Contacts of the strand formed by residues 78 - 83 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29I VAL* 4.2 16.8 - - + -
30I LYS 4.1 3.8 - - - +
31I LEU* 4.4 2.5 - - + +
32I LYS* 4.2 1.0 - - - +
49I PHE* 4.6 6.5 - - + +
51I LEU* 5.3 2.9 - - + -
73I ILE* 4.2 8.5 - - + -
74I ARG 3.6 13.2 - - - +
75I SER* 2.6 30.6 + - - +
76I ASN 3.2 1.5 - - - +
77I ASN* 1.3 71.6 - - - +
79I LEU* 1.3 64.0 + - - +
80I TYR* 3.5 19.7 - - - +
81I ILE* 4.2 17.9 - - + -
74J ARG* 3.9 21.4 + - + +
77J ASN* 3.0 18.4 + - - -
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LYS* 2.7 29.1 + - + +
31I LEU 3.8 13.7 - - - +
32I LYS* 3.8 7.9 - - - +
78I VAL* 1.3 75.9 - - - +
80I TYR* 1.3 79.1 + - + +
31J LEU* 4.2 17.5 - - + -
33J PHE* 4.1 18.4 - - + -
38J TYR* 3.5 24.9 - - + +
73J ILE* 4.0 3.9 - - + +
74J ARG* 3.5 19.9 + - - +
77J ASN* 3.4 32.0 + - + +
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Residues in contact with TYR 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I GLY 4.4 0.9 - - - -
30I LYS* 2.8 65.2 + - + +
37I GLU* 4.5 1.4 + - - -
78I VAL* 3.5 5.9 - - - +
79I LEU* 1.3 101.8 - - + +
81I ILE* 1.3 70.9 - - - +
82I ARG* 3.7 32.1 + - + -
38J TYR* 3.8 27.6 - + - -
58J GLU* 5.6 1.1 - - - -
68J LEU* 4.0 29.9 - - + +
71J ILE* 4.7 9.6 - - + -
72J PHE 3.1 20.4 - - - +
73J ILE* 4.1 8.1 - - + -
74J ARG* 4.9 0.7 - - - +
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Residues in contact with ILE 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU* 3.8 10.3 - - + -
22I LEU* 4.4 8.5 - - + -
27I VAL* 3.8 27.1 - - + -
28I GLY 3.2 9.2 - - - +
29I VAL* 4.1 15.0 - - + -
42I LEU* 5.0 3.6 - - + -
49I PHE* 3.5 32.3 - - + -
51I LEU* 3.3 32.1 - - + -
78I VAL* 4.2 9.4 - - + -
80I TYR* 1.3 83.5 - - - +
82I ARG* 1.3 60.8 + - - +
71J ILE* 3.5 0.3 - - - -
72J PHE* 2.7 44.8 + - + +
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Residues in contact with ARG 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LEU* 5.1 0.9 - - - -
27I VAL* 3.2 6.5 - - - -
28I GLY 2.5 41.6 + - - +
37I GLU* 2.7 38.1 + - - -
39I ARG* 3.8 11.5 - - - +
80I TYR* 3.7 19.9 + - + -
81I ILE* 1.3 75.0 - - - +
83I GLU* 1.3 61.8 + - - +
84I LEU* 3.2 38.2 + - - +
68J LEU* 4.6 21.4 - - - +
69J GLY 5.1 6.3 - - - +
70J GLU 3.3 16.8 - - - +
71J ILE* 3.8 11.7 - - + -
72J PHE* 5.3 0.9 - - - -
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I GLY 5.2 0.5 - - - +
22I LEU* 3.6 30.0 - - + +
25I HIS* 3.2 32.0 + - + -
26I ARG 3.9 7.0 - - - +
27I VAL* 4.4 0.7 - - - +
82I ARG* 1.3 72.0 - - - +
84I LEU* 1.3 71.6 + - - +
85I PRO* 3.9 2.8 - - - +
69J GLY* 5.5 6.4 - - - -
70J GLU* 3.7 29.9 + - + +
72J PHE* 5.7 0.4 - - - -
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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