Contacts of the strand formed by residues 141 - 147 (chain D) in PDB entry 3IU3
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 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D LEU* 4.3 17.7 - - + -
136D PHE* 4.2 9.6 - - + -
139D ARG 3.0 10.8 + - - +
140D GLU* 1.3 78.2 - - - +
142D LYS* 1.3 61.3 + - - +
143D VAL* 4.3 0.6 + - + -
158D GLU* 5.0 6.4 - - - +
172D LEU* 4.3 14.9 - - + +
194D THR 3.5 9.0 - - - +
195D HIS* 3.9 15.0 - - + +
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Residues in contact with LYS 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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141D ALA* 1.3 75.0 - - - +
143D VAL* 1.3 65.4 + - - +
144D GLN* 3.4 35.5 + - + -
192D GLU 3.6 1.2 - - - +
193D VAL* 3.5 3.5 - - - +
194D THR* 2.8 58.0 + - + +
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Residues in contact with VAL 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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133D LEU* 3.7 37.7 - - + -
141D ALA 4.3 0.4 + - - -
142D LYS* 1.3 80.8 - - - +
144D GLN* 1.3 67.7 + - - +
145D TRP* 4.5 7.9 - - - +
158D GLU* 4.4 14.4 + - - +
172D LEU* 4.2 13.9 - - + -
174D SER* 3.8 27.8 + - - +
191D CYS* 3.8 28.3 - - - -
192D GLU 3.4 3.4 - - - +
193D VAL* 4.3 3.4 - - + -
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Residues in contact with GLN 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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142D LYS* 3.4 37.7 + - + -
143D VAL* 1.3 80.5 - - - +
145D TRP* 1.3 64.3 + - - +
146D LYS* 4.9 2.0 - - + +
151D LEU* 3.6 32.0 - - + +
152D GLN 6.1 0.4 - - - +
191D CYS* 3.9 2.8 - - - -
192D GLU* 2.9 63.7 + - + +
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Residues in contact with TRP 145 (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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114D ILE* 4.3 11.2 - - + -
129D VAL* 3.6 42.8 - - + -
130D VAL 4.3 0.2 - - - -
131D CYS* 3.5 26.5 - - + -
143D VAL* 4.5 6.6 - - + +
144D GLN* 1.3 80.9 - - - +
146D LYS* 1.3 67.5 + - - +
147D VAL* 5.5 2.0 - - + -
151D LEU* 3.5 4.2 - - - +
152D GLN* 3.1 48.1 + - + +
156D SER* 3.8 27.1 - - - -
174D SER* 2.8 44.4 + - - -
176D LEU* 3.7 23.1 - - + -
189D TYR* 5.5 5.4 - + + -
190D ALA 3.4 23.8 - - - -
191D CYS* 4.4 2.9 - - + -
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Residues in contact with LYS 146 (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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144D GLN* 4.3 1.8 + - - +
145D TRP* 1.3 79.6 - - - +
147D VAL* 1.3 65.5 + - - +
148D ASP 3.7 2.4 + - - -
149D ASN* 3.8 38.3 + - - +
150D ALA 3.3 5.4 - - - +
151D LEU* 4.2 24.7 - - + -
188D VAL* 3.8 1.7 - - - +
190D ALA* 3.0 46.2 + - + +
192D GLU* 3.3 34.2 + - + +
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Residues in contact with VAL 147 (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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145D TRP* 4.2 2.6 - - + -
146D LYS* 1.3 69.4 - - - +
148D ASP* 1.3 62.4 + - - +
149D ASN 3.0 0.2 - - - -
150D ALA* 2.8 37.2 + - - +
152D GLN* 3.8 32.5 - - + +
176D LEU* 4.6 10.5 - - + -
178D LEU* 4.8 4.7 - - + -
186D HIS* 3.7 35.6 + - + +
188D VAL 3.5 5.2 - - - +
189D TYR* 3.6 37.7 - - + -
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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