Contacts of the strand formed by residues 97 - 105 (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 SER 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D SER* 4.3 2.6 - - - -
92D LEU* 4.3 4.5 - - - -
96D ASP* 1.3 94.4 + - - +
98D LYS* 1.3 67.3 + - - +
400D GLU* 4.0 19.4 + - - -
401D ALA 3.1 17.5 - - - -
402D LYS* 3.7 19.7 - - - -
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Residues in contact with LYS 98 (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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59D SER* 4.2 20.3 + - - +
60D GLU* 3.0 34.1 - - - +
61D ALA* 3.6 15.0 - - + -
90D LEU* 3.9 14.6 - - + -
92D LEU* 4.4 6.7 - - + +
97D SER* 1.3 77.6 - - - +
99D ASN* 1.3 85.1 + - - +
100D PHE* 4.5 3.2 - - - -
400D GLU* 3.2 5.4 - - - -
401D ALA* 2.7 35.1 + - - +
1007D NAG 5.3 6.1 + - - +
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Residues in contact with ASN 99 (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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61D ALA* 4.8 1.9 - - - +
98D LYS* 1.3 103.1 + - - +
100D PHE* 1.3 65.7 + - - +
398D SER* 4.8 3.9 + - - +
399D ILE 3.0 11.9 - - - +
400D GLU* 4.3 3.6 - - + -
1007D NAG 1.4 76.8 + - - +
1013D NAG 3.8 20.6 - - + +
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Residues in contact with PHE 100 (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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61D ALA* 5.1 5.4 - - + +
63D VAL* 6.5 0.9 - - + -
88D ILE* 3.5 32.3 - - + -
90D LEU* 4.3 21.3 - - + -
98D LYS 4.5 0.2 - - - -
99D ASN* 1.3 81.9 - - - +
101D SER* 1.3 62.7 + - - +
368D LEU* 4.9 4.9 - - + -
398D SER* 4.7 2.2 - - - -
399D ILE* 2.8 71.8 + - + +
401D ALA* 4.3 20.0 - - + -
414D PHE* 5.0 0.4 - + - -
416D ILE* 4.3 7.6 - - + -
425D LEU* 4.1 17.9 - - + -
427D VAL* 4.3 15.7 - - + -
1007D NAG 4.0 11.0 - - + -
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Residues in contact with SER 101 (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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85D PRO* 4.0 18.9 - - - +
88D ILE* 5.8 0.9 - - - +
100D PHE* 1.3 81.0 - - - +
102D ILE* 1.3 63.8 + - - +
103D GLN* 5.8 2.7 - - - +
396D SER* 6.0 2.9 - - - -
397D PHE 3.2 13.2 - - - -
398D SER* 4.3 6.7 - - - +
399D ILE* 4.5 0.4 - - - -
425D LEU* 5.3 0.7 - - - +
1007D NAG 4.4 14.4 + - - +
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Residues in contact with ILE 102 (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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83D VAL* 4.0 15.7 - - + -
84D SER* 4.2 17.9 - - - +
85D PRO 4.9 0.4 - - - -
101D SER* 1.3 75.9 - - - +
103D GLN* 1.3 64.6 + - - +
104D VAL* 4.7 7.4 - - + -
357D LEU* 4.5 7.6 - - + -
396D SER* 3.3 2.8 - - - -
397D PHE* 2.7 68.8 + - + +
399D ILE* 3.7 13.7 - - + -
416D ILE* 4.5 15.7 - - + +
418D PRO* 6.1 0.9 - - + -
425D LEU* 3.4 42.2 - - + -
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Residues in contact with GLN 103 (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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69D LEU* 4.1 21.1 - - + +
82D GLN 3.9 0.4 - - - +
83D VAL* 3.3 5.9 - - - +
84D SER* 2.7 53.6 + - - +
101D SER* 5.8 2.9 - - - +
102D ILE* 1.3 71.6 - - - +
104D VAL* 1.3 66.3 + - - +
394D THR* 4.2 14.1 - - + +
395D VAL 3.5 3.4 - - - +
396D SER* 3.8 22.0 - - - -
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Residues in contact with VAL 104 (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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69D LEU* 5.0 0.2 - - - -
82D GLN 3.4 11.2 - - - +
83D VAL* 4.1 10.1 - - + -
102D ILE* 4.7 8.7 - - + -
103D GLN* 1.3 80.5 - - - +
105D ARG* 1.3 62.5 + - - +
355D VAL* 3.8 37.7 - - + +
357D LEU* 4.5 9.9 - - + -
389D LEU* 5.5 0.2 - - - +
393D ASP 4.1 0.2 - - - +
394D THR* 3.4 2.5 - - - -
395D VAL* 2.6 48.2 + - - +
397D PHE* 4.3 12.8 - - + -
418D PRO* 4.1 16.2 - - + -
421D PHE* 4.2 13.9 - - + -
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Residues in contact with ARG 105 (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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69D LEU* 3.1 48.7 + - + +
70D SER 3.0 28.8 + - - +
71D ASP* 3.7 12.1 + - - -
82D GLN* 3.0 42.2 + - + +
104D VAL* 1.3 78.4 - - - +
106D GLN* 1.3 60.6 + - - +
107D VAL* 4.3 11.9 - - - -
355D VAL* 5.9 0.9 - - - -
389D LEU* 5.7 0.7 - - - -
392D GLY* 3.4 18.2 + - - -
393D ASP 3.0 15.3 - - - +
394D THR* 2.9 26.8 + - + +
421D PHE* 4.2 2.7 - - - -
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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