Contacts of the strand formed by residues 75 - 83 (chain C) in PDB entry 5NC5
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 LEU 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C MET 4.5 13.5 - - - +
71C GLY 6.4 0.4 - - - +
72C ILE* 3.8 25.0 + - + +
73C ASP 3.5 0.4 - - - -
74C ASN* 1.4 73.7 - - - +
76C MET* 1.3 65.8 + - - +
77C TYR* 3.6 24.7 - - - +
78C MET* 4.6 15.3 - - + -
92C LEU* 3.8 31.0 - - + -
93C THR 3.7 7.9 - - - +
94C PHE* 4.1 10.8 - - + -
820C ASN* 5.9 0.2 - - - +
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PRO* 4.0 20.2 - - + -
74C ASN 3.5 0.4 + - - -
75C LEU* 1.3 76.3 - - - +
77C TYR* 1.3 91.7 + - + +
93C THR* 2.9 14.3 + - + +
94C PHE 3.7 18.6 - - - +
95C GLU* 3.4 44.0 - - + +
96C SER 5.1 0.9 - - - -
820C ASN* 4.8 2.8 + - - +
864C TYR* 3.5 36.7 + - - +
865C GLN* 4.2 8.5 - - - +
868C LEU* 5.8 1.6 - - - -
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Residues in contact with TYR 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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75C LEU* 3.6 9.8 - - - +
76C MET* 1.3 108.5 - - + +
78C MET* 1.3 68.2 + - - +
79C SER* 5.2 4.5 - - - -
91C THR 3.9 0.2 - - - +
93C THR* 3.2 51.6 + - + +
674C LEU* 3.6 16.3 - - + +
819C TYR* 3.3 31.2 - + + +
820C ASN* 3.4 16.2 - - - +
860C THR* 3.3 13.7 - - - -
861C GLY* 3.2 29.7 + - - -
864C TYR* 3.8 28.7 - + + -
865C GLN* 4.8 1.0 + - - -
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Residues in contact with MET 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU* 3.7 40.8 - - + +
69C MET* 3.9 28.9 - - + +
75C LEU* 4.6 9.2 - - + -
77C TYR* 1.3 79.0 - - - +
79C SER* 1.3 67.5 + - - +
90C ILE* 4.2 13.0 - - + -
91C THR 3.4 5.8 - - - +
92C LEU* 4.0 23.3 - - + -
819C TYR* 3.6 5.5 - - - -
820C ASN* 2.9 36.8 + - - +
821C GLY* 3.9 19.1 - - - +
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Residues in contact with SER 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU* 4.6 2.9 - - - -
77C TYR* 5.2 5.4 - - - -
78C MET* 1.3 78.1 - - - +
80C SER* 1.3 63.6 + - - +
89C GLN 3.9 0.2 - - - +
90C ILE* 3.4 2.4 - - - +
91C THR* 2.7 46.0 + - - +
93C THR* 5.3 0.7 + - - -
683C GLU* 5.5 3.6 - - - -
818C ARG 3.5 11.0 - - - -
819C TYR* 4.1 15.4 - - - -
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C THR* 3.6 14.5 - - - +
66C GLU* 2.9 24.9 + - - -
79C SER* 1.3 78.1 - - - +
81C ASN* 1.3 65.5 + - - +
82C SER* 4.7 0.5 + - - -
89C GLN 3.1 12.3 - - - -
90C ILE* 3.8 15.7 - - - -
816C LEU 3.7 0.2 - - - +
817C GLU* 3.3 5.8 - - - +
818C ARG* 2.9 39.1 + - - +
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Residues in contact with ASN 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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80C SER* 1.3 76.8 - - - +
82C SER* 1.3 64.9 + - - +
83C ASP* 4.3 6.3 - - + +
87C THR 3.9 1.3 - - - +
88C VAL* 3.4 6.1 - - - +
89C GLN* 3.1 51.4 + - - +
815C ARG* 3.3 48.2 + - + +
816C LEU 3.3 7.9 - - - +
817C GLU* 4.6 4.9 - - + +
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Residues in contact with SER 82 (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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54C ALA* 3.4 11.1 - - - +
57C VAL* 4.1 9.9 - - - -
58C GLN* 4.0 22.1 + - - +
62C THR* 2.7 37.2 + - - +
80C SER* 4.7 0.5 + - - -
81C ASN* 1.3 76.2 + - - +
83C ASP* 1.3 59.9 + - - +
87C THR 3.6 5.6 - - - -
88C VAL* 4.6 0.7 - - - +
815C ARG* 3.3 1.5 - - - -
816C LEU* 2.7 40.3 + - - -
818C ARG* 5.6 0.2 - - - -
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASP 4.1 0.7 - - - -
54C ALA* 3.7 12.9 + - - -
57C VAL* 4.3 2.5 - - - +
81C ASN* 5.2 6.7 - - - +
82C SER* 1.3 75.0 - - - +
84C SER* 1.3 58.1 + - - +
85C THR* 2.5 34.3 + - - +
86C GLY* 3.0 21.3 + - - -
87C THR* 3.0 31.0 + - - +
619C GLY* 5.6 2.9 - - - -
620C ARG* 5.2 9.3 + - - +
814C PRO 3.2 16.2 - - - +
815C ARG* 4.2 14.0 + - + -
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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