Contacts of the strand formed by residues 89 - 96 (chain Y) in PDB entry 1T6B
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 ALA 89 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83Y ILE* 4.8 0.2 - - + -
84Y VAL 3.3 8.3 - - - +
85Y PHE* 4.2 1.8 - - + -
88Y GLN* 1.3 81.4 + - - +
90Y THR* 1.3 66.3 + - - +
122Y GLU* 3.3 44.2 - - + +
123Y GLY* 3.7 6.3 - - - +
126Y LEU* 3.6 17.1 - - + +
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Residues in contact with THR 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y ILE* 3.5 2.1 - - - -
84Y VAL* 2.8 45.5 + - - +
88Y GLN* 5.0 5.9 - - - +
89Y ALA* 1.3 80.5 + - - +
91Y ILE* 1.3 76.2 + - - +
92Y ILE* 3.4 9.5 + - + +
126Y LEU* 3.9 5.8 - - - -
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Residues in contact with ILE 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Y SER* 4.4 2.2 - - - +
82Y PHE 3.8 4.9 - - - +
83Y ILE* 4.4 4.9 - - + +
90Y THR* 1.3 80.0 - - - +
92Y ILE* 1.3 60.4 + - - +
93Y LEU 3.6 4.7 - - - +
94Y PRO* 3.4 41.7 - - + +
126Y LEU* 3.9 36.2 - - + +
130Y GLN* 4.0 29.6 - - + +
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Residues in contact with ILE 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Y PHE* 2.9 22.2 + - + +
84Y VAL* 3.7 37.5 - - + -
90Y THR* 3.4 8.0 + - + +
91Y ILE* 1.3 76.5 - - - +
93Y LEU* 1.3 59.5 + - - +
94Y PRO* 4.3 3.9 - - - +
105Y GLY* 3.9 11.8 - - - +
108Y ASP* 3.6 43.8 - - + +
109Y LEU* 4.5 6.3 - - + -
112Y VAL* 5.1 10.3 - - + -
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Residues in contact with LEU 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y LEU 4.0 12.6 - - - +
81Y SER* 2.7 26.7 + - - -
82Y PHE* 3.0 56.5 + - + +
91Y ILE* 3.6 3.6 - - - -
92Y ILE* 1.3 80.4 - - - +
94Y PRO* 1.3 68.4 - - + +
96Y THR* 3.6 21.8 - - + -
101Y LYS* 3.6 26.5 - - + +
102Y ILE* 3.9 25.4 - - + -
105Y GLY* 4.4 4.9 - - - -
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Residues in contact with PRO 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y LEU 3.5 1.2 - - - +
91Y ILE* 3.4 17.6 - - + +
92Y ILE 4.3 3.8 - - - +
93Y LEU* 1.3 91.2 - - + +
95Y LEU* 1.3 72.0 + - - +
96Y THR* 3.1 17.9 + - - +
130Y GLN* 3.5 9.4 - - - +
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Residues in contact with LEU 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Y ASP* 3.6 26.2 - - + +
45Y LEU 4.3 1.3 - - - +
46Y TYR* 3.4 39.0 - - + +
79Y ARG* 3.6 50.2 - - + +
80Y LEU* 3.2 13.7 - - - -
81Y SER* 3.5 5.8 - - - +
94Y PRO* 1.3 74.0 - - - +
96Y THR* 1.3 61.0 + - - +
130Y GLN* 2.7 21.6 + - + +
134Y ALA* 4.4 9.2 - - + -
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Residues in contact with THR 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y ARG* 3.2 11.1 - - - +
80Y LEU 2.8 27.4 + - - +
93Y LEU* 3.6 27.4 - - + -
94Y PRO* 3.4 12.1 - - - +
95Y LEU* 1.3 79.7 - - - +
97Y GLY* 1.3 61.1 + - - +
98Y ASP* 3.3 15.5 + - - +
101Y LYS* 3.4 35.0 + - + +
102Y ILE* 3.7 8.4 - - + +
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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