Contacts of the strand formed by residues 97 - 105 (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 SER 97 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F SER* 4.8 0.3 - - - -
92F LEU* 5.1 2.5 - - - -
95F ASP 4.5 1.0 + - - -
96F ASP* 1.3 90.7 + - - +
98F LYS* 1.3 67.1 + - - +
400F GLU* 3.7 24.8 + - - -
401F ALA 3.1 10.3 - - - -
402F LYS* 3.3 28.4 - - - +
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Residues in contact with LYS 98 (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* 4.5 18.5 + - - +
60F GLU* 3.1 28.9 - - - +
61F ALA* 3.5 24.5 - - + +
90F LEU* 4.3 11.7 - - + -
91F ARG 5.0 0.4 - - - +
92F LEU* 4.8 6.7 - - + +
97F SER* 1.3 79.9 - - - +
99F ASN* 1.3 91.0 + - - +
100F PHE* 4.0 5.9 - - - -
399F ILE 4.0 0.3 - - - +
400F GLU* 3.4 3.9 - - - +
401F ALA* 2.9 31.5 + - - +
1015F NAG 4.8 7.1 + - - -
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Residues in contact with ASN 99 (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* 5.2 1.6 - - - +
98F LYS* 1.3 101.3 + - - +
100F PHE* 1.3 64.8 + - - +
398F SER* 5.0 3.3 + - - +
399F ILE 3.1 11.2 - - - +
400F GLU* 4.0 16.1 - - + +
1015F NAG 1.5 73.6 + - + +
1020F NAG 4.5 12.7 + - + +
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Residues in contact with PHE 100 (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* 5.0 9.4 - - + +
88F ILE* 3.7 33.9 - - + -
90F LEU* 4.0 24.7 - - + -
98F LYS 4.0 9.6 - - - -
99F ASN* 1.3 79.1 - - - +
101F SER* 1.3 67.5 + - - +
368F LEU* 4.9 5.8 - - + -
398F SER* 3.5 6.2 + - - -
399F ILE* 2.8 74.3 + - + -
401F ALA* 4.5 9.0 - - + -
414F PHE* 5.2 1.6 - + - -
416F ILE* 4.9 4.9 - - + -
425F LEU* 4.7 7.4 - - + -
427F VAL* 4.4 16.8 - - + -
1015F NAG 3.4 11.9 - - - -
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Residues in contact with SER 101 (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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85F PRO* 5.0 11.2 - - - +
88F ILE* 6.0 2.1 - - - +
100F PHE* 1.3 86.3 - - - +
102F ILE* 1.3 79.0 + - - +
103F GLN* 4.3 14.9 + - - +
396F SER* 5.6 1.4 - - - -
397F PHE 3.8 7.6 + - - -
398F SER* 4.9 0.7 - - - +
425F LEU* 4.8 3.3 - - - +
1015F NAG 3.5 16.1 - - - +
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Residues in contact with ILE 102 (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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83F VAL* 5.2 6.3 - - + -
84F SER* 3.9 24.9 - - - +
101F SER* 1.3 81.5 + - - +
103F GLN* 1.3 70.2 + - - +
104F VAL* 4.8 12.3 - - + -
357F LEU* 5.0 12.6 - - + -
396F SER* 3.3 2.9 - - - -
397F PHE* 2.8 61.5 + - + +
399F ILE* 3.5 19.3 - - + -
416F ILE* 5.1 7.2 - - + +
425F LEU* 3.4 34.3 - - + -
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Residues in contact with GLN 103 (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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69F LEU* 3.9 8.3 - - + +
83F VAL* 3.3 3.6 - - - +
84F SER* 2.7 52.8 + - - +
85F PRO* 5.7 1.2 - - - +
101F SER* 4.3 12.8 + - - +
102F ILE* 1.3 79.7 - - - +
104F VAL* 1.3 64.1 + - - +
394F THR* 4.4 17.4 - - + +
395F VAL 3.4 7.4 - - - +
396F SER* 3.7 16.8 - - - -
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Residues in contact with VAL 104 (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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69F LEU* 4.4 0.2 - - - -
82F GLN 3.4 11.0 - - - +
83F VAL* 4.1 16.8 - - + -
102F ILE* 4.8 11.0 - - + -
103F GLN* 1.3 78.6 - - - +
105F ARG* 1.3 64.7 + - - +
355F VAL* 3.9 39.7 - - + -
357F LEU* 4.9 2.7 - - + -
393F ASP 4.0 0.2 - - - +
394F THR* 3.2 5.8 - - - +
395F VAL* 2.6 44.1 + - - +
397F PHE* 4.3 14.4 - - + -
418F PRO* 4.6 6.3 - - + -
421F PHE* 4.1 23.6 - - + -
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Residues in contact with ARG 105 (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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69F LEU* 3.2 43.8 + - + +
70F SER 3.1 26.0 + - - -
71F ASP* 4.3 9.7 + - - -
82F GLN* 2.9 37.4 + - + +
104F VAL* 1.3 82.1 - - - +
106F GLN* 1.3 63.7 + - - +
107F VAL* 3.0 12.3 + - + +
392F GLY* 3.5 17.7 + - - +
393F ASP 3.2 15.9 - - - +
394F THR* 2.7 24.3 + - - +
421F PHE* 4.1 1.2 - - - -
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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