Contacts of the strand formed by residues 42 - 48 (chain A) in PDB entry 5TF6
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 2.8 28.2 + - - +
39A GLU 4.1 5.2 - - - +
40A LEU 3.7 1.0 - - - -
41A THR* 1.3 84.6 + - - +
43A VAL* 1.3 65.7 + - - +
84A ARG* 3.7 45.7 + - + +
85A ILE 3.2 11.4 - - - +
86A GLU* 4.0 11.2 - - - +
93A ALA* 4.5 0.2 - - - +
113A HIS* 3.8 3.5 - - - -
114A LEU* 3.0 33.6 + - + +
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Residues in contact with VAL 43 (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 THR* 1.3 77.9 - - - +
44A LEU* 1.3 60.8 + - - +
45A VAL* 4.4 3.4 - - + -
83A ALA 3.7 0.3 - - - +
84A ARG* 3.3 9.2 - - - +
85A ILE* 2.8 58.6 + - + -
87A PHE* 3.9 11.2 - - + -
93A ALA* 3.7 38.1 - - + +
96A ALA* 4.3 3.6 - - + -
97A ILE* 4.2 12.1 - - + -
111A VAL* 4.1 17.3 - - + -
112A SER 3.2 13.7 - - - +
113A HIS* 4.7 1.1 - - + -
114A LEU* 4.1 4.7 - - - +
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Residues in contact with LEU 44 (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 VAL* 1.3 73.7 - - - +
45A VAL* 1.3 66.0 + - - +
46A LYS* 4.7 5.4 - - + +
82A PHE* 4.0 24.0 - - + -
83A ALA 3.4 10.8 - - - +
110A ILE 3.4 2.1 - - - +
111A VAL* 3.3 4.9 - - - -
112A SER* 2.8 45.6 + - - +
113A HIS 5.7 0.4 - - - +
114A LEU* 4.0 19.9 - - + +
117A CYS* 5.7 1.1 - - - -
145A LEU* 3.6 30.5 - - + -
166A THR* 3.4 31.0 - - + +
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Residues in contact with VAL 45 (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 VAL* 4.4 6.7 - - + -
44A LEU* 1.3 76.5 - - - +
46A LYS* 1.3 60.9 + - - +
48A LEU* 3.6 32.1 - - + -
61A PHE* 3.7 29.8 - - + -
81A ARG 3.9 0.5 - - - +
82A PHE* 3.2 8.7 - - - -
83A ALA* 2.8 46.7 + - + +
85A ILE* 4.0 19.7 - - + -
109A ILE* 4.4 12.8 - - + -
110A ILE 3.3 7.0 - - - +
111A VAL* 4.2 7.6 - - + -
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Residues in contact with LYS 46 (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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44A LEU* 4.0 7.6 - - + +
45A VAL* 1.3 74.5 - - - +
47A ASN* 1.3 77.1 + - + +
48A LEU 3.6 1.1 - - - -
80A PHE* 3.8 22.7 - - + -
82A PHE* 3.4 29.8 - - + -
109A ILE* 3.3 6.2 - - - +
110A ILE* 2.8 58.7 + - + +
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Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS* 1.3 86.8 - - + +
48A LEU* 1.3 65.3 + - - +
80A PHE* 3.4 35.8 - - + +
81A ARG 3.4 5.1 + - - -
107A ASN* 3.2 35.5 + - - +
108A GLU* 3.1 27.8 + - - +
109A ILE* 3.9 5.5 - - - +
110A ILE* 5.7 1.8 - - + -
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Residues in contact with LEU 48 (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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45A VAL* 3.6 33.2 - - + -
47A ASN* 1.3 79.6 - - - +
49A PRO* 1.3 79.2 - - + +
52A TYR* 4.2 19.1 - - + -
57A VAL* 3.6 29.8 - - + -
60A TYR* 6.2 0.4 - - + -
61A PHE* 5.0 8.1 - - + -
72A VAL* 5.6 0.2 - - + -
80A PHE* 3.3 5.5 - - - +
81A ARG* 2.7 37.8 + - + +
82A PHE 4.8 1.1 - - - +
83A ALA* 3.7 18.8 - - + +
104A VAL* 4.4 9.9 - - + -
107A ASN* 3.9 0.7 - - - -
109A ILE* 3.9 15.0 - - + -
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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