Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 1N6U
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 TYR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.2 20.5 - + - -
44A THR 3.2 21.1 - - - -
45A ILE* 3.7 15.0 - - + +
71A GLU 2.7 14.7 + - - -
72A TRP* 2.9 75.1 - + + -
73A ARG* 3.8 6.6 + - - +
74A SER* 2.8 37.2 + - - -
77A GLU 3.6 4.2 + - - -
78A ALA* 1.3 66.4 - - - +
80A VAL* 1.3 64.8 + - - +
81A THR* 3.0 11.8 + - - -
99A PHE* 2.7 22.9 + - - +
101A LEU* 3.4 19.0 - - + +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.6 0.5 - - - -
44A THR* 2.5 76.6 + - + +
45A ILE 3.2 3.1 - - - +
46A MET* 3.1 34.1 - - + +
49A PRO* 4.5 8.3 - - + -
78A ALA 2.6 11.1 + - - +
79A TYR* 1.3 71.5 - - - +
81A THR* 1.3 54.5 + - - +
82A VAL* 6.3 0.2 - - + -
96A SER* 5.0 4.9 - - - +
97A HIS 3.4 5.2 - - - +
98A ASN* 3.6 29.6 - - + +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 4.4 2.8 - - - -
25A LEU* 4.0 17.0 - - + -
41A LEU* 4.6 3.6 - - + -
42A LEU 2.9 20.4 - - - +
43A TYR* 3.1 23.8 - - + +
44A THR 4.4 0.2 - - - +
72A TRP* 3.1 12.1 - - + -
79A TYR 3.0 5.7 + - - -
80A VAL* 1.3 72.6 - - - +
82A VAL* 1.3 54.1 + - - +
83A LEU* 4.0 2.2 - - + +
95A CYS 3.8 0.2 - - - +
96A SER* 2.5 38.8 + - - -
97A HIS 2.8 11.2 + - - -
99A PHE* 2.7 36.0 - - - -
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 2.6 51.4 + - + +
44A THR* 5.7 0.2 - - + -
52A LEU* 3.6 30.0 - - + +
80A VAL* 6.3 0.2 - - + -
81A THR* 1.3 71.6 - - - +
83A LEU* 1.3 54.4 + - - +
84A GLU* 3.4 29.8 - - + +
94A SER* 4.6 4.0 - - - -
95A CYS 3.1 14.6 - - - +
96A SER* 3.1 25.1 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.1 24.3 - - + -
27A TRP* 3.0 72.7 - - + -
29A LEU* 3.2 13.9 - - + -
39A TYR* 3.8 13.9 - - + -
40A THR 3.7 4.0 - - - -
41A LEU* 3.8 26.7 - - + +
42A LEU 4.0 2.4 + - - +
81A THR* 4.0 2.0 - - + -
82A VAL* 1.3 70.7 - - - +
84A GLU* 1.3 59.3 + - - +
85A GLY 3.6 3.6 + - - +
93A PHE* 4.1 5.4 - - + -
94A SER* 3.8 0.3 - - - -
95A CYS* 2.6 28.5 + - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR 2.8 25.2 + - - +
42A LEU* 3.1 29.6 - - + +
82A VAL* 3.3 15.3 + - + +
83A LEU* 1.3 70.5 - - - +
85A GLY* 1.3 57.7 + - - +
86A PHE* 2.7 37.8 - - + -
91A THR* 4.7 6.9 - - + +
93A PHE 3.2 5.6 - - - +
94A SER* 3.0 33.8 - - - +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.6 15.0 - - - -
83A LEU 3.6 2.0 + - - -
84A GLU* 1.3 69.6 - - - +
86A PHE* 1.3 63.8 + - - -
92A LEU 2.8 19.8 + - - -
93A PHE* 2.9 53.8 + - - +
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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