Contacts of the strand formed by residues 394 - 403 (chain B) 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 THR 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.9 20.4 - - + -
103B GLN* 4.1 18.4 - - + +
104B VAL 3.3 12.8 - - - +
105B ARG* 2.9 34.1 + - - +
374B CYS 5.1 4.2 - - - +
375B LEU* 5.5 2.9 - - - +
392B GLY 3.5 1.6 + - - -
393B ASP* 1.3 73.2 - - - +
395B VAL* 1.3 74.1 + - - +
396B SER* 6.0 0.2 - - - -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 3.2 3.9 - - - +
104B VAL* 2.8 47.6 + - + +
355B VAL* 4.9 3.1 - - + -
373B THR 3.7 8.7 - - - +
374B CYS* 4.4 4.7 - - - -
375B LEU* 4.2 20.6 - - + -
386B CYS* 3.4 42.0 - - + -
389B LEU* 4.5 15.5 - - + +
393B ASP* 5.9 0.2 - - + -
394B THR* 1.3 81.1 - - - +
396B SER* 1.3 63.4 + - - +
397B PHE* 3.8 21.1 - - + -
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Residues in contact with SER 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 6.5 0.4 - - - -
102B ILE 3.5 5.4 - - - -
103B GLN* 3.5 24.5 - - - -
373B THR* 2.8 51.7 + - - +
395B VAL* 1.3 76.5 - - - +
397B PHE* 1.3 71.8 + - - +
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Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 3.8 4.7 + - - -
102B ILE* 2.8 49.8 + - + +
103B GLN* 5.4 0.2 - - - -
104B VAL* 4.6 6.5 - - + -
355B VAL* 3.9 28.0 - - + -
357B LEU* 3.5 44.2 - - + -
370B PHE* 4.8 3.8 - - + -
371B ASN 3.8 5.2 - - - -
372B ALA* 3.5 32.5 - - + -
383B LEU 4.6 0.4 - - - -
384B LYS* 3.7 20.6 - - + -
385B SER 3.8 1.6 - - - -
386B CYS* 4.3 6.5 - - - -
395B VAL* 3.8 22.2 - - + -
396B SER* 1.3 78.3 - - - +
398B SER* 1.3 61.6 + - - +
399B ILE* 4.0 4.3 - - + -
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Residues in contact with SER 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 5.2 5.2 + - - -
100B PHE 3.9 7.2 + - - -
101B SER* 4.8 6.0 + - - -
370B PHE* 3.2 5.0 - - - -
371B ASN* 2.9 51.0 + - - -
397B PHE* 1.3 72.6 - - - +
399B ILE* 1.3 62.3 + - - +
1001B NAG 5.2 3.5 - - - +
1006B NAG 2.9 26.9 + - - +
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Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN* 3.1 4.2 - - - +
100B PHE* 2.8 77.3 + - + +
102B ILE* 3.6 32.3 - - + -
368B LEU* 4.3 16.2 - - + -
369B SER 3.5 4.7 - - - +
370B PHE* 3.6 35.7 - - + -
397B PHE 4.6 0.4 - - - +
398B SER* 1.3 77.8 - - - +
400B GLU* 1.3 62.5 + - - +
416B ILE* 3.6 21.8 - - + -
425B LEU* 5.0 0.4 - - + -
1006B NAG 3.8 1.3 - - - -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B SER* 4.5 17.0 + - - -
98B LYS 3.8 5.4 - - - +
99B ASN* 4.0 15.7 - - + +
367B SER 3.7 0.9 - - - +
368B LEU* 3.3 6.9 - - - -
369B SER* 3.1 46.4 + - - +
399B ILE* 1.3 77.1 - - - +
401B ALA* 1.3 67.8 + - - +
402B LYS* 5.3 6.4 - - + +
1001B NAG 5.0 2.8 + - - -
1006B NAG 3.4 38.9 + - + -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.9 27.6 - - + -
92B LEU* 4.3 5.3 - - + +
96B ASP 4.2 0.2 - - - +
97B SER* 3.2 26.1 - - - -
98B LYS 3.0 16.4 + - - +
100B PHE* 4.2 8.2 - - + -
366B LEU* 3.9 8.1 - - + -
367B SER 3.7 3.6 - - - -
368B LEU* 3.8 17.9 - - + -
399B ILE 4.3 0.4 - - - -
400B GLU* 1.3 73.6 - - - +
402B LYS* 1.3 60.2 + - - +
414B PHE* 5.4 0.9 - - + -
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 4.4 16.4 + - - -
96B ASP 4.0 1.6 - - - +
97B SER* 3.0 22.7 - - - +
366B LEU* 3.3 5.5 - - - +
367B SER* 2.9 48.7 + - - +
400B GLU* 5.3 6.7 - - + +
401B ALA* 1.3 74.7 - - - +
403B VAL* 1.3 78.8 + - - +
404B ARG* 5.6 1.0 - - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.5 23.3 - - + -
93B ARG 3.9 2.9 - - - +
95B ASP* 3.6 33.0 - - - +
96B ASP 3.4 18.2 + - - +
365B GLU 3.6 8.3 - - - +
366B LEU* 3.9 15.5 - - + -
402B LYS* 1.3 95.8 + - - +
404B ARG* 1.3 60.8 + - - +
405B GLY 4.0 9.2 - - - +
407B PRO* 5.6 1.3 - - + -
431B PHE* 3.5 30.7 - - + -
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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