Contacts of the strand formed by residues 44 - 50 (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 ASP 44 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42Y ALA 4.3 0.2 + - - -
43Y PHE* 1.3 74.8 - - - +
45Y LEU* 1.3 59.1 + - - +
46Y TYR* 4.0 5.9 + - + -
77Y GLU 5.2 1.2 - - - +
79Y ARG* 2.5 58.7 + - - +
95Y LEU* 3.6 18.9 - - + +
134Y ALA* 4.4 2.9 - - - +
139Y THR* 3.9 14.4 - - - +
140Y SER 2.8 16.3 + - - +
141Y SER* 3.4 11.5 + - - +
142Y ILE* 2.9 30.8 + - - +
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Residues in contact with LEU 45 (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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43Y PHE* 5.3 4.9 - - + +
44Y ASP* 1.3 73.2 - - - +
46Y TYR* 1.3 63.6 + - - +
47Y PHE* 3.8 30.6 + - + -
69Y LEU* 4.9 1.8 - - + +
73Y PHE* 3.8 32.1 - - + -
78Y MET* 5.8 3.4 - - + -
79Y ARG 2.7 15.1 + - - +
80Y LEU* 3.1 19.5 - - + +
81Y SER 3.0 24.3 + - - +
95Y LEU* 4.3 0.4 - - - +
142Y ILE* 3.6 28.5 - - + +
144Y ILE* 3.6 26.2 - - + -
210Y ILE* 5.6 2.5 - - + -
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Residues in contact with TYR 46 (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* 4.0 9.2 + - + -
45Y LEU* 1.3 73.8 - - - +
47Y PHE* 1.3 64.1 + - - +
48Y VAL* 3.6 1.5 + - + -
81Y SER* 3.7 15.3 - - - -
83Y ILE* 4.7 3.4 - - + -
95Y LEU* 3.4 39.5 - - + +
127Y ALA* 4.1 17.9 - - + -
130Y GLN* 3.5 36.9 + - + -
131Y ILE* 3.4 44.1 + - + +
134Y ALA* 4.2 2.9 - - - +
141Y SER* 3.8 11.7 + - - -
142Y ILE 2.8 23.0 + - - +
143Y ILE* 3.4 14.0 - - + +
144Y ILE* 2.8 28.3 + - - +
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Residues in contact with PHE 47 (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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45Y LEU* 3.8 28.9 - - + -
46Y TYR* 1.3 73.6 - - - +
48Y VAL* 1.3 59.3 + - - +
49Y LEU* 3.9 15.7 - - + -
65Y PHE* 4.7 3.4 - + - -
66Y VAL* 3.9 28.3 - - + -
69Y LEU* 3.6 46.4 - - + -
70Y ALA 5.3 1.6 - - - -
80Y LEU* 4.7 9.4 - - + -
81Y SER 2.9 16.3 + - - +
82Y PHE* 3.6 33.2 - + + -
83Y ILE* 2.6 37.1 + - - +
144Y ILE* 3.5 23.8 - - + -
146Y LEU* 4.7 1.1 - - + -
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Residues in contact with VAL 48 (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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46Y TYR 4.3 1.1 - - - +
47Y PHE* 1.3 75.4 - - - +
49Y LEU* 1.3 56.0 + - - +
83Y ILE* 3.6 14.4 - - + -
85Y PHE* 3.8 24.7 - - + -
120Y ILE* 4.7 2.7 - - + +
123Y GLY* 3.9 32.8 - - - +
124Y LEU* 4.1 7.6 - - + +
127Y ALA* 4.2 6.1 - - + -
143Y ILE* 3.7 23.1 - - + -
144Y ILE 2.8 12.1 + - - +
145Y ALA* 3.1 13.7 - - + +
146Y LEU 2.8 32.4 + - - +
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Residues in contact with LEU 49 (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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47Y PHE* 4.1 13.9 - - + -
48Y VAL* 1.3 86.2 - - - +
50Y ASP* 1.3 61.9 + - - +
51Y LYS 3.4 0.5 + - - -
59Y TRP* 3.9 20.6 - - + -
62Y ILE* 4.3 4.5 - - + -
66Y VAL* 3.6 28.9 - - + -
82Y PHE* 5.2 1.6 - - + -
83Y ILE 2.7 19.0 + - - +
84Y VAL* 3.3 6.2 - - + +
85Y PHE* 2.9 30.9 + - - -
109Y LEU* 3.9 30.3 - - + -
146Y LEU* 3.7 33.0 - - + -
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Residues in contact with ASP 50 (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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49Y LEU* 1.3 69.9 - - - +
51Y LYS* 1.3 58.1 + - - +
52Y SER* 2.6 32.9 + - - -
55Y VAL* 3.2 23.1 - - + +
59Y TRP* 3.3 12.9 - - - -
62Y ILE* 3.9 4.1 - - + +
85Y PHE* 3.5 24.7 - - + -
118Y THR* 3.6 10.7 - - - +
146Y LEU* 2.8 24.3 + - - +
147Y THR* 2.8 27.7 + - - -
148Y ASP* 3.7 9.2 + - - +
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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