Contacts of the strand formed by residues 366 - 371 (chain A) in PDB entry 1TF5
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 LYS 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A THR* 5.2 0.8 + - - -
93A HIS* 2.9 40.1 + - - -
94A ASP 4.7 0.7 - - - -
95A GLY* 4.3 12.1 - - - +
117A ASN* 2.6 31.2 + - - +
202A HIS* 2.8 18.7 + - + +
203A PHE* 3.3 31.1 - - + -
204A ALA 3.2 18.4 + - - -
364A TYR* 3.2 1.7 - - - +
365A GLU* 1.3 81.3 - - + +
367A LEU* 1.3 74.8 + - - +
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Residues in contact with LEU 367 (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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95A GLY* 3.1 30.5 - - - +
203A PHE* 4.0 2.7 - - - -
204A ALA* 3.6 14.8 - - + -
206A ILE* 4.4 14.1 - - + -
213A LEU* 5.2 0.7 - - + -
361A PHE* 3.3 31.9 - - + +
362A ARG* 4.7 2.9 - - + +
364A TYR* 3.3 31.0 - - + +
366A LYS* 1.3 86.6 - - - +
368A ALA* 1.3 60.8 + - - +
385A TYR* 4.4 30.1 - - + +
387A MET* 3.6 17.3 - - + +
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Residues in contact with ALA 368 (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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92A LEU* 3.3 38.6 - - + +
96A ASN 3.4 7.4 - - - +
203A PHE* 3.6 17.0 - - + -
204A ALA 3.1 8.7 + - - +
205A VAL* 4.3 6.3 - - + -
206A ILE* 2.9 27.9 + - - +
367A LEU* 1.3 73.4 - - - +
369A GLY* 1.3 59.6 + - - +
387A MET* 3.3 10.5 - - - +
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Residues in contact with GLY 369 (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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92A LEU* 3.0 6.8 - - - +
96A ASN 3.3 6.5 + - - -
97A ILE* 3.3 1.8 - - - -
98A ALA 2.9 26.3 + - - -
205A VAL 5.1 0.2 - - - -
206A ILE 3.3 11.7 - - - -
209A VAL* 3.9 21.5 - - - -
368A ALA* 1.3 77.6 - - - +
370A MET* 1.3 64.4 + - - -
387A MET* 3.4 3.7 - - - +
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Residues in contact with MET 370 (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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92A LEU* 3.8 23.1 - - + -
98A ALA 3.6 8.1 - - - +
100A MET* 4.1 9.2 - - + -
106A LYS* 3.3 41.9 + - + +
107A THR* 5.1 2.7 - - - -
110A SER* 3.9 25.1 - - - +
126A VAL* 5.9 3.8 - - + -
205A VAL* 4.4 11.7 - - + +
206A ILE 3.0 6.6 + - - +
207A ASP* 3.7 32.1 - - + +
208A GLU 2.9 27.0 + - - -
209A VAL* 3.2 3.8 + - - +
369A GLY* 1.3 78.4 - - - +
371A THR* 1.3 63.8 + - - +
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Residues in contact with THR 371 (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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97A ILE* 4.2 3.8 - - + -
98A ALA 3.5 3.0 + - - -
99A GLU* 2.9 27.2 - - - -
100A MET* 3.0 7.0 + - - +
106A LYS* 3.8 11.8 - - - +
208A GLU* 4.4 7.0 + - - -
209A VAL* 3.7 16.6 - - + -
210A ASP* 2.8 24.1 + - - +
370A MET* 1.3 79.6 - - - +
372A GLY* 1.3 62.8 + - - +
373A THR* 3.0 15.0 + - - +
374A ALA* 3.4 32.8 - - + -
521A GLN* 4.4 2.3 + - - -
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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