Contacts of the strand formed by residues 59 - 64 (chain C) in PDB entry 6NMY
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 VAL 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PRO* 4.2 12.3 - - + -
47C TRP* 3.8 27.5 - - + -
49C ASP* 4.6 9.1 + - + +
57C VAL* 5.2 8.3 - - + +
58C ASN* 1.3 82.3 - - - +
60C THR* 1.3 66.0 + - - +
94C ARG* 5.2 4.0 + - - -
113C PHE* 3.7 24.9 - - + -
114C GLN 3.4 14.6 - - - +
115C PRO* 4.1 17.0 - - + -
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Residues in contact with THR 60 (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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47C TRP* 5.0 2.2 - - - -
59C VAL* 1.3 76.0 + - - +
61C LEU* 1.3 75.1 + - - +
62C ILE* 3.5 10.0 - - - +
72C PRO* 4.6 11.7 - - + -
73C VAL 3.8 15.7 - - - +
75C CYS* 5.7 1.8 - - - -
113C PHE* 3.3 8.1 - - - -
114C GLN* 2.9 37.2 + - - -
116C ASP* 5.2 7.4 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.1 11.7 - - + -
45C CYS* 3.9 28.3 - - + -
47C TRP* 4.0 25.0 - - - +
60C THR* 1.3 77.1 - - - +
62C ILE* 1.3 66.3 + - - +
72C PRO* 3.5 0.5 - - - +
73C VAL* 2.9 43.1 + - + -
75C CYS* 4.4 5.5 - - - -
96C CYS* 4.1 7.6 - - - -
111C PHE* 3.9 27.1 - - + -
112C SER 3.3 18.4 - - - +
113C PHE* 3.7 25.8 - - + -
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Residues in contact with ILE 62 (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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60C THR* 3.5 18.8 - - - +
61C LEU* 1.3 86.6 - - - +
63C ARG* 1.3 62.3 + - - +
70C LEU* 3.7 34.1 - - + +
71C GLU 3.4 14.4 - - - +
72C PRO* 4.2 14.6 - - + -
73C VAL* 4.5 0.9 - - - -
111C PHE* 3.3 10.3 - - - -
112C SER* 2.9 45.1 + - - +
113C PHE 4.3 1.6 - - - -
114C GLN* 3.6 40.6 - - + +
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 5.3 3.1 - - - +
62C ILE* 1.3 72.8 - - - +
64C ARG* 1.3 72.8 + - - +
65C VAL* 3.2 21.3 + - - +
70C LEU* 4.5 2.9 - - - -
71C GLU* 2.9 70.9 + - + +
73C VAL* 4.2 7.1 - - + +
98C ILE* 4.4 17.6 - - - +
99C PRO 5.7 0.8 + - - -
100C CYS* 4.1 26.6 - - - +
109C ASP* 3.5 29.2 + - - +
110C TYR 3.5 7.6 - - - +
111C PHE* 3.9 29.8 - - + -
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Residues in contact with ARG 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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62C ILE 4.2 0.2 - - - -
63C ARG* 1.3 78.8 + - - +
65C VAL* 1.3 60.0 + - - +
66C ASN 3.1 26.4 + - - +
67C GLU* 3.1 39.7 + - - +
68C ASP 5.4 0.7 - - - -
69C LEU 3.9 3.6 - - - +
70C LEU* 3.7 30.7 - - + +
109C ASP* 5.2 1.7 - - - +
110C TYR* 2.9 66.4 + - + +
112C SER* 6.0 0.2 - - - +
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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