Contacts of the strand formed by residues 87 - 92 (chain F) in PDB entry 1TYE
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 ARG 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.3 1.2 - - - +
64F LEU* 3.4 28.1 + - + -
65F GLU* 3.2 61.6 + - + +
85F PRO 3.2 2.0 + - - +
86F GLN* 1.3 82.5 - - - +
88F ILE* 1.3 73.9 + - - +
426F ILE* 3.4 44.7 - - - +
428F GLN* 3.4 30.2 - - - +
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ALA* 5.6 4.3 - - + +
62F ARG 3.9 7.4 - - - +
63F VAL* 4.1 19.5 - - + -
64F LEU* 3.9 7.6 - - - -
85F PRO* 4.2 18.2 - - + +
87F ARG* 1.3 85.8 - - - +
89F ALA* 1.3 62.3 + - - +
90F LEU* 5.3 3.8 - - + -
100F PHE* 3.7 41.5 - - + -
101F SER 6.0 2.0 - - - +
425F LEU* 4.3 5.4 - - + -
426F ILE 3.1 9.1 + - - +
427F VAL* 3.8 30.7 - - + -
428F GLN* 2.9 29.3 + - - +
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Residues in contact with ALA 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F GLU* 5.5 0.3 - - - +
61F ALA* 2.9 25.2 - - - +
62F ARG* 3.1 21.4 + - + +
64F LEU* 4.1 22.6 - - + +
88F ILE* 1.3 72.6 - - - +
90F LEU* 1.3 59.9 + - - +
91F ARG* 3.7 6.3 + - + +
428F GLN* 3.7 9.9 - - + +
430F THR* 5.0 6.3 - - - +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ALA* 3.5 23.6 - - + +
88F ILE* 3.7 1.7 + - + -
89F ALA* 1.3 69.8 - - - +
91F ARG* 1.3 58.0 + - - +
92F LEU* 3.8 16.3 + - + -
98F LYS* 4.3 14.4 - - + -
100F PHE* 4.0 22.7 - - + -
366F LEU* 5.2 1.8 - - + -
401F ALA* 3.9 22.9 - - + -
414F PHE* 4.8 2.9 - - + -
427F VAL* 3.8 25.8 - - + -
428F GLN 2.8 15.3 + - - +
429F VAL* 3.5 22.6 - - + +
430F THR* 2.7 30.3 + - - +
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F PRO* 5.3 2.0 - - - +
58F VAL* 3.5 32.5 + - - +
59F SER* 3.2 5.7 - - - -
60F GLU* 2.9 63.1 + - + +
61F ALA* 3.9 7.1 + - - +
89F ALA* 3.7 8.7 + - + +
90F LEU* 1.3 72.0 - - - +
92F LEU* 1.3 61.8 + - - +
98F LYS* 5.0 1.2 - - - +
430F THR* 3.4 32.5 + - + +
431F PHE 5.6 0.4 + - - -
432F ASP* 2.7 33.1 + - + +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F SER* 3.2 13.0 - - - +
90F LEU* 3.8 31.6 + - + +
91F ARG* 1.3 76.8 - - - +
93F ARG* 1.3 60.7 + - - +
96F ASP* 4.5 10.3 - - + +
98F LYS* 4.8 8.5 - - + -
366F LEU* 5.6 0.7 - - + -
401F ALA* 4.1 25.8 - - + +
403F VAL* 3.4 44.0 - - + -
406F CYS* 5.4 1.3 - - - -
429F VAL* 5.0 1.8 - - + -
430F THR 3.4 5.1 + - - -
431F PHE* 3.9 16.7 - - + -
432F ASP* 3.6 21.1 + - - +
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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