Contacts of the strand formed by residues 139 - 144 (chain D) in PDB entry 6WNX
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 LYS 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D TYR* 3.2 2.9 - - - +
136D ASP* 2.7 66.7 + - - +
138D GLU* 1.3 84.2 + - + +
140D ILE* 1.3 64.8 + - - +
141D ILE* 3.8 24.2 - - + -
151D ILE* 4.2 15.9 - - + -
152D TRP 3.3 13.7 - - - +
153D ASP* 5.3 0.4 - - - -
154D LYS* 3.6 3.7 - - - +
160D LEU* 5.3 3.1 - - + -
175D TYR* 3.7 24.1 - - - +
176D ASP 5.7 0.8 + - - -
194D VAL* 4.3 13.9 - - - +
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Residues in contact with ILE 140 (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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120D ILE* 4.3 22.9 - - + -
133D LEU* 4.7 9.0 - - + -
134D GLN 3.5 11.7 - - - +
135D TYR* 3.8 16.6 - - + -
139D LYS* 1.3 76.7 - - - +
141D ILE* 1.3 69.3 + - - +
151D ILE* 3.4 2.8 - - - +
152D TRP* 2.7 53.5 + - + -
154D LYS* 3.9 21.5 - - + +
157D LEU* 4.9 2.9 - - + -
393D ILE* 4.0 29.6 - - + -
401D ILE* 4.7 9.6 - - + -
403D ILE* 4.4 10.8 - - + -
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Residues in contact with ILE 141 (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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133D LEU* 3.2 4.5 - - - +
134D GLN 2.8 33.5 + - - +
139D LYS* 3.8 24.9 - - + -
140D ILE* 1.3 75.2 - - - +
142D SER* 1.3 63.3 + - - +
149D ILE* 3.6 25.1 - - + -
150D LYS 3.6 2.9 - - - -
151D ILE* 4.0 18.6 - - + +
173D LEU* 4.1 16.1 - - + +
175D TYR* 3.5 38.4 - - + -
180D ILE* 3.9 26.7 - - + -
194D VAL* 4.3 2.9 - - + -
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Residues in contact with SER 142 (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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130D VAL* 4.0 8.3 - - - -
132D CYS 3.4 11.9 - - - -
133D LEU* 4.5 2.9 - - - -
140D ILE* 5.1 0.4 - - - -
141D ILE* 1.3 75.9 - - - +
143D GLY* 1.3 59.6 + - - +
144D LEU* 3.6 10.0 - - - +
149D ILE* 3.3 8.5 - - - +
150D LYS 2.8 40.7 + - - -
152D TRP* 3.1 15.3 + - - -
173D LEU* 3.5 6.3 - - - -
401D ILE* 3.8 23.0 - - - +
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Residues in contact with GLY 143 (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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130D VAL* 3.5 5.5 - - - +
131D TYR 2.9 25.5 + - - -
132D CYS* 3.1 25.5 + - - -
142D SER* 1.3 70.8 - - - +
144D LEU* 1.3 62.6 + - - -
148D SER 3.9 2.2 - - - -
149D ILE* 4.7 0.7 - - - -
170D VAL* 3.6 23.1 - - - -
173D LEU* 3.5 4.6 - - - +
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Residues in contact with LEU 144 (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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122D CYS* 3.9 28.7 - - + -
124D SER* 4.7 7.9 - - - -
129D GLY 3.5 11.9 - - - +
130D VAL* 4.1 9.4 - - + +
131D TYR* 4.6 2.0 - - - -
142D SER* 3.6 32.5 - - - +
143D GLY* 1.3 80.2 - - - +
145D ARG* 1.3 59.9 + - - +
146D ASP* 3.2 20.2 - - - +
147D ASN* 3.1 15.9 + - - -
148D SER* 3.1 16.6 + - - +
150D LYS* 3.9 30.7 - - + +
170D VAL* 3.2 20.4 + - - +
399D ASP* 4.8 0.2 - - - +
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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