Contacts of the strand formed by residues 134 - 139 (chain D) in PDB entry 1Y9D
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 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D TYR 3.2 18.7 + - - +
131D ALA 3.7 12.1 - - - +
132D ASP 3.3 1.9 - - - +
133D VAL* 1.3 79.3 - - + +
135D ASP* 1.3 64.7 + - - +
136D TYR 3.5 20.6 - - - +
137D ASN* 3.9 9.1 - - + +
163D VAL* 3.6 7.6 - - - +
165D VAL* 3.8 22.7 - - + -
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Residues in contact with ASP 135 (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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98D ARG* 5.2 7.9 - - - +
133D VAL 3.9 2.8 + - - +
134D ALA* 1.3 75.6 - - - +
136D TYR* 1.3 61.0 + - + +
156D ARG* 5.2 6.4 + - - +
160D HIS* 3.5 56.3 + - + +
161D GLN 4.9 0.2 - - - +
162D GLY* 3.8 17.6 - - - -
163D VAL 2.8 12.5 + - - +
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Residues in contact with TYR 136 (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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134D ALA* 3.3 3.1 - - - +
135D ASP* 1.3 80.5 - - + +
137D ASN* 1.3 58.2 + - - +
138D VAL* 3.7 38.5 - - + +
149D VAL* 4.0 12.8 + - - +
152D GLU* 3.9 29.5 - - + +
153D ALA* 3.6 35.0 - - + -
156D ARG* 3.4 52.9 - - + -
163D VAL 3.6 1.4 + - - -
164D ALA* 3.4 8.7 - - + -
165D VAL 2.7 35.1 + - - -
166D VAL* 4.6 1.3 - - + -
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Residues in contact with ASN 137 (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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125A ASN* 3.3 15.2 + - - +
128A PRO* 5.4 0.8 - - - +
127D ASN* 2.8 46.2 + - - +
130D TYR* 3.6 13.1 - - - +
131D ALA* 3.5 20.4 - - - +
134D ALA* 3.9 13.0 - - + +
136D TYR* 1.3 79.3 - - - +
138D VAL* 1.3 64.3 + - - +
165D VAL* 3.3 4.8 - - - +
167D GLN* 2.7 32.4 + - - -
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Residues in contact with VAL 138 (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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123A GLU 6.1 0.7 - - - +
125A ASN* 5.1 12.1 - - + +
127D ASN* 4.2 1.3 - - - +
136D TYR* 3.7 37.7 - - + +
137D ASN* 1.3 82.2 + - - +
139D THR* 1.3 63.6 + - - +
149D VAL* 3.5 33.4 - - + -
165D VAL 2.9 11.7 + - - +
166D VAL* 3.1 9.4 - - + +
167D GLN* 2.9 28.0 + - - -
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Residues in contact with THR 139 (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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125A ASN* 6.2 0.2 - - - -
141A VAL* 5.9 7.2 - - + -
110D GLN* 4.1 23.0 + - - +
127D ASN* 4.1 13.5 + - - +
138D VAL* 1.3 76.9 - - - +
140D ALA* 1.3 74.7 + - - +
141D VAL* 3.4 16.0 + - + +
167D GLN* 2.8 33.1 + - + +
169D PRO* 4.2 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