Contacts of the helix formed by residues 69 - 73 (chain A) in PDB entry 1YRT
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 TRP 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 3.3 6.4 + - - -
68A ASP* 1.3 97.1 - - - +
70A GLY* 1.3 79.0 + - - +
72A GLN* 3.2 34.4 - - - -
73A ALA* 3.1 16.4 + - - +
81A ASN 3.5 23.8 - - - -
82A LEU* 3.3 9.4 + - + -
83A SER 2.9 21.6 + - - -
84A LYS* 4.5 0.7 - - - -
86A PHE* 3.7 15.0 - + + +
128A LEU* 4.3 5.8 - - + -
141A HIS* 3.4 46.0 - + + -
143A GLY* 3.7 24.9 - - - -
144A TYR* 3.9 24.0 - + - -
147A PHE* 4.3 7.6 - + - -
149A PHE* 3.9 15.3 - + - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TRP* 1.3 92.6 - - - +
71A LEU* 1.3 62.3 + - - -
72A GLN* 3.0 8.1 - - - -
73A ALA* 3.1 13.2 + - - +
123A LEU* 4.0 7.6 - - - +
128A LEU* 4.3 18.1 + - - +
129A VAL* 4.6 6.1 - - - -
139A SER* 5.0 1.6 + - - -
144A TYR* 3.8 18.4 - - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY* 1.3 71.6 - - - -
72A GLN* 1.3 63.5 + - - +
73A ALA 3.2 2.7 + - - +
75A TYR* 4.5 1.2 - - - -
113A LEU* 3.8 2.0 - - - +
115A LEU* 3.5 47.1 - - + +
119A ARG* 5.1 0.2 - - - -
120A LEU* 3.9 16.6 - - + -
123A LEU* 3.7 12.2 - - + +
129A VAL* 3.7 22.4 - - + +
137A VAL* 3.9 20.6 - - + -
144A TYR* 3.9 5.0 + - - +
149A PHE* 3.9 26.4 - - + -
150A ARG 4.3 9.0 - - - +
151A VAL* 4.8 7.2 - - + -
161A VAL* 3.9 29.2 - - + -
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 3.3 23.2 - - - +
69A TRP* 3.2 41.9 + - - +
70A GLY* 3.6 2.4 - - - -
71A LEU* 1.3 87.7 + - - +
73A ALA* 1.3 65.0 + - - +
74A GLY 3.3 0.2 + - - -
75A TYR* 3.1 25.4 + - + +
77A PRO* 4.7 5.2 - - + -
82A LEU* 2.9 36.6 + - + +
113A LEU* 3.9 18.6 - - + -
149A PHE* 4.1 15.7 - - - -
161A VAL* 5.4 1.0 - - + +
174A VAL* 4.5 13.1 - - + +
176A VAL* 5.4 0.9 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A HIS* 4.4 6.1 - - + -
67A SER 3.7 6.3 - - - -
68A ASP 4.0 5.2 - - - -
69A TRP 3.1 20.9 + - - +
70A GLY 3.1 17.3 + - - +
71A LEU 3.2 1.6 - - - -
72A GLN* 1.3 78.5 - - - +
74A GLY* 1.3 58.3 + - - +
75A TYR* 3.5 8.8 + - - -
119A ARG* 2.8 23.3 + - - +
123A LEU* 4.3 3.6 - - + +
128A LEU* 3.9 24.9 - - + -
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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