Contacts of the strand formed by residues 78 - 83 (chain C) in PDB entry 1N9S
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 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 3.9 24.2 - - + -
30C LYS 3.7 3.4 - - - +
31C LEU* 4.6 2.0 - - + +
32C LYS* 4.5 1.1 - - - -
49C PHE* 4.7 13.2 - - + +
51C LEU* 5.3 3.1 - - + -
73C ILE* 3.8 18.2 - - + -
74C ARG 3.2 21.5 - - - +
75C SER* 2.5 24.1 + - - +
76C ASN 3.2 2.6 - - - +
77C ASN* 1.3 73.2 - - - +
79C LEU* 1.3 67.5 + - - +
80C TYR* 3.7 18.6 - - - +
81C ILE* 4.3 10.1 - - + -
74D ARG* 3.4 18.5 - - + +
77D ASN* 3.5 5.4 + - - -
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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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30C LYS* 2.7 23.7 + - + +
31C LEU 3.8 18.8 - - - +
32C LYS* 4.2 2.4 - - - +
77C ASN 3.7 2.6 + - - -
78C VAL* 1.3 75.8 - - - +
80C TYR* 1.3 72.9 + - + +
31D LEU* 4.2 14.6 - - + -
33D PHE* 4.0 22.7 - - + -
38D TYR* 3.8 22.9 - - + +
73D ILE* 4.0 3.5 - - + +
74D ARG* 3.0 26.7 + - - +
77D ASN* 3.1 43.2 + - + +
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Residues in contact with TYR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.8 0.3 - - - -
30C LYS* 2.9 59.2 + - + +
37C GLU* 5.0 2.1 + - - -
49C PHE* 5.8 0.4 - - - -
78C VAL* 3.6 4.4 - - - -
79C LEU* 1.3 99.1 - - + +
81C ILE* 1.3 71.2 + - - +
82C ARG* 4.1 25.7 + - + -
38D TYR* 3.1 39.7 - + - -
58D GLU* 4.4 3.2 + - - -
68D LEU* 3.9 24.1 - - + +
71D ILE* 4.4 13.7 - - + -
72D PHE 3.2 16.2 - - - +
73D ILE* 4.1 11.9 - - + -
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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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19C LEU* 3.3 31.9 - - + -
22C LEU* 4.8 5.2 - - + -
27C VAL* 3.9 27.8 - - + -
28C GLY 3.1 12.6 - - - +
29C VAL* 4.1 7.4 - - + -
42C LEU* 5.3 2.7 - - + -
49C PHE* 3.8 20.2 - - + -
51C LEU* 3.6 29.4 - - + -
78C VAL* 4.3 9.4 - - + -
80C TYR* 1.3 79.9 - - - +
82C ARG* 1.3 65.5 + - - +
71D ILE* 3.4 3.8 - - - -
72D PHE* 2.8 36.5 + - + +
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 5.0 3.8 - - - -
27C VAL* 3.0 11.2 - - - +
28C GLY* 2.6 44.9 + - - +
37C GLU* 2.9 36.6 + - - +
39C ARG* 3.8 12.3 - - - +
80C TYR* 4.1 15.7 + - + -
81C ILE* 1.3 75.1 - - - +
83C GLU* 1.3 63.9 + - - +
84C LEU* 3.4 26.3 - - + +
68D LEU* 4.6 26.1 - - - +
69D GLY 5.2 5.6 - - - +
70D GLU 3.7 13.5 - - - +
71D ILE* 4.0 12.1 - - + -
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Residues in contact with GLU 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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22C LEU* 4.0 25.6 - - + +
25C HIS* 3.4 27.1 + - + -
26C ARG 3.6 7.2 - - - +
27C VAL* 4.2 3.8 - - - +
82C ARG* 1.3 79.1 + - - +
84C LEU* 1.3 79.2 + - - +
69D GLY* 5.4 6.7 + - - -
70D GLU* 3.9 23.7 + - + +
72D PHE* 6.3 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