 25.1 - - + +
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Residues in contact with PHE 79 (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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38C LEU* 3.2 43.7 - - + -
42C CYS* 3.6 23.1 - - - -
64C ILE* 3.8 21.1 - - + -
67C SER* 3.7 15.7 - - - +
68C LEU* 4.0 13.0 - - + +
77C LEU* 3.4 20.6 - - + -
78C GLN* 1.3 77.7 - - - +
80C LYS* 1.3 72.7 + - - +
81C TYR* 4.2 9.0 - - + -
93C LEU* 3.9 5.6 - - + -
102C PHE* 4.8 0.7 - + - -
103C THR 3.5 1.2 + - - -
104C ILE* 3.0 35.2 - - + -
105C ILE* 2.9 26.8 + - - -
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Residues in contact with LYS 80 (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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63C ILE* 3.8 18.0 - - + +
64C ILE* 3.6 12.8 - - - +
67C SER* 2.8 31.1 + - - +
79C PHE* 1.3 83.1 - - - +
81C TYR* 1.3 64.6 + - - +
105C ILE* 3.1 34.3 - - + +
106C PRO 5.1 2.2 - - - -
107C TYR* 4.5 30.1 + - + -
108C ASN 5.8 0.2 + - - -
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Residues in contact with TYR 81 (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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39C THR* 4.7 5.2 - - + -
42C CYS* 3.6 29.8 + - + -
43C TRP* 3.5 39.0 - - - +
46C THR* 3.8 12.0 + - + -
47C HIS* 4.6 1.3 - + - -
60C TYR* 3.6 29.7 - + + -
63C ILE* 4.8 3.8 - - - -
64C ILE* 4.4 18.4 - - + -
79C PHE* 4.1 4.7 + - + -
80C LYS* 1.3 75.9 - - - +
82C LYS* 1.3 84.2 + - - +
83C THR* 2.7 34.8 + - + +
89C LEU* 4.3 7.9 - - + -
104C ILE* 3.8 17.3 - - + -
105C ILE 3.2 6.6 + - - +
106C PRO* 3.8 0.5 - - - +
107C TYR* 3.2 21.2 + - - +
21I G 5.3 1.3 - - - -
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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