Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1TX6
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 GLN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL 3.3 5.2 - - - +
66A ARG* 3.3 2.1 - - - -
67A LEU* 2.8 46.4 + - + +
79A ASN 4.6 4.8 + - - +
80A GLU* 1.3 77.0 - - - +
82A PHE* 1.3 62.7 + - - +
83A ILE* 3.8 10.3 - - + +
111A PRO 4.9 0.2 - - - +
112A ALA* 3.8 8.2 - - - -
113A THR* 3.0 54.6 + - - -
115A ASN* 4.1 6.9 + - - -
118A VAL* 3.5 22.5 - - + +
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Residues in contact with PHE 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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64A GLN* 3.4 26.6 + - - +
65A VAL 3.5 5.2 - - - -
66A ARG* 3.1 50.9 - - + -
70A GLU* 4.1 8.7 - - - -
76A LEU* 5.0 12.1 - - + -
80A GLU* 3.4 30.5 - - + -
81A GLN* 1.3 78.0 - - - +
83A ILE* 1.3 62.2 + - - +
84A ASN* 5.8 0.7 + - - -
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Residues in contact with ILE 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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64A GLN* 4.5 0.4 - - - +
65A VAL* 2.7 44.6 + - - +
67A LEU* 4.2 14.1 - - + -
81A GLN* 4.2 10.1 - - + +
82A PHE* 1.3 82.0 - - - +
84A ASN* 1.3 58.2 + - - +
108A LEU* 3.9 16.8 - - + +
109A SER* 3.4 21.1 - - - +
110A SER* 3.5 34.3 - - - +
111A PRO 3.8 3.8 - - - +
112A ALA* 3.7 36.6 - - + -
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Residues in contact with ASN 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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63A ILE 3.7 5.0 - - - +
64A GLN* 3.4 35.1 + - - +
82A PHE 5.8 0.6 + - - -
83A ILE* 1.3 77.7 - - - +
85A ALA* 1.3 61.5 + - - +
108A LEU* 3.7 2.5 - - - -
109A SER* 2.7 45.3 + - - +
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Residues in contact with ALA 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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63A ILE* 2.9 30.0 + - + +
65A VAL* 5.0 1.9 - - + +
83A ILE 3.9 1.0 + - - -
84A ASN* 1.3 73.3 - - - +
86A ALA* 1.3 61.1 + - - +
87A LYS 4.4 0.2 - - - +
88A ILE* 3.9 23.0 - - + +
106A ILE* 3.3 28.7 - - + -
107A LYS 3.6 6.1 - - - -
108A LEU* 4.8 0.2 - - - +
109A SER* 5.0 0.7 - - - -
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Residues in contact with ALA 86 (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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84A ASN 3.4 2.2 + - - -
85A ALA* 1.3 73.3 - - - +
87A LYS* 1.3 69.2 + - + +
88A ILE* 5.5 0.4 - - - -
107A LYS* 2.6 21.9 + - + +
108A LEU 3.9 3.4 - - - +
109A SER* 3.6 26.2 - - - +
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Residues in contact with LYS 87 (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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51A TRP* 4.5 1.1 - - + -
85A ALA 3.5 0.2 - - - -
86A ALA* 1.3 85.9 - - + +
88A ILE* 1.3 65.9 + - - +
89A ILE* 4.1 12.1 - - + -
105A LEU 4.4 0.4 - - - -
106A ILE* 3.3 7.6 - - - +
107A LYS* 2.9 57.8 + - + +
245A ASN* 3.5 47.4 + - + +
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Residues in contact with ILE 88 (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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59A TYR* 3.5 37.1 - - + +
60A LYS 3.0 28.3 - - - +
61A SER* 3.7 18.4 - - - +
62A ARG* 4.4 0.4 - - - +
63A ILE* 4.1 15.0 - - + +
85A ALA* 3.9 20.0 - - + +
87A LYS* 1.3 80.5 - - - +
89A ILE* 1.3 63.2 + - - +
90A THR 4.1 1.4 + - - -
104A MET* 3.6 25.1 - - + -
105A LEU 3.6 1.8 - - - -
106A ILE* 4.4 7.2 - - + +
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Residues in contact with ILE 89 (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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51A TRP* 4.1 13.7 - - + -
87A LYS* 4.6 8.1 - - + -
88A ILE* 1.3 81.5 - - - +
90A THR* 1.3 69.7 + - - +
92A PRO* 5.7 1.3 - - + -
104A MET* 3.3 3.2 - - - -
105A LEU* 2.8 38.9 + - + +
237A TRP* 3.7 17.1 - - + -
241A THR* 3.5 18.2 - - + -
245A ASN* 3.4 34.5 - - - +
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Residues in contact with THR 90 (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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56A ALA* 4.1 15.7 - - - +
59A TYR* 3.5 38.1 - - + -
88A ILE 4.1 1.0 + - - -
89A ILE* 1.3 79.3 - - - +
91A HIS* 1.3 71.5 + - - +
92A PRO* 3.1 8.1 - - - +
94A PHE* 5.2 6.3 - - + +
103A ILE 4.0 4.0 - - - -
104A MET* 3.8 16.8 - - + -
237A TRP* 4.2 0.9 - - - -
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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