Contacts of the strand formed by residues 394 - 403 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.6 26.5 - - + -
103D GLN* 4.2 15.5 - - + +
104D VAL 3.4 12.3 - - - +
105D ARG* 2.9 35.3 + - + +
374D CYS 4.7 5.2 - - - +
375D LEU* 5.1 4.9 - - - +
392D GLY 3.6 1.1 + - - -
393D ASP* 1.3 74.0 - - - +
395D VAL* 1.3 76.0 + - - +
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Residues in contact with VAL 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE 4.2 0.5 - - - +
103D GLN* 3.5 0.4 - - - -
104D VAL* 2.6 46.3 + - + +
355D VAL* 4.7 7.2 - - + -
373D THR 3.4 10.8 - - - +
374D CYS* 3.8 19.7 - - - -
375D LEU* 3.8 20.9 - - + -
386D CYS* 3.5 29.2 - - + -
389D LEU* 3.9 11.4 - - + -
394D THR* 1.3 82.1 - - - +
396D SER* 1.3 62.8 + - - +
397D PHE* 3.7 20.1 - - + -
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Residues in contact with SER 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D SER* 6.0 3.1 - - - -
102D ILE 3.3 9.9 - - - -
103D GLN* 3.8 20.6 - - - -
373D THR* 2.9 49.8 + - - +
395D VAL* 1.3 78.0 - - - +
397D PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D SER* 3.2 6.4 - - - -
102D ILE* 2.7 58.4 + - + -
104D VAL* 4.3 6.1 - - + -
355D VAL* 3.8 36.8 - - + -
357D LEU* 3.7 25.1 - - + -
370D PHE* 5.1 2.7 - + + -
371D ASN 3.3 6.7 - - - +
372D ALA* 3.6 28.5 - - + -
373D THR* 5.2 0.4 - - - -
383D LEU 4.5 0.4 - - - -
384D LYS* 3.6 31.6 - - + -
385D SER* 3.7 2.5 - - - -
386D CYS* 4.4 1.8 - - - -
395D VAL* 3.7 25.6 - - + -
396D SER* 1.3 77.7 - - - +
398D SER* 1.3 62.7 + - - +
399D ILE* 3.8 8.1 - - + +
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Residues in contact with SER 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASN* 4.8 7.3 + - - -
100D PHE 3.9 4.9 + - - -
101D SER* 4.3 5.6 - - - +
369D SER 3.5 0.7 - - - +
370D PHE* 3.5 4.7 - - - +
371D ASN* 2.8 45.2 + - - +
373D THR* 5.6 0.9 + - - -
397D PHE* 1.3 74.7 - - - +
399D ILE* 1.3 61.2 + - - +
1007D NAG 4.9 6.9 + - - -
1013D NAG 2.9 26.6 + - - +
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Residues in contact with ILE 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASN* 3.0 5.9 - - - +
100D PHE* 2.8 81.5 + - + +
102D ILE* 3.7 35.0 - - + -
357D LEU* 5.1 1.3 - - + -
368D LEU* 4.1 19.5 - - + -
369D SER 3.2 9.0 - - - +
370D PHE* 3.5 35.7 - - + -
397D PHE* 3.8 8.1 - - + +
398D SER* 1.3 78.1 - - - +
400D GLU* 1.3 62.2 + - - +
401D ALA 4.3 0.2 - - - -
416D ILE* 4.6 7.2 - - + -
1013D NAG 4.7 0.7 - - - -
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Residues in contact with GLU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D SER* 4.0 22.7 + - - +
98D LYS* 3.2 18.2 - - - +
99D ASN* 4.1 1.4 - - + +
367D SER 3.6 1.4 - - - +
368D LEU* 3.2 5.6 - - - -
369D SER* 2.8 56.3 + - - +
399D ILE* 1.3 77.1 - - - +
401D ALA* 1.3 59.5 + - - +
402D LYS* 3.9 9.5 + - - +
1007D NAG 5.0 2.8 + - - -
1013D NAG 3.5 35.1 + - + +
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Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 3.7 30.5 - - + -
92D LEU* 3.8 6.1 - - + +
97D SER* 3.1 5.3 - - - -
98D LYS 2.7 33.8 + - - +
100D PHE* 4.3 6.4 - - + -
366D LEU* 4.7 8.5 - - + -
367D SER 3.4 4.9 - - - +
368D LEU* 3.5 20.0 - - + -
399D ILE 4.3 0.8 + - - -
400D GLU* 1.3 71.4 - - - +
402D LYS* 1.3 60.2 + - - +
414D PHE* 5.2 0.2 - - + -
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Residues in contact with LYS 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ASP* 4.1 17.8 + - - +
96D ASP 4.1 3.1 - - - +
97D SER* 3.7 19.1 - - - -
365D GLU 4.0 0.2 - - - +
366D LEU* 3.6 3.8 - - - +
367D SER* 2.9 47.0 + - - +
369D SER* 5.9 1.8 - - - +
400D GLU* 3.9 9.6 + - - +
401D ALA* 1.3 73.4 - - - +
403D VAL* 1.3 78.2 + - - +
404D ARG* 5.5 1.4 - - - +
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Residues in contact with VAL 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU* 3.3 42.8 - - + +
93D ARG 3.8 9.9 - - - +
94D PRO* 4.4 0.2 - - + -
95D ASP* 3.4 29.3 - - - +
96D ASP 3.2 12.2 + - - +
365D GLU 3.6 7.4 - - - +
366D LEU* 4.0 20.0 - - + -
402D LYS* 1.3 89.7 + - - +
404D ARG* 1.3 58.3 + - - +
405D GLY 3.3 21.5 - - - +
407D PRO* 5.8 2.2 - - + -
431D PHE* 4.6 5.6 - - + -
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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