Contacts of the strand formed by residues 78 - 84 (chain C) in PDB entry 3N1Y
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 THR 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A ASP* 2.8 23.6 + - - +
418A GLN* 3.0 21.3 - - - +
427A HIS* 3.2 13.3 + - - -
7C MET* 3.2 18.1 - - - +
9C ASN* 4.1 17.0 - - + -
16C ILE* 4.1 12.3 - - + -
55C ARG* 4.5 0.3 - - - +
56C HIS* 3.1 42.1 + - + +
77C GLU* 1.3 78.8 - - - +
79C LEU* 1.3 68.2 + - - +
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Residues in contact with LEU 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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6C ILE* 4.0 34.8 - - + -
7C MET 2.7 12.4 + - - +
8C SER* 3.8 1.7 - - - -
9C ASN* 2.9 26.7 + - - +
27C MET* 5.7 1.1 - - - -
30C VAL* 4.4 11.0 - - + -
53C VAL* 3.9 22.2 - - + -
54C ARG 3.3 5.2 - - - +
55C ARG* 4.0 14.8 - - - -
62C PHE* 4.1 8.7 - - + -
73C LEU* 3.9 35.0 - - + -
77C GLU* 4.1 11.0 - - + +
78C THR* 1.3 81.9 - - - +
80C ASP* 1.3 64.8 + - - +
81C ILE* 3.8 6.6 + - + +
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Residues in contact with ASP 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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412A TRP* 4.3 3.8 - - + -
9C ASN* 2.7 37.6 + - - +
52C ARG 3.5 1.9 - - - +
54C ARG* 2.6 78.7 + - + +
56C HIS* 2.9 32.7 + - - +
59C GLY* 5.6 0.2 - - - -
79C LEU* 1.3 72.4 - - - +
81C ILE* 1.3 65.7 + - - +
82C ILE* 3.8 8.5 + - + -
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Residues in contact with ILE 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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8C SER* 3.9 10.1 - - - +
9C ASN 3.1 7.9 + - - +
10C PHE* 3.5 35.2 - - + -
11C GLU* 2.9 25.3 + - - +
30C VAL* 4.7 2.7 - - + -
31C ALA* 3.9 25.1 - - + +
34C CYS* 3.8 32.5 - - + -
51C LEU* 4.5 7.2 - - + -
52C ARG 3.4 5.8 - - - +
53C VAL* 4.1 24.0 - - + -
79C LEU* 4.2 12.6 - - + +
80C ASP* 1.3 79.4 - - - +
82C ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 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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412A TRP* 4.3 11.7 - - + -
11C GLU* 3.3 13.0 - - - +
50C ILE 3.4 0.9 - - - +
51C LEU* 3.3 7.5 - - - -
52C ARG* 2.7 46.1 + - + +
54C ARG* 3.5 54.5 - - + +
61C LEU* 4.7 4.7 - - + -
80C ASP* 4.0 11.0 - - + -
81C ILE* 1.3 77.5 - - - +
83C PHE* 1.3 62.5 + - - +
84C MET* 3.8 33.2 - - + -
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Residues in contact with PHE 83 (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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10C PHE* 3.8 22.4 - + - -
11C GLU* 2.7 58.0 + - + +
12C ARG* 4.5 1.1 - - - -
39C ILE* 3.9 15.0 - - + -
43C VAL* 4.3 7.9 - - + -
44C HIS 4.3 2.5 - - - -
46C GLN* 3.7 63.0 - - + +
49C LYS* 4.1 23.4 + - + +
50C ILE 3.6 1.8 - - - -
51C LEU* 3.5 20.4 - - + -
82C ILE* 1.3 73.2 - - - +
84C MET* 1.3 64.9 + - - +
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Residues in contact with MET 84 (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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49C LYS* 3.4 13.5 - - - +
50C ILE* 2.5 42.4 + - - -
52C ARG* 3.6 38.1 - - + +
61C LEU* 4.2 21.8 - - + -
82C ILE* 3.8 29.4 - - + -
83C PHE* 1.3 80.8 - - - +
85C ASP* 1.3 64.4 + - - +
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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