Contacts of the strand formed by residues 141 - 147 (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 SER 141 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44Y ASP* 3.4 10.1 + - - +
46Y TYR* 3.8 8.3 + - - -
131Y ILE* 3.8 25.6 - - - +
134Y ALA* 5.8 0.2 - - - +
139Y THR* 3.1 26.5 + - - -
140Y SER* 1.3 71.0 - - - +
142Y ILE* 1.3 67.2 + - - +
169Y LEU 5.5 0.4 - - - -
170Y GLY 4.0 4.9 + - - +
171Y ALA* 3.2 37.7 - - - -
172Y SER* 3.2 6.6 + - - -
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Residues in contact with ILE 142 (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* 4.1 33.9 - - + -
44Y ASP 2.9 12.2 + - - +
45Y LEU* 3.6 24.5 - - + -
46Y TYR* 2.8 31.0 + - - +
141Y SER* 1.3 82.2 - - - +
143Y ILE* 1.3 64.3 + - - +
144Y ILE* 4.1 8.5 - - + -
172Y SER* 3.6 12.8 - - - +
174Y TYR* 4.1 27.8 - - + +
210Y ILE* 4.6 25.6 - - + -
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Residues in contact with ILE 143 (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* 3.4 15.5 - - + +
48Y VAL* 3.7 26.9 - - + -
124Y LEU* 3.9 19.3 - - + -
127Y ALA* 3.9 13.9 - - + -
128Y ASN* 3.7 9.0 - - - +
131Y ILE* 4.0 13.9 - - + -
142Y ILE* 1.3 75.2 - - - +
144Y ILE* 1.3 65.6 + - - +
145Y ALA 4.3 1.8 - - - +
166Y SER* 3.1 32.8 - - - +
171Y ALA* 4.8 3.3 - - + +
172Y SER 2.8 14.0 + - - +
173Y VAL* 4.4 12.8 - - + -
174Y TYR* 2.8 35.0 + - - +
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Residues in contact with ILE 144 (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* 3.6 25.1 - - + -
46Y TYR 2.8 11.2 + - - +
47Y PHE* 3.5 16.6 - - + -
48Y VAL 2.8 29.7 + - - +
65Y PHE* 4.5 5.2 - - + -
69Y LEU* 3.8 25.4 - - + -
142Y ILE* 4.1 11.2 - - + -
143Y ILE* 1.3 77.3 - - - +
145Y ALA* 1.3 55.8 + - - +
146Y LEU* 3.7 23.1 + - + +
174Y TYR* 3.5 14.6 - - + +
176Y VAL* 3.7 20.0 - - + -
206Y LEU* 3.8 13.7 - - + -
210Y ILE* 5.5 3.1 - - + -
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Residues in contact with ALA 145 (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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48Y VAL* 3.1 20.6 - - + +
120Y ILE* 4.5 21.1 - - + -
124Y LEU* 4.8 11.0 - - + -
143Y ILE* 4.0 1.5 - - + -
144Y ILE* 1.3 73.1 - - - +
146Y LEU* 1.3 59.6 + - - +
147Y THR* 4.1 2.6 + - + -
173Y VAL* 5.5 0.9 - - + -
174Y TYR 2.9 12.6 + - - +
175Y CYS* 3.4 13.8 - - - +
176Y VAL* 2.8 32.2 + - - +
189Y ILE* 5.6 0.7 - - + -
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Residues in contact with LEU 146 (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* 4.7 3.4 - - + -
48Y VAL 2.8 8.8 + - - +
49Y LEU* 3.7 26.9 - - + -
50Y ASP* 2.8 31.9 + - - +
62Y ILE* 4.2 25.6 - - + +
65Y PHE* 3.9 25.6 - - + -
66Y VAL* 5.2 0.2 - - + -
85Y PHE* 4.6 0.5 - - - -
144Y ILE* 3.7 27.6 - - + +
145Y ALA* 1.3 72.9 - - - +
147Y THR* 1.3 61.1 + - - +
176Y VAL* 3.6 17.5 - - + +
178Y VAL* 4.2 4.5 - - + -
199Y VAL* 3.7 30.1 - - + -
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Residues in contact with THR 147 (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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50Y ASP* 2.8 27.2 + - - -
118Y THR* 4.5 5.5 - - - +
120Y ILE* 3.8 30.4 - - + +
145Y ALA* 4.8 6.1 - - + +
146Y LEU* 1.3 78.2 - - - +
148Y ASP* 1.3 64.3 + - - +
149Y GLY* 3.1 16.7 + - - +
151Y LEU* 5.0 0.3 - - - +
175Y CYS* 5.4 1.1 - - + -
176Y VAL 3.4 8.9 + - - +
177Y GLY* 3.5 4.2 - - - -
178Y VAL* 2.8 29.5 + - - +
181Y PHE* 4.2 0.2 - - - +
186Y LEU* 3.8 20.7 - - + +
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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