Contacts of the strand formed by residues 129 - 134 (chain D) in PDB entry 3HN3
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 TYR 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D TRP* 4.0 9.4 - + + -
127D HIS 4.3 3.1 - - - -
128D SER* 1.3 82.6 - - - +
130D ALA* 1.3 86.2 + - - +
131D ILE* 3.8 15.9 - - + -
141D GLU* 2.6 37.0 + - + +
142D HIS* 3.5 10.3 - - - -
143D GLU* 4.0 23.6 - - + -
171D ALA 4.6 0.2 - - - -
172D ILE* 3.3 6.4 - - - +
173D ASN* 2.7 37.1 + - + +
1G NAG 3.6 33.9 - - + +
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Residues in contact with ALA 130 (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 TRP* 4.8 0.2 - - - -
126D ALA* 3.6 28.9 - - + -
129D TYR* 1.3 78.8 - - - +
131D ILE* 1.3 64.0 + - - +
132D VAL* 5.2 0.7 - - - -
141D GLU* 3.2 7.7 - - - +
142D HIS 2.9 32.4 + - - +
149D PHE* 3.8 17.5 - - + -
170D ILE* 4.6 5.2 - - + -
171D ALA 3.2 10.8 - - - +
172D ILE* 4.3 5.6 - - + -
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Residues in contact with ILE 131 (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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59D PHE* 3.9 21.8 - - + -
98D TRP* 3.8 23.6 - - + -
129D TYR* 3.8 17.9 - - + -
130D ALA* 1.3 78.4 - - - +
132D VAL* 1.3 64.8 + - - +
133D TRP* 3.6 30.6 - - + -
138D ASP* 3.7 22.9 - - - +
140D LEU 3.5 2.9 - - - -
141D GLU* 3.9 14.6 - - + +
170D ILE* 3.4 3.6 - - - +
171D ALA 2.9 32.6 + - - +
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.9 26.2 - - + -
123D ILE* 4.7 2.9 - - + -
130D ALA 5.2 0.2 - - - -
131D ILE* 1.3 78.9 - - - +
133D TRP* 1.3 71.9 + - - +
134D VAL* 4.5 4.3 - - + -
138D ASP* 3.7 3.3 - - - +
139D THR* 2.9 25.1 + - - -
140D LEU* 2.7 35.0 + - + +
149D PHE* 4.1 24.0 - - + -
168D ILE* 4.2 7.0 - - + -
169D THR 3.3 8.7 - - - +
170D ILE* 4.1 19.1 - - + -
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Residues in contact with TRP 133 (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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59D PHE* 3.7 26.9 - + - -
64D TYR* 3.4 58.0 - + + -
100D TRP* 3.7 17.0 - + - -
131D ILE* 3.6 30.1 - - + -
132D VAL* 1.3 76.0 - - - +
134D VAL* 1.3 65.0 + - - +
135D ASN 4.1 0.2 - - - -
136D GLY* 3.7 13.9 - - - +
137D VAL 3.2 6.3 - - - +
138D ASP* 3.4 34.2 - - + +
167D ARG 3.7 0.9 - - - +
168D ILE* 3.6 3.8 - - - -
169D THR* 2.7 55.8 + - - +
171D ALA* 3.6 27.1 - - + -
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Residues in contact with VAL 134 (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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121D LEU* 4.4 17.7 - - + -
132D VAL* 4.5 2.9 - - + -
133D TRP* 1.3 76.6 - - - +
135D ASN* 1.3 73.3 + - - +
137D VAL* 2.8 26.4 + - - +
139D THR* 3.7 18.8 - - - +
153D ILE* 4.1 24.0 - - + -
156D LEU* 4.0 26.4 - - + +
166D LEU* 3.2 32.5 - - + -
167D ARG 3.5 2.9 - - - +
168D ILE* 4.9 3.6 - - + -
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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